Publications

Scientific Papers, Journals, Presentations, Posters, and Technical Reports

Presentations
Posters

2025

  1. Deelman, E., Dongarra, J., Hendrickson, B., Randles, A., Reed, D., Seidel, E., & Yelick, K. (2025). High-performance computing at a crossroads. Science, 387(6736), 829–831. https://doi.org/10.1126/science.adu0801 
    @article{deelman-science-2025,
  author = {Deelman, Ewa and Dongarra, Jack and Hendrickson, Bruce and Randles, Amanda and Reed, Daniel and Seidel, Edward and Yelick, Katherine},
  title = {High-performance computing at a crossroads},
  journal = {Science},
  volume = {387},
  number = {6736},
  pages = {829-831},
  year = {2025},
  doi = {10.1126/science.adu0801},
  url = {https://www.science.org/doi/abs/10.1126/science.adu0801},
  eprint = {https://www.science.org/doi/pdf/10.1126/science.adu0801}
}
  2. Poczekajlo, P., Moroz, L., Deelman, E., & Gepner, P. (2025). Evaluation of new CORDIC algorithms implemented on FPGA for the Givens Rotator. Journal of Computational Science, 87, 102567. https://doi.org/https://doi.org/10.1016/j.jocs.2025.102567 (Funding Acknowledgments: NSF #2331153) 
    @article{poczekajlo-jocs-2025,
  title = {Evaluation of new CORDIC algorithms implemented on FPGA for the Givens Rotator},
  journal = {Journal of Computational Science},
  volume = {87},
  pages = {102567},
  year = {2025},
  issn = {1877-7503},
  doi = {https://doi.org/10.1016/j.jocs.2025.102567},
  url = {https://www.sciencedirect.com/science/article/pii/S1877750325000444},
  author = {Poczekajlo, Pawel and Moroz, Leonid and Deelman, Ewa and Gepner, Pawel},
  keywords = {CORDIC, FPGA, Computer arithmetic},
  note = {Funding Acknowledgments: NSF #2331153}
}
  3. Raghavan, K., Papadimitriou, G., Jin, H., Mandal, A., Kiran, M., Balaprakash, P., & Deelman, E. (2025). Advancing anomaly detection in computational workflows with active learning. Future Generation Computer Systems, 166, 107608. https://doi.org/https://doi.org/10.1016/j.future.2024.107608 (Funding Acknowledgments: DE-SC0022328 ) 
    @article{raghavan-fgcs-2025,
  title = {Advancing anomaly detection in computational workflows with active learning},
  journal = {Future Generation Computer Systems},
  volume = {166},
  pages = {107608},
  year = {2025},
  issn = {0167-739X},
  doi = {https://doi.org/10.1016/j.future.2024.107608},
  url = {https://www.sciencedirect.com/science/article/pii/S0167739X24005727},
  author = {Raghavan, Krishnan and Papadimitriou, George and Jin, Hongwei and Mandal, Anirban and Kiran, Mariam and Balaprakash, Prasanna and Deelman, Ewa},
  keywords = {Active learning, Artificial intelligence, Computational workflows, Automated experimentation},
  note = {Funding Acknowledgments: DE-SC0022328 }
}

2024

  1. Callaghan, S., Maechling, P. J., Silva, F., Su, M.-H., Milner, K. R., Graves, R. W., Olsen, K. B., Cui, Y., Vahi, K., Kottke, A., Goulet, C. A., Deelman, E., Jordan, T. H., & Ben-Zion, Y. (2024). Using open-science workflow tools to produce SCEC CyberShake physics-based probabilistic seismic hazard models. Frontiers in High Performance Computing, 2. https://doi.org/10.3389/fhpcp.2024.1497384 (Funding Acknowledgments: NSF OAC SI2-SSI program, grant #1664162 ) 
    @article{callaghan-fhpcp-2024,
  author = {Callaghan, Scott and Maechling, Philip J. and Silva, Fabio and Su, Mei-Hui and Milner, Kevin R. and Graves, Robert W. and Olsen, Kim B. and Cui, Yifeng and Vahi, Karan and Kottke, Albert and Goulet, Christine A. and Deelman, Ewa and Jordan, Thomas H. and Ben-Zion, Yehuda},
  title = {Using open-science workflow tools to produce SCEC CyberShake physics-based probabilistic seismic hazard models},
  journal = {Frontiers in High Performance Computing},
  volume = {2},
  year = {2024},
  url = {https://www.frontiersin.org/journals/high-performance-computing/articles/10.3389/fhpcp.2024.1497384},
  doi = {10.3389/fhpcp.2024.1497384},
  issn = {2813-7337},
  note = {Funding Acknowledgments: NSF OAC SI2-SSI program, grant #1664162 }
}
  2. Catalfamo, A., Aral, A., Brandic, I., Deelman, E., & Villari, M. (2024). Machine Learning Workflows in the Computing Continuum for Environmental Monitoring. Computational Science – ICCS 2024: 24th International Conference, Malaga, Spain, July 2–4, 2024, Proceedings, Part V, 368–382. https://doi.org/10.1007/978-3-031-63775-9_27 (Funding Acknowledgments: NSF #2331153 and #2103508; DE-SC0024387) 
    @inproceedings{catalfamo-iccs-2024,
  author = {Catalfamo, Alessio and Aral, Atakan and Brandic, Ivona and Deelman, Ewa and Villari, Massimo},
  title = {Machine Learning Workflows in the Computing Continuum for Environmental Monitoring},
  year = {2024},
  isbn = {978-3-031-63774-2},
  publisher = {Springer-Verlag},
  address = {Berlin, Heidelberg},
  url = {https://doi.org/10.1007/978-3-031-63775-9_27},
  doi = {10.1007/978-3-031-63775-9_27},
  booktitle = {Computational Science – ICCS 2024: 24th International Conference, Malaga, Spain, July 2–4, 2024, Proceedings, Part V},
  pages = {368–382},
  numpages = {15},
  keywords = {Continuum, Worfklow, Pegasus, Cloud-Edge, Machine Learning},
  location = {Malaga, Spain},
  note = {Funding Acknowledgments: NSF #2331153 and #2103508; DE-SC0024387}
}
  3. Cranganore, S. S., De Maio, V., Brandic, I., & Deelman, E. (2024). Paving the way to hybrid quantum–classical scientific workflows. Future Generation Computer Systems, 158, 346–366. https://doi.org/https://doi.org/10.1016/j.future.2024.04.030 (Funding Acknowledgments: NSF #2331153) 
    @article{cranganore-fgcs-2024,
  title = {Paving the way to hybrid quantum–classical scientific workflows},
  journal = {Future Generation Computer Systems},
  volume = {158},
  pages = {346-366},
  year = {2024},
  issn = {0167-739X},
  doi = {https://doi.org/10.1016/j.future.2024.04.030},
  url = {https://www.sciencedirect.com/science/article/pii/S0167739X24001596},
  author = {Cranganore, Sandeep Suresh and {De Maio}, Vincenzo and Brandic, Ivona and Deelman, Ewa},
  keywords = {Quantum computing, Scientific computing, Post-Moore computing, Scientific workflows, Molecular dynamics, Hybrid quantum-classical systems},
  note = {Funding Acknowledgments: NSF #2331153}
}
  4. Ferreira Da Silva, R., Moore II, R., Mintz, B., Advincula, R., Alnajjar, A., Baldwin, L., Bridges, C. A., Coffee, R., Deelman, E., Engelmann, C., & others. (2024). Shaping the Future of Self-Driving Autonomous Laboratories Workshop. Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF). https://doi.org/10.2172/2481197 
    @techreport{silva-osti-2024,
  author = {Ferreira Da Silva, Rafael and Moore II, Rob and Mintz, Ben and Advincula, Rigoberto and Alnajjar, Anees and Baldwin, Luke and Bridges, Craig A. and Coffee, Ryan and Deelman, Ewa and Engelmann, Christian and others},
  title = {Shaping the Future of Self-Driving Autonomous Laboratories Workshop},
  institution = {Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF)},
  annote = {The "Shaping the Future of Self-Driving Autonomous Laboratories" workshop, held in Denver on November 7-8, 2024, brought together leading experts from materials science and computing to address the growing need to revolutionize scientific research through AI-driven autonomous laboratories. The workshop identified critical challenges, including the integration of heterogeneous data, development of AI systems that understand fundamental physical principles, and comprehensive safety protocols. Key recommendations emerged around developing universal laboratory equipment interfaces, implementing automated metadata collection systems, and creating hybrid AI approaches that combine data-driven learning with scientific principles. The workshop emphasized maintaining human oversight while leveraging automation, transforming scientific education to prepare the next generation of researchers, and establishing a national consortium leveraging DOE facilities as anchors for broader collaboration with academia and industry. Participants stressed the urgency of addressing the growing disconnect between human decision-making timescales and modern instrumentation capabilities, highlighting the need for strategic automation while preserving essential human insight and oversight in the research process.},
  doi = {10.2172/2481197},
  url = {https://www.osti.gov/biblio/2481197},
  place = {United States},
  year = {2024},
  month = nov
}
  5. Hasan, M., Kee, K. F., Okunloye, O., & Deelman, E. (2024). Decision Strategies during a Science Crisis: How Science Organizations Made Adaptations during the Pandemic. https://wearecrisiscomm.com/2024-icrcc-proceedings/enzc7642/ (Funding Acknowledgments: NSF #12127548, #2042054) 
    @inproceedings{hasan-icrcc-2024,
  author = {Hasan, Mahedi and Kee, Kerk F and Okunloye, Oluwabusayo and Deelman, Ewa},
  title = {Decision Strategies during a Science Crisis: How Science Organizations Made Adaptations during the Pandemic},
  year = {2024},
  series = {ICRCC '24},
  url = {https://wearecrisiscomm.com/2024-icrcc-proceedings/enzc7642/},
  note = {Funding Acknowledgments: NSF #12127548, #2042054}
}
  6. Jin, H., Papadimitriou, G., Raghavan, K., Zuk, P., Balaprakash, P., Wang, C., Mandal, A., & Deelman, E. (2024). Large Language Models for Anomaly Detection in Computational Workflows: From Supervised Fine-Tuning to In-Context Learning. In SC24: International Conference for High Performance Computing, Networking, Storage and Analysis (pp. 1–17). https://doi.org/10.1109/SC41406.2024.00098 (Funding Acknowledgments: DE-SC0022328 ) 
    @inproceeding{jin-sc24-2024,
  author = {Jin, Hongwei and Papadimitriou, George and Raghavan, Krishnan and Zuk, Pawel and Balaprakash, Prasanna and Wang, Cong and Mandal, Anirban and Deelman, Ewa},
  booktitle = {SC24: International Conference for High Performance Computing, Networking, Storage and Analysis},
  title = {Large Language Models for Anomaly Detection in Computational Workflows: From Supervised Fine-Tuning to In-Context Learning},
  year = {2024},
  volume = {},
  number = {},
  pages = {1-17},
  keywords = {Training;Analytical models;Accuracy;Large language models;Computational modeling;High performance computing;Transfer learning;Reliability;Security;Anomaly detection;anomaly detection;large language models;supervised fine-tuning;in-context learning;computational workflows},
  doi = {10.1109/SC41406.2024.00098},
  note = {Funding Acknowledgments: DE-SC0022328 }
}
  7. Jin, H., Papadimitriou, G., Raghavan, K., Zuk, P., Balaprakash, P., Wang, C., Mandal, A., & Deelman, E. (2024). Large Language Models for Anomaly Detection in Computational Workflows: From Supervised Fine-Tuning to In-Context Learning. Proceedings of the International Conference for High Performance Computing, Networking, Storage, and Analysis. https://doi.org/10.1109/SC41406.2024.00098 (Funding Acknowledgments: DE-SC0022328 ) 
    @inproceedings{10.1109/SC41406.2024.00098,
  author = {Jin, Hongwei and Papadimitriou, George and Raghavan, Krishnan and Zuk, Pawel and Balaprakash, Prasanna and Wang, Cong and Mandal, Anirban and Deelman, Ewa},
  title = {Large Language Models for Anomaly Detection in Computational Workflows: From Supervised Fine-Tuning to In-Context Learning},
  year = {2024},
  isbn = {9798350352917},
  publisher = {IEEE Press},
  url = {https://doi.org/10.1109/SC41406.2024.00098},
  doi = {10.1109/SC41406.2024.00098},
  booktitle = {Proceedings of the International Conference for High Performance Computing, Networking, Storage, and Analysis},
  articleno = {92},
  numpages = {17},
  keywords = {anomaly detection, computational workflows, in-context learning, large language models, supervised fine-tuning},
  location = {Atlanta, GA, USA},
  series = {SC '24},
  note = {Funding Acknowledgments: DE-SC0022328 }
}
  8. Jin, H., Papadimitriou, G., Raghavan, K., Zuk, P., Balaprakash, P., Wang, C., Mandal, A., & Deelman, E. (2024). Large Language Models for Anomaly Detection in Computational Workflows: from Supervised Fine-Tuning to In-Context Learning. https://arxiv.org/abs/2407.17545 (Funding Acknowledgments: DE-SC0022328, NSF award #2138286 and #2106147 ) 
    @misc{jin-arxiv-2024,
  title = {Large Language Models for Anomaly Detection in Computational Workflows: from Supervised Fine-Tuning to In-Context Learning},
  author = {Jin, Hongwei and Papadimitriou, George and Raghavan, Krishnan and Zuk, Pawel and Balaprakash, Prasanna and Wang, Cong and Mandal, Anirban and Deelman, Ewa},
  year = {2024},
  eprint = {2407.17545},
  archiveprefix = {arXiv},
  primaryclass = {cs.SE},
  url = {https://arxiv.org/abs/2407.17545},
  note = {Funding Acknowledgments: DE-SC0022328, NSF award #2138286 and #2106147 }
}
  9. Mahmud, I., Zuk, P., Wang, C., Kiran, M., Wu, K., Thareja, K., Raghavan, K., Mandal, A., & Deelman, E. (2024). DISTRI: Development and Integration of Simulation Tools for Resilient Infrastructure. 2024 IEEE International Conference on Big Data (BigData), 4167–4177. https://doi.org/10.1109/BigData62323.2024.10825783 (Funding Acknowledgments: DE-SC0024387 ) 
    @inproceedings{mahmud-bigdata-2024,
  author = {Mahmud, Imtiaz and Zuk, Pawel and Wang, Cong and Kiran, Mariam and Wu, Kesheng and Thareja, Komal and Raghavan, Krishnan and Mandal, Anirban and Deelman, Ewa},
  booktitle = {2024 IEEE International Conference on Big Data (BigData)},
  title = {DISTRI: Development and Integration of Simulation Tools for Resilient Infrastructure},
  year = {2024},
  volume = {},
  number = {},
  pages = {4167-4177},
  keywords = {Measurement;Protocols;Processor scheduling;Solids;Scheduling;Resource management;Research and development;Optimization;Testing;Resilience;Distributed Computing;Resilient Computing;Multi-Facility Simulator;HPC Network Simulator;Fault-Tolerant Algorithms},
  doi = {10.1109/BigData62323.2024.10825783},
  note = {Funding Acknowledgments: DE-SC0024387 }
}
  10. Poczekajlo, P., Moroz, L., Deelman, E., & Gepner, P. (2024). Modified CORDIC Algorithm for Givens Rotator. In L. Franco, C. de Mulatier, M. Paszynski, V. V. Krzhizhanovskaya, J. J. Dongarra, & P. M. A. Sloot (Eds.), Computational Science – ICCS 2024 (pp. 101–114). Springer Nature Switzerland. https://doi.org/10.1007/978-3-031-63778-0_8 (Funding Acknowledgments: NSF #2331153) 
    @inproceedings{poczekajlo-iccs-2024,
  doi = {10.1007/978-3-031-63778-0_8},
  author = {Poczekajlo, Pawel and Moroz, Leonid and Deelman, Ewa and Gepner, Pawel},
  editor = {Franco, Leonardo and de Mulatier, Cl{\'e}lia and Paszynski, Maciej and Krzhizhanovskaya, Valeria V. and Dongarra, Jack J. and Sloot, Peter M. A.},
  title = {Modified CORDIC Algorithm for Givens Rotator},
  booktitle = {Computational Science -- ICCS 2024},
  year = {2024},
  publisher = {Springer Nature Switzerland},
  address = {Cham},
  pages = {101--114},
  isbn = {978-3-031-63778-0},
  note = {Funding Acknowledgments: NSF #2331153}
}
  11. Raghavan, K., Papadimitriou, G., Jin, H., Mandal, A., Kiran, M., Balaprakash, P., & Deelman, E. (2024). Advancing Anomaly Detection in Computational Workflows with Active Learning. https://arxiv.org/abs/2405.06133 (Funding Acknowledgments: DE-SC0022328 ) 
    @misc{raghavan-arxiv-2024,
  title = {Advancing Anomaly Detection in Computational Workflows with Active Learning},
  author = {Raghavan, Krishnan and Papadimitriou, George and Jin, Hongwei and Mandal, Anirban and Kiran, Mariam and Balaprakash, Prasanna and Deelman, Ewa},
  year = {2024},
  eprint = {2405.06133},
  archiveprefix = {arXiv},
  primaryclass = {cs.DC},
  url = {https://arxiv.org/abs/2405.06133},
  note = {Funding Acknowledgments: DE-SC0022328 }
}
  12. Roa, C., Rynge, M., Olaya, P., Vahi, K., Miller, T., Griffioen, J., Knuth, S., Goodhue, J., Hudak, D., Romanella, A., Llamas, R., Vargas, R., Livny, M., Deelman, E., & Taufer, M. (2024). End-to-end Integration of Scientific Workflows on Distributed Cyberinfrastructures: Challenges and Lessons Learned with an Earth Science Application. Proceedings of the IEEE/ACM 16th International Conference on Utility and Cloud Computing. https://doi.org/10.1145/3603166.3632142 (Funding Acknowledgments: NSF 1664162, 1841758, 2028923, 2103845, 2103836, 2138811, 2223704, 2330582, 2331152, 2334945, 2138286) 
    @inproceedings{roa-ucc-2023,
  author = {Roa, Camila and Rynge, Mats and Olaya, Paula and Vahi, Karan and Miller, Todd and Griffioen, James and Knuth, Shelley and Goodhue, John and Hudak, David and Romanella, Alana and Llamas, Ricardo and Vargas, Rodrigo and Livny, Miron and Deelman, Ewa and Taufer, Michela},
  title = {End-to-end Integration of Scientific Workflows on Distributed Cyberinfrastructures: Challenges and Lessons Learned with an Earth Science Application},
  year = {2024},
  isbn = {9798400702341},
  publisher = {Association for Computing Machinery},
  address = {New York, NY, USA},
  url = {https://doi.org/10.1145/3603166.3632142},
  doi = {10.1145/3603166.3632142},
  booktitle = {Proceedings of the IEEE/ACM 16th International Conference on Utility and Cloud Computing},
  articleno = {17},
  numpages = {9},
  keywords = {workflows, machine learning, soil moisture, high throughput computing, containers},
  location = {, Taormina (Messina), Italy, },
  series = {UCC '23},
  note = {Funding Acknowledgments: NSF 1664162, 1841758, 2028923, 2103845, 2103836, 2138811, 2223704, 2330582, 2331152, 2334945, 2138286}
}
  13. Safri, H., Papadimitriou, G., & Deelman, E. (2024). Dynamic Tracking, MLOps, and Workflow Integration: Enabling Transparent Reproducibility in Machine Learning. 2024 IEEE 20th International Conference on e-Science (e-Science), 1–10. https://doi.org/10.1109/e-Science62913.2024.10678658 (Funding Acknowledgments: DOE award #DE-SC0022328 and NSF award #2138286 and #2106147 ) 
    @inproceedings{hamza-escience-2024,
  author = {Safri, Hamza and Papadimitriou, George and Deelman, Ewa},
  booktitle = {2024 IEEE 20th International Conference on e-Science (e-Science)},
  title = {Dynamic Tracking, MLOps, and Workflow Integration: Enabling Transparent Reproducibility in Machine Learning},
  year = {2024},
  volume = {},
  number = {},
  pages = {1-10},
  keywords = {Concurrent computing;Codes;Runtime;Federated learning;Refining;Pipelines;Metadata;Workflow Management System;Tracking;Versionning;MLops;Machine learning},
  doi = {10.1109/e-Science62913.2024.10678658},
  note = {Funding Acknowledgments:  DOE award #DE-SC0022328 and NSF award #2138286 and #2106147 }
}
  14. Safri, H., Papadimitriou, G., Desprez, F., & Deelman, E. (2024). A Workflow Management System Approach To Federated Learning: Application to Industry 4.0. 2024 20th International Conference on Distributed Computing in Smart Systems and the Internet of Things (DCOSS-IoT). https://doi.org/https://doi.org/10.1109/DCOSS-IoT61029.2024.00047 (Funding Acknowledgments: DE-SC0022328 and NSF #2138286, #2106147) 
    @inproceedings{safri-dcoss-iot-2024,
  author = {Safri, Hamza and Papadimitriou, George and Desprez, Frédéric and Deelman, Ewa},
  booktitle = {2024 20th International Conference on Distributed Computing in Smart Systems and the Internet of Things (DCOSS-IoT)},
  title = {A Workflow Management System Approach To Federated Learning: Application to Industry 4.0},
  year = {2024},
  volume = {},
  number = {},
  pages = {},
  doi = {https://doi.org/10.1109/DCOSS-IoT61029.2024.00047},
  note = {Funding Acknowledgments: DE-SC0022328 and NSF #2138286, #2106147}
}
  15. Seidel, E., Randles, A., Arthur, R., Bergman, K., Carlson, B., Deelman, E., Grout, R., Hendrickson, B., & Reed, D. (2024). 2024 Advanced Scientific Computing Advisory Committee (ASCR): Facilities Subcommittee Recommendations. https://doi.org/10.2172/2370379 (Funding Acknowledgments: XXX ) 
    @article{raghavan-osti-2024,
  title = {2024 Advanced Scientific Computing Advisory Committee (ASCR): Facilities Subcommittee Recommendations},
  author = {Seidel, Ed and Randles, Amanda and Arthur, Rick and Bergman, Keren and Carlson, Bill and Deelman, Ewa and Grout, Ray and Hendrickson, Bruce and Reed, Dan},
  abstractnote = {We were given a charge to assess the necessity for new or upgraded facilities to ensure the Office of Science (SC) remains at the forefront of scientific discovery. This effort included evaluating five specific ASCR facilities for their potential to contribute to this goal and to rate the readiness for construction of each.},
  doi = {10.2172/2370379},
  url = {https://www.osti.gov/biblio/2370379},
  place = {United States},
  year = {2024},
  month = may,
  note = {Funding Acknowledgments: XXX }
}
  16. Wyrzykowski, R., & Deelman, E. (2024). Guest Editor’s note: Special issue on challenges and solutions for porting applications to next-generation high performance computing systems. The International Journal of High Performance Computing Applications, 38(1), 3–4. https://doi.org/10.1177/10943420231224509 
    @article{wyrzykowski-ijhpca-2024,
  author = {Wyrzykowski, Roman and Deelman, Ewa},
  title = {Guest Editor’s note: Special issue on challenges and solutions for porting applications to next-generation high performance computing systems},
  journal = {The International Journal of High Performance Computing Applications},
  volume = {38},
  number = {1},
  pages = {3-4},
  year = {2024},
  doi = {10.1177/10943420231224509},
  url = {https://doi.org/10.1177/10943420231224509},
  eprint = { 
          https://doi.org/10.1177/10943420231224509
  }
}

2023

  1. Afle, C., Miles, P. R., Caino-Lores, S., Capano, C. D., Tews, I., Vahi, K., Deelman, E., Taufer, M., & Brown, D. A. (2023). Reproducing the results for NICER observation of PSR J0030+0451. (Funding Acknowledgments: NSF 2207264, 2041977, 2041901, 2028923, 2028930, 1841399, and 1941443; DOE DE-AC52-06NA25396 ) 
    @article{afle-arxiv-2023,
  author = {Afle, Chaitanya and Miles, Patrick R. and Caino-Lores, Silvina and Capano, Collin D. and Tews, Ingo and Vahi, Karan and Deelman, Ewa and Taufer, Michela and Brown, Duncan A.},
  title = {{Reproducing the results for NICER observation of PSR J0030+0451}},
  eprint = {2304.01035},
  archiveprefix = {arXiv},
  primaryclass = {astro-ph.HE},
  reportnumber = {LA-UR-22-29359},
  month = apr,
  year = {2023},
  note = {Funding Acknowledgments: NSF 2207264, 2041977, 2041901, 2028923, 2028930, 1841399, and 1941443; DOE DE-AC52-06NA25396 }
}
  2. Afle, C., Miles, P. R., Caíno-Lores, S., Capano, C. D., Tews, I., Vahi, K., Deelman, E., Taufer, M., & Brown, D. A. (2023). Reproducing the Results for Neutron Star Interior Composition Explorer Observation of PSR J0030 + 0451. Computing in Science & Engineering, 25(6), 16–26. https://doi.org/10.1109/MCSE.2024.3381080 
    @article{afle-cise-2023,
  author = {Afle, Chaitanya and Miles, Patrick R. and Caíno-Lores, Silvina and Capano, Collin D. and Tews, Ingo and Vahi, Karan and Deelman, Ewa and Taufer, Michela and Brown, Duncan A.},
  journal = {Computing in Science & Engineering},
  title = {Reproducing the Results for Neutron Star Interior Composition Explorer Observation of PSR J0030 + 0451},
  year = {2023},
  volume = {25},
  number = {6},
  pages = {16-26},
  keywords = {Software;Extraterrestrial measurements;Reproducibility of results;Temperature measurement;Neutron stars;Data models;Containers},
  doi = {10.1109/MCSE.2024.3381080}
}
  3. Caino-Lores, S., Cuendet, M., Marquez, J., Kots, E., Estrada, T., Deelman, E., Weinstein, H., & Taufer, M. (2023). Runtime Steering of Molecular Dynamics Simulations Through In Situ Analysis and Annotation of Collective Variables. Proceedings of the Platform for Advanced Scientific Computing Conference. https://doi.org/10.1145/3592979.3593420 (Funding Acknowledgments: NSF 1741057, 1841758, 2138811, 2223704; ORLCF CSC427; XSEDE TG-CIS200053; IBM Shared University Research Award) 
    @inproceedings{10.1145/3592979.3593420,
  author = {Caino-Lores, Silvina and Cuendet, Michel and Marquez, Jack and Kots, Ekaterina and Estrada, Trilce and Deelman, Ewa and Weinstein, Harel and Taufer, Michela},
  title = {Runtime Steering of Molecular Dynamics Simulations Through In Situ Analysis and Annotation of Collective Variables},
  year = {2023},
  isbn = {9798400701900},
  publisher = {Association for Computing Machinery},
  address = {New York, NY, USA},
  url = {https://doi.org/10.1145/3592979.3593420},
  doi = {10.1145/3592979.3593420},
  booktitle = {Proceedings of the Platform for Advanced Scientific Computing Conference},
  articleno = {21},
  numpages = {11},
  keywords = {molecular dynamics, scientific workflows, simulation ensembles, in situ analysis, collective variables},
  location = {Davos, Switzerland},
  series = {PASC '23},
  note = {Funding Acknowledgments: NSF 1741057, 1841758, 2138811, 2223704; ORLCF CSC427; XSEDE TG-CIS200053; IBM Shared University Research Award}
}
  4. Caino-Lores, S., Cuendet, M., Marquez, J., Kots, E., Estrada, T., Deelman, E., Weinstein, H., & Taufer, M. (2023). Runtime Steering of Molecular Dynamics Simulations Through In Situ Analysis and Annotation of Collective Variables. Proceedings of the Platform for Advanced Scientific Computing Conference. https://doi.org/10.1145/3592979.3593420 (Funding Acknowledgments: NSF 1741057, 1841758, 2138811 and 2223704) 
    @inproceedings{lores-pasc-2023,
  author = {Caino-Lores, Silvina and Cuendet, Michel and Marquez, Jack and Kots, Ekaterina and Estrada, Trilce and Deelman, Ewa and Weinstein, Harel and Taufer, Michela},
  title = {Runtime Steering of Molecular Dynamics Simulations Through In Situ Analysis and Annotation of Collective Variables},
  year = {2023},
  isbn = {9798400701900},
  publisher = {Association for Computing Machinery},
  address = {New York, NY, USA},
  url = {https://doi.org/10.1145/3592979.3593420},
  doi = {10.1145/3592979.3593420},
  booktitle = {Proceedings of the Platform for Advanced Scientific Computing Conference},
  articleno = {21},
  numpages = {11},
  keywords = {molecular dynamics, scientific workflows, collective variables, simulation ensembles, in situ analysis},
  location = {Davos, Switzerland},
  series = {PASC '23},
  note = {Funding Acknowledgments: NSF 1741057, 1841758, 2138811 and 2223704}
}
  5. Deelman, E. (2023). How is Artificial Intelligence Changing Science? 2023 IEEE 19th International Conference on e-Science (e-Science), 1–4. https://doi.org/10.1109/e-Science58273.2023.10254913 (Funding Acknowledgments: DOE DE-SC0022328 and NSF 1664162, 2138286) 
    @inproceedings{deelman-escience-2023,
  author = {Deelman, Ewa},
  booktitle = {2023 IEEE 19th International Conference on e-Science (e-Science)},
  title = {How is Artificial Intelligence Changing Science?},
  year = {2023},
  volume = {},
  number = {},
  pages = {1-4},
  doi = {10.1109/e-Science58273.2023.10254913},
  note = {Funding Acknowledgments: DOE DE-SC0022328 and NSF 1664162, 2138286}
}
  6. Dongarra, J., Deelman, E., Hey, T., Matsuoka, S., Sarakar, V., Bell, G., Foster, I., Keyes, D., & Kranzlmueller, D. et-al. (2023). Can the United States Maintain Its Leadership in High-Performance Computing?-A report from the ASCAC Subcommittee on American Competitiveness and Innovation to the ASCR Office. OSTI. https://doi.org/10.2172/1989107 
    @article{dongarra-osti-2023,
  author = {Dongarra, Jack and Deelman, Ewa and Hey, Tony and Matsuoka, Satoshi and Sarakar, Vivek and Bell, Greg and Foster, Ian and Keyes, David and Kranzlmueller, Dieter et-al},
  journal = {OSTI},
  title = {Can the United States Maintain Its Leadership in High-Performance Computing?-A report from the ASCAC Subcommittee on American Competitiveness and Innovation to the ASCR Office},
  year = {2023},
  volume = {},
  number = {},
  pages = {},
  doi = {10.2172/1989107}
}
  7. Esquivel Morel, A., Calyam, P., Qu, C., Gafurov, D., Wang, C., Thareja, K., Mandal, A., Lyons, E., Zink, M., Papadimitriou, G., & Deelman, E. (2023). Network Services Management using Programmable Data Planes for Visual Cloud Computing. 2023 International Conference on Computing, Networking and Communications (ICNC), 130–136. https://doi.org/10.1109/ICNC57223.2023.10074183 (Funding Acknowledgments: NSF 1950873, 2018074) 
    @inproceedings{esquivel-morel-icnc-2023,
  author = {Esquivel Morel, Alicia and Calyam, Prasad and Qu, Chengyi and Gafurov, Durbek and Wang, Cong and Thareja, Komal and Mandal, Anirban and Lyons, Eric and Zink, Michael and Papadimitriou, George and Deelman, Ewa},
  booktitle = {2023 International Conference on Computing, Networking and Communications (ICNC)},
  title = {Network Services Management using Programmable Data Planes for Visual Cloud Computing},
  year = {2023},
  volume = {},
  issn = {},
  pages = {130-136},
  doi = {10.1109/ICNC57223.2023.10074183},
  note = {Funding Acknowledgments: NSF 1950873, 2018074}
}
  8. Gesing, S., Deelman, E., Hildreth, M., Makhija, R., McDowell, M. A., Meyers, N. K., & Thain, D. (2023). VisDict: Improving Communication Via a Visual Dictionary in a Science Gateway. Computing in Science & Engineering, 25(2), 7–11. https://doi.org/10.1109/MCSE.2023.3275711 (Funding Acknowledgments: NSF 2216851, 2100561, and 2100636 ) 
    @article{gesing-cise-2023,
  author = {Gesing, Sandra and Deelman, Ewa and Hildreth, Michael and Makhija, Ramandeep and McDowell, Mary Ann and Meyers, Natalie K. and Thain, Douglas},
  journal = {Computing in Science & Engineering},
  title = {VisDict: Improving Communication Via a Visual Dictionary in a Science Gateway},
  year = {2023},
  volume = {25},
  number = {2},
  pages = {7-11},
  doi = {10.1109/MCSE.2023.3275711},
  note = {Funding Acknowledgments: NSF 2216851, 2100561, and 2100636 }
}
  9. Grote, A., Lyons, E., Thareja, K., Papadimitriou, G., Deelman, E., Mandal, A., Calyam, P., & Zink, M. (2023). FlyPaw: Optimized Route Planning for Scientific UAVMissions. 2023 IEEE 19th International Conference on e-Science (e-Science), 1–10. https://doi.org/10.1109/e-Science58273.2023.10254831 (Funding Acknowledgments: NSF 2018074, 1939334) 
    @inproceedings{grote-escience-2023,
  author = {Grote, Andrew and Lyons, Eric and Thareja, Komal and Papadimitriou, George and Deelman, Ewa and Mandal, Anirban and Calyam, Prasad and Zink, Michael},
  booktitle = {2023 IEEE 19th International Conference on e-Science (e-Science)},
  title = {FlyPaw: Optimized Route Planning for Scientific UAVMissions},
  year = {2023},
  volume = {},
  number = {},
  pages = {1-10},
  doi = {10.1109/e-Science58273.2023.10254831},
  note = {Funding Acknowledgments: NSF 2018074, 1939334}
}
  10. Jin, H., Raghavan, K., Papadimitriou, G., Wang, C., Mandal, A., Kiran, M., Deelman, E., & Balaprakash, P. (2023). Graph neural networks for detecting anomalies in scientific workflows. The International Journal of High Performance Computing Applications. https://doi.org/10.1177/10943420231172140 (Funding Acknowledgments: DOE DE-SC0022328, DE-AC02-06CH11357) 
    @article{jin-ijhpca-2023,
  author = {Jin, Hongwei and Raghavan, Krishnan and Papadimitriou, George and Wang, Cong and Mandal, Anirban and Kiran, Mariam and Deelman, Ewa and Balaprakash, Prasanna},
  title = {Graph neural networks for detecting anomalies in scientific workflows},
  journal = {The International Journal of High Performance Computing Applications},
  volume = {},
  number = {},
  pages = {},
  year = {2023},
  doi = {10.1177/10943420231172140},
  url = {https://doi.org/10.1177/10943420231172140},
  eprint = {https://doi.org/10.1177/10943420231172140},
  note = {Funding Acknowledgments: DOE DE-SC0022328, DE-AC02-06CH11357}
}
  11. Mahmud, I., Papadimitriou, G., Wang, C., Kiran, M., Mandal, A., & Deelman, E. (2023). Elephants Sharing the Highway: Studying TCP Fairness in Large Transfers over High Throughput Links. Proceedings of the SC ’23 Workshops of The International Conference on High Performance Computing, Network, Storage, and Analysis, 806–818. https://doi.org/10.1145/3624062.3624594 (Funding Acknowledgments: DOE DE-SC0022328. Best Paper Award.) 
    @inproceedings{mahmud-indis-2023,
  author = {Mahmud, Imtiaz and Papadimitriou, George and Wang, Cong and Kiran, Mariam and Mandal, Anirban and Deelman, Ewa},
  title = {Elephants Sharing the Highway: Studying TCP Fairness in Large Transfers over High Throughput Links},
  year = {2023},
  isbn = {9798400707858},
  publisher = {Association for Computing Machinery},
  address = {New York, NY, USA},
  url = {https://doi.org/10.1145/3624062.3624594},
  doi = {10.1145/3624062.3624594},
  booktitle = {Proceedings of the SC '23 Workshops of The International Conference on High Performance Computing, Network, Storage, and Analysis},
  pages = {806–818},
  numpages = {13},
  keywords = {Buffer Size, FABRIC, High-Speed Internet, TCP Congestion Control, Elephant Flows, Active Queue Management, High-Bandwidth, Fairness},
  location = {Denver, CO, USA},
  series = {SC-W '23},
  note = {Funding Acknowledgments: DOE DE-SC0022328. Best Paper Award.}
}
  12. Morel, A. E., Gafurov, D., Calyam, P., Wang, C., Thareja, K., Mandal, A., Lyons, E., Zink, M., Papadimitriou, G., & Deelman, E. (2023). Experiments on Network Services for Video Transmission using FABRIC Instrument Resources. IEEE INFOCOM 2023 - IEEE Conference on Computer Communications Workshops (INFOCOM WKSHPS), 1–6. https://doi.org/10.1109/INFOCOMWKSHPS57453.2023.10225817 (Funding Acknowledgments: NSF CNS-1950873, CNS-1647182 and OAC-2018074) 
    @inproceedings{morel-infocom-2023,
  author = {Morel, Alicia Esquivel and Gafurov, Durbek and Calyam, Prasad and Wang, Cong and Thareja, Komal and Mandal, Anirban and Lyons, Eric and Zink, Michael and Papadimitriou, George and Deelman, Ewa},
  booktitle = {IEEE INFOCOM 2023 - IEEE Conference on Computer Communications Workshops (INFOCOM WKSHPS)},
  title = {Experiments on Network Services for Video Transmission using FABRIC Instrument Resources},
  year = {2023},
  volume = {},
  number = {},
  pages = {1-6},
  doi = {10.1109/INFOCOMWKSHPS57453.2023.10225817},
  note = {Funding Acknowledgments: NSF CNS-1950873, CNS-1647182 and OAC-2018074}
}
  13. Morel, A. E., Qu, C., Calyam, P., Wang, C., Thareja, K., Mandal, A., Lyons, E., Zink, M., Papadimitriou, G., & Deelman, E. (2023). FlyNet: Drones on the Horizon. IEEE Internet Computing, 27(3), 35–43. https://doi.org/10.1109/MIC.2023.3260440 (Funding Acknowledgments: NSF 1950873, 1647182, 2018074) 
    @article{morel-mic-2023,
  author = {Morel, Alicia Esquivel and Qu, Chengyi and Calyam, Prasad and Wang, Cong and Thareja, Komal and Mandal, Anirban and Lyons, Eric and Zink, Michael and Papadimitriou, George and Deelman, Ewa},
  journal = {IEEE Internet Computing},
  title = {FlyNet: Drones on the Horizon},
  year = {2023},
  volume = {27},
  number = {3},
  pages = {35-43},
  doi = {10.1109/MIC.2023.3260440},
  note = {Funding Acknowledgments: NSF 1950873, 1647182, 2018074}
}
  14. Murillo, A., Brower, D., Hossain, S., Kee, K., Mandal, A., Nabrzyski, J., Scott, E., Virdone, N., Ewing, R., & Deelman, E. (2023). Broadening Student Engagement To Build the Next Generation of Cyberinfrastructure Professionals. Practice and Experience in Advanced Research Computing, 470–473. https://doi.org/10.1145/3569951.3597567 (Funding Acknowledgments: NSF 2127548) 
    @inproceedings{murillo-pearc-2023,
  author = {Murillo, Angela and Brower, Don and Hossain, Sarowar and Kee, Kerk and Mandal, Anirban and Nabrzyski, Jarek and Scott, Erik and Virdone, Nicole and Ewing, Rodney and Deelman, Ewa},
  title = {Broadening Student Engagement To Build the Next Generation of Cyberinfrastructure Professionals},
  year = {2023},
  isbn = {9781450399852},
  publisher = {Association for Computing Machinery},
  address = {New York, NY, USA},
  url = {https://doi.org/10.1145/3569951.3597567},
  doi = {10.1145/3569951.3597567},
  booktitle = {Practice and Experience in Advanced Research Computing},
  pages = {470–473},
  numpages = {4},
  keywords = {workforce development, cyberinfrastructure, Student fellowships, Major Facilities},
  location = {Portland, OR, USA},
  series = {PEARC '23},
  note = {Funding Acknowledgments: NSF 2127548}
}
  15. Papadimitriou, G., Jin, H., Wang, C., Raghavan, K., Mandal, A., Balaprakash, P., & Deelman, E. (2023). Flow-Bench: A Dataset for Computational Workflow Anomaly Detection. https://doi.org/10.48550/ARXIV.2306.09930 
    @article{flow-bench,
  author = {Papadimitriou, George and Jin, Hongwei and Wang, Cong and Raghavan, Krishnan and Mandal, Anirban and Balaprakash, Prasanna and Deelman, Ewa},
  title = {Flow-Bench: A Dataset for Computational Workflow Anomaly Detection},
  publisher = {arXiv},
  year = {2023},
  doi = {10.48550/ARXIV.2306.09930},
  url = {https://arxiv.org/abs/2306.09930},
  copyright = {arXiv.org perpetual,  non-exclusive license}
}
  16. Papadimitriou, G., Wang, C., Lyons, E., Thareja, K., Ruth, P., Villalobos, J. J., Rodero, I., Deelman, E., Zink, M., & Mandal, A. (2023). Dynamic Network-Centric Multi-cloud Platform for Real-Time and Data-Intensive Science Workflows. In F. Darema, E. P. Blasch, S. Ravela, & A. J. Aved (Eds.), Handbook of Dynamic Data Driven Applications Systems: Volume 2 (pp. 835–868). Springer International Publishing. https://doi.org/10.1007/978-3-031-27986-7_32 (Funding Acknowledgments: NSF 1826997) 
    @inbook{papadimitriou-dddas-2023,
  author = {Papadimitriou, George and Wang, Cong and Lyons, Eric and Thareja, Komal and Ruth, Paul and Villalobos, J. J. and Rodero, Ivan and Deelman, Ewa and Zink, Michael and Mandal, Anirban},
  editor = {Darema, Frederica and Blasch, Erik P. and Ravela, Sai and Aved, Alex J.},
  title = {Dynamic Network-Centric Multi-cloud Platform for Real-Time and Data-Intensive Science Workflows},
  booktitle = {Handbook of Dynamic Data Driven Applications Systems: Volume 2},
  year = {2023},
  publisher = {Springer International Publishing},
  address = {Cham},
  pages = {835--868},
  isbn = {978-3-031-27986-7},
  doi = {10.1007/978-3-031-27986-7_32},
  url = {https://doi.org/10.1007/978-3-031-27986-7_32},
  note = {Funding Acknowledgments: NSF 1826997}
}
  17. Rynge, M., Vahi, K., Alam, M. Z., Deelman, E., Miller, T., Livny, M., Knuth, S., Griffioen, J., Goodhue, J., Hudak, D., Ma, J., Pasquale, A., & Fein, L. (2023). ACCESS Pegasus: Bringing Workflows to the ACCESS Masses. Practice and Experience in Advanced Research Computing, 478–480. https://doi.org/10.1145/3569951.3597590 (Funding Acknowledgments: NSF 2138286, 1664162) 
    @inproceedings{rynge-pearc-2023,
  author = {Rynge, Mats and Vahi, Karan and Alam, Mohammad Zaiyan and Deelman, Ewa and Miller, Todd and Livny, Miron and Knuth, Shelley and Griffioen, James and Goodhue, John and Hudak, David and Ma, Julie and Pasquale, Andrew and Fein, Lissie},
  title = {ACCESS Pegasus: Bringing Workflows to the ACCESS Masses},
  year = {2023},
  isbn = {9781450399852},
  publisher = {Association for Computing Machinery},
  address = {New York, NY, USA},
  url = {https://doi.org/10.1145/3569951.3597590},
  doi = {10.1145/3569951.3597590},
  booktitle = {Practice and Experience in Advanced Research Computing},
  pages = {478–480},
  numpages = {3},
  location = {Portland, OR, USA},
  series = {PEARC '23},
  note = {Funding Acknowledgments: NSF 2138286, 1664162}
}
  18. Sahni, H., Carrillo-Cabada, H., Kots, E., Caino-Lores, S., Marquez, J., Deelman, E., Cuendet, M., Weinstein, H., Taufer, M., & Estrada, T. (2023). Online Boosted Gaussian Learners for In-Situ Detection and Characterization of Protein Folding States in Molecular Dynamics Simulations. 2023 IEEE 19th International Conference on e-Science (e-Science), 1–10. https://doi.org/10.1109/e-Science58273.2023.10254895 (Funding Acknowledgments: NSF 1757207, 1741057, 1841758, 2138811 and 2223704) 
    @inproceedings{sahni-esciences-2023,
  author = {Sahni, Harshita and Carrillo-Cabada, Hector and Kots, Ekaterina and Caino-Lores, Silvina and Marquez, Jack and Deelman, Ewa and Cuendet, Michel and Weinstein, Harel and Taufer, Michela and Estrada, Trilce},
  booktitle = {2023 IEEE 19th International Conference on e-Science (e-Science)},
  title = {Online Boosted Gaussian Learners for In-Situ Detection and Characterization of Protein Folding States in Molecular Dynamics Simulations},
  year = {2023},
  volume = {},
  number = {},
  pages = {1-10},
  doi = {10.1109/e-Science58273.2023.10254895},
  note = {Funding Acknowledgments:  NSF 1757207, 1741057, 1841758, 2138811 and 2223704}
}

2022

  1. Abhinit, I., Adams, E. K., Alam, K., Chase, B., Deelman, E., Gorenstein, L., Hudson, S., Islam, T., Larson, J., Lentner, G., Mandal, A., Navarro, J.-L., Nicolae, B., Pouchard, L., Ross, R., Roy, B., Rynge, M., Serebrenik, A., Vahi, K., … Filgueira, R. (2022). Novel Proposals for FAIR, Automated, Recommendable, and Robust Workflows. 2022 IEEE/ACM Workshop on Workflows in Support of Large-Scale Science (WORKS), 84–92. https://doi.org/10.1109/WORKS56498.2022.00016 (Funding Acknowledgments: NSF 1839900 and DOE DE-AC02-06CH11357, DE-AC05-00OR22725) 
    @inproceedings{novel-fair-works-2022,
  author = {Abhinit, Ishan and Adams, Emily K. and Alam, Khairul and Chase, Brian and Deelman, Ewa and Gorenstein, Lev and Hudson, Stephen and Islam, Tanzima and Larson, Jeffrey and Lentner, Geoffrey and Mandal, Anirban and Navarro, John-Luke and Nicolae, Bogdan and Pouchard, Line and Ross, Rob and Roy, Banani and Rynge, Mats and Serebrenik, Alexander and Vahi, Karan and Wild, Stefan and Xin, Yufeng and da Silva, Rafael Ferreira and Filgueira, Rosa},
  booktitle = {2022 IEEE/ACM Workshop on Workflows in Support of Large-Scale Science (WORKS)},
  title = {Novel Proposals for FAIR, Automated, Recommendable, and Robust Workflows},
  year = {2022},
  volume = {},
  number = {},
  pages = {84-92},
  doi = {10.1109/WORKS56498.2022.00016},
  note = {Funding Acknowledgments: NSF 1839900 and DOE DE-AC02-06CH11357, DE-AC05-00OR22725}
}
  2. Casanova, H., Ching Wong, Y., Pottier, L., & Ferreira da Silva, R. (2022). On the Feasibility of Simulation-driven Portfolio Scheduling for Cyberinfrastructure Runtime Systems. 2022 Job Scheduling Strategies for Parallel Processing (JSSPP), To appear. (Funding Acknowledgments: NSF 2106059 and 2106147, DOE DE-AC05-00OR22725) 
    @inproceedings{casanova-jssp-2022,
  title = {On the Feasibility of Simulation-driven Portfolio Scheduling for Cyberinfrastructure Runtime Systems},
  author = {Casanova, Henri and Ching Wong, Yick and Pottier, Lo\"ic and Ferreira da Silva, Rafael},
  booktitle = {2022 Job Scheduling Strategies for Parallel Processing (JSSPP)},
  doi = {},
  pages = {To appear},
  year = {2022},
  publisher = {Springer Nature},
  note = {Funding Acknowledgments: NSF 2106059 and 2106147, DOE DE-AC05-00OR22725}
}
  3. Choudhary, K., Nersisyan, N., Lin, E., Chandrasekaran, S., Mayani, R., Pottier, L., Murillo, A. P., Virdone, N. K., Kee, K., & Deelman, E. (2022). Application of Edge-to-Cloud Methods Toward Deep Learning. 2022 IEEE 18th International Conference on e-Science (e-Science), 415–416. https://doi.org/10.1109/eScience55777.2022.00065 (Funding Acknowledgments: NSF 2127548) 
    @inproceedings{choudhary-escience-2022,
  author = {Choudhary, Khushi and Nersisyan, Nona and Lin, Edward and Chandrasekaran, Shobana and Mayani, Rajiv and Pottier, Loïc and Murillo, Angela P. and Virdone, Nicole K. and Kee, Kerk and Deelman, Ewa},
  booktitle = {2022 IEEE 18th International Conference on e-Science (e-Science)},
  title = {Application of Edge-to-Cloud Methods Toward Deep Learning},
  year = {2022},
  volume = {},
  number = {},
  pages = {415-416},
  doi = {10.1109/eScience55777.2022.00065},
  note = {Funding Acknowledgments: NSF 2127548}
}
  4. Coleman, T., Casanova, H., Pottier, L., Kaushik, M., Deelman, E., & Ferreira da Silva, R. (2022). WfCommons: A framework for enabling scientific workflow research and development. Future Generation Computer Systems, 128, 16–27. https://doi.org/10.1016/j.future.2021.09.043 (Funding Acknowledgments: NSF 1923539, 2016610, 2016619, 2103489, 2103508, 1923621, 1664162, DOE DE-SC0012636) 
    @article{coleman-fgcs-2022,
  title = {WfCommons: A framework for enabling scientific workflow research and development},
  journal = {Future Generation Computer Systems},
  volume = {128},
  pages = {16-27},
  year = {2022},
  issn = {0167-739X},
  doi = {10.1016/j.future.2021.09.043},
  url = {https://www.sciencedirect.com/science/article/pii/S0167739X21003897},
  author = {Coleman, Tain\=a and Casanova, Henri and Pottier, Lo\"ic and Kaushik, Manav and Deelman, Ewa and {Ferreira da Silva}, Rafael},
  keywords = {Scientific workflows, Workflow management systems, Simulation, Distributed computing, Workflow instances},
  note = {Funding Acknowledgments: NSF 1923539, 2016610, 2016619, 2103489, 2103508, 1923621, 1664162, DOE DE-SC0012636}
}
  5. Cranganore, S. S., De Maio, V., Brandic, I., Do, T. M. A., & Deelman, E. (2022). Molecular Dynamics Workflow Decomposition for Hybrid Classic/Quantum Systems. 2022 IEEE 18th International Conference on e-Science (e-Science), 346–356. https://doi.org/10.1109/eScience55777.2022.00048 (Funding Acknowledgments: NSF 1664162 and 1741040) 
    @inproceedings{cranganore-escience-2022,
  author = {Cranganore, Sandeep Suresh and De Maio, Vincenzo and Brandic, Ivona and Do, Tu Mai Anh and Deelman, Ewa},
  booktitle = {2022 IEEE 18th International Conference on e-Science (e-Science)},
  title = {Molecular Dynamics Workflow Decomposition for Hybrid Classic/Quantum Systems},
  year = {2022},
  volume = {},
  number = {},
  pages = {346-356},
  doi = {10.1109/eScience55777.2022.00048},
  note = {Funding Acknowledgments: NSF 1664162 and 1741040}
}
  6. Do, T. M. A., Pottier, L., Ferreira da Silva, R., Caı́no-Lores Silvina, Taufer, M., & Deelman, E. (2022). Performance assessment of ensembles of in situ workflows under resource constraints. Concurrency and Computation: Practice and Experience. https://doi.org/10.1002/cpe.7111 (Funding Acknowledgments: NSF 1664162) 
    @article{do-ccpe-2022,
  author = {Do, Tu Mai Anh and Pottier, Lo\"ic and Ferreira da Silva, Rafael and Ca\'{\i}no-Lores, Silvina and Taufer, Michela and Deelman, Ewa},
  title = {Performance assessment of ensembles of in situ workflows under resource constraints},
  journal = {Concurrency and Computation: Practice and Experience},
  year = {2022},
  doi = {10.1002/cpe.7111},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cpe.7111},
  note = {Funding Acknowledgments: NSF 1664162}
}
  7. Do, T. M. A., Pottier, L., Yildiz, O., Vahi, K., Krawczuk, P., Peterka, T., & Deelman, E. (2022). Accelerating Scientific Workflows on HPC Platforms with In Situ Processing. 2022 IEEE/ACM 22nd International Symposium on Cluster, Cloud and Internet Computing (CCGrid), 1–10. https://doi.org/10.1109/CCGrid54584.2022.00009 (Funding Acknowledgments: NSF 1664162, DOE DE-AC02-06CH11357, DE-AC02-05CH11231, DE-SC0012636 and DE-SC0022328) 
    @inproceedings{do-pottier-ccgrid-2022,
  title = {Accelerating Scientific Workflows on HPC Platforms with In Situ Processing},
  author = {Do, Tu Mai Anh and Pottier, Lo\"ic and Yildiz, Orcun and Vahi, Karan and Krawczuk, Patrycja and Peterka, Tom and Deelman, Ewa},
  booktitle = {2022 IEEE/ACM 22nd International Symposium on Cluster, Cloud and Internet Computing (CCGrid)},
  doi = {10.1109/CCGrid54584.2022.00009},
  pages = {1--10},
  year = {2022},
  organization = {IEEE},
  note = {Funding Acknowledgments: NSF 1664162, DOE DE-AC02-06CH11357, DE-AC02-05CH11231, DE-SC0012636 and DE-SC0022328}
}
  8. Do, T. M. A., Pottier, L., da Silva, R. F., Suter, F., Caíno-Lores, S., Taufer, M., & Deelman, E. (2022). Co-scheduling Ensembles of In Situ Workflows. 2022 IEEE/ACM Workshop on Workflows in Support of Large-Scale Science (WORKS), 43–51. https://doi.org/10.1109/WORKS56498.2022.00011 (Funding Acknowledgments: NSF 1741040, 1741057, 1841758 and DOE DE-AC05-00OR22725) 
    @inproceedings{do-works-2022,
  author = {Do, Tu Mai Anh and Pottier, Loïc and da Silva, Rafael Ferreira and Suter, Frédéric and Caíno-Lores, Silvina and Taufer, Michela and Deelman, Ewa},
  booktitle = {2022 IEEE/ACM Workshop on Workflows in Support of Large-Scale Science (WORKS)},
  title = {Co-scheduling Ensembles of In Situ Workflows},
  year = {2022},
  volume = {},
  number = {},
  pages = {43-51},
  doi = {10.1109/WORKS56498.2022.00011},
  note = {Funding Acknowledgments: NSF 1741040, 1741057, 1841758 and DOE DE-AC05-00OR22725}
}
  9. Gesing, S., Deelman, E., Ferreira da Silva, R., Hildreth, M., McDowell, M. A., Meyers, N., Taylor, I., & Tain, D. (2022). VisDict: A Visual Dictionary in a Science Gateway. In Gateways 2022. Zenodo. https://doi.org/10.5281/zenodo.7098353 (Funding Acknowledgments: NSF 2216851) 
    @proceedings{gesing-gateways-2022,
  title = {VisDict: A Visual Dictionary in a Science Gateway},
  author = {Gesing, Sandra and Deelman, Ewa and Ferreira da Silva, Rafael and Hildreth, Michael and McDowell, Mary Ann and Meyers, Natalie and Taylor, Ian and Tain, Douglas},
  year = {2022},
  booktitle = {Gateways 2022},
  publisher = {Zenodo},
  month = sep,
  doi = {10.5281/zenodo.7098353},
  url = {https://doi.org/10.5281/zenodo.7098353},
  note = {Funding Acknowledgments: NSF 2216851}
}
  10. Hacker, T., Smith, P., Brunson, D., Arafune, L., Cheatham, T., & Deelman, E. (2022). Building the Research Innovation Workforce: Challenges and Recommendations from a Virtual Workshop to Advance the Research Computing Community*. Practice and Experience in Advanced Research Computing. https://doi.org/10.1145/3491418.3530288 (Funding Acknowledgments: NSF 2036534) 
    @inproceedings{deelman-pearc-2022,
  author = {Hacker, Thomas and Smith, Preston and Brunson, Dana and Arafune, Lisa and Cheatham, Thomas and Deelman, Ewa},
  title = {Building the Research Innovation Workforce: Challenges and Recommendations from a Virtual Workshop to Advance the Research Computing Community*},
  year = {2022},
  isbn = {9781450391610},
  publisher = {Association for Computing Machinery},
  address = {New York, NY, USA},
  url = {https://doi.org/10.1145/3491418.3530288},
  doi = {10.1145/3491418.3530288},
  booktitle = {Practice and Experience in Advanced Research Computing},
  articleno = {26},
  numpages = {7},
  keywords = {cyberinfrastructure, research computing, workforce},
  location = {Boston, MA, USA},
  series = {PEARC '22},
  note = {Funding Acknowledgments: NSF 2036534}
}
  11. Hamed, A. A., Jonczyk, J., Alam, M. Z., Deelman, E., & Lee, B. S. (2022). Mining Literature-Based Knowledge Graph for Predicting Combination Therapeutics: A COVID-19 Use Case. 2022 IEEE International Conference on Knowledge Graph (ICKG), 79–86. https://doi.org/10.1109/ICKG55886.2022.00018 
    @inproceedings{hamed-ickg-2022,
  author = {Hamed, Ahmed Abdeen and Jonczyk, Jakub and Alam, Mohammad Zaiyan and Deelman, Ewa and Lee, Byung Suk},
  booktitle = {2022 IEEE International Conference on Knowledge Graph (ICKG)},
  title = {Mining Literature-Based Knowledge Graph for Predicting Combination Therapeutics: A COVID-19 Use Case},
  year = {2022},
  volume = {},
  number = {},
  pages = {79-86},
  doi = {10.1109/ICKG55886.2022.00018}
}
  12. Honoré, V., Do, T. M. A., Pottier, L., Da Silva, R. F., Deelman, E., & Suter, F. (2022). SIM-SITU: A Framework for the Faithful Simulation of in situ Processing. 2022 IEEE 18th International Conference on e-Science (e-Science), 182–191. https://doi.org/10.1109/eScience55777.2022.00032 (Funding Acknowledgments: DOE DE-AC05-00OR22725) 
    @inproceedings{honore-escience-2022,
  author = {Honoré, Valentin and Do, Tu Mai Anh and Pottier, Loïc and Da Silva, Rafael Ferreira and Deelman, Ewa and Suter, Frédéric},
  booktitle = {2022 IEEE 18th International Conference on e-Science (e-Science)},
  title = {SIM-SITU: A Framework for the Faithful Simulation of in situ Processing},
  year = {2022},
  volume = {},
  number = {},
  pages = {182-191},
  doi = {10.1109/eScience55777.2022.00032},
  note = {Funding Acknowledgments: DOE DE-AC05-00OR22725}
}
  13. Jin, H., Raghavan, K., Papadimitriou, G., Wang, C., Mandal, A., Krawczuk, P., Pottier, L., Kiran, M., Deelman, E., & Balaprakash, P. (2022). Workflow Anomaly Detection with Graph Neural Networks. 2022 IEEE/ACM Workshop on Workflows in Support of Large-Scale Science (WORKS), 35–42. https://doi.org/10.1109/WORKS56498.2022.00010 (Funding Acknowledgments: DOE DE-SC0022328, DE-AC02-06CH11357) 
    @inproceedings{jin-works-2022,
  author = {Jin, Hongwei and Raghavan, Krishnan and Papadimitriou, George and Wang, Cong and Mandal, Anirban and Krawczuk, Patrycja and Pottier, Loïc and Kiran, Mariam and Deelman, Ewa and Balaprakash, Prasanna},
  booktitle = {2022 IEEE/ACM Workshop on Workflows in Support of Large-Scale Science (WORKS)},
  title = {Workflow Anomaly Detection with Graph Neural Networks},
  year = {2022},
  volume = {},
  number = {},
  pages = {35-42},
  doi = {10.1109/WORKS56498.2022.00010},
  note = {Funding Acknowledgments: DOE DE-SC0022328, DE-AC02-06CH11357}
}
  14. Knuth, S. L., Ma, J., Adams, J. C., Chalker, A., Deelman, E., Freeborn, L., Gazula, V., Goodhue, J., Griffioen, J., Hudak, D., Pasquale, A., Perkins, D., Romanella, A., & Rynge, M. (2022). The Multi-Tier Assistance, Training, and Computational Help (MATCH) Project, a Track 2 NSF ACCESS Initiative. The Journal of Computational Science Education, 13(2), 17–20. https://doi.org/https://doi.org/10.22369/issn.2153-4136/13/2/4 (Funding Acknowledgments: NSF 2138286) 
    @article{jocse-13-2-4,
  author = {Knuth, Shelley L. and Ma, Julie and Adams, Joel C. and Chalker, Alan and Deelman, Ewa and Freeborn, Layla and Gazula, Vikram and Goodhue, John and Griffioen, James and Hudak, David and Pasquale, Andrew and Perkins, Dylan and Romanella, Alana and Rynge, Mats},
  title = {The Multi-Tier Assistance, Training, and Computational Help (MATCH) Project, a Track 2 NSF ACCESS Initiative},
  journal = {The Journal of Computational Science Education},
  year = {2022},
  month = dec,
  volume = {13},
  issue = {2},
  pages = {17--20},
  doi = {https://doi.org/10.22369/issn.2153-4136/13/2/4},
  note = {Funding Acknowledgments: NSF 2138286}
}
  15. Murillo, A., Deelman, E., Nabrzyski, J., & Pottier, L. (2022). Broadening Student Participation in Cyberinfrastructure Research and Development. Practice and Experience in Advanced Research Computing. https://doi.org/10.1145/3491418.3535175 (Funding Acknowledgments: NSF 2127548 and 1842042) 
    @inproceedings{deelman-pearc-2023,
  author = {Murillo, Angela and Deelman, Ewa and Nabrzyski, Jarek and Pottier, Loic},
  title = {Broadening Student Participation in Cyberinfrastructure Research and Development.},
  year = {2022},
  isbn = {9781450391610},
  publisher = {Association for Computing Machinery},
  address = {New York, NY, USA},
  url = {https://doi.org/10.1145/3491418.3535175},
  doi = {10.1145/3491418.3535175},
  booktitle = {Practice and Experience in Advanced Research Computing},
  articleno = {82},
  numpages = {2},
  keywords = {cyberinfrastructure, research computing, workforce},
  location = {Boston, MA, USA},
  series = {PEARC '22},
  note = {Funding Acknowledgments: NSF 2127548 and 1842042}
}
  16. Murillo, A. P., Deelman, E., Nabrzyski, J., & Pottier Loı̈c. (2022). Broadening Student Participation in Cyberinfrastructure Research and Development. Practice and Experience in Advanced Research Computing. https://doi.org/10.1145/3491418.3535175 (Funding Acknowledgments: NSF 2127548, 1842042) 
    @inproceedings{murillo-pearc-2022,
  author = {Murillo, Angela Patricia and Deelman, Ewa and Nabrzyski, Jarek and Pottier, Lo\"{\i}c},
  title = {Broadening Student Participation in Cyberinfrastructure Research and Development},
  year = {2022},
  isbn = {9781450391610},
  publisher = {Association for Computing Machinery},
  address = {New York, NY, USA},
  url = {https://doi.org/10.1145/3491418.3535175},
  doi = {10.1145/3491418.3535175},
  booktitle = {Practice and Experience in Advanced Research Computing},
  articleno = {82},
  numpages = {2},
  keywords = {workforce development, student fellowships, cyberinfrastructure, Major Facilities},
  location = {Boston, MA, USA},
  series = {PEARC '22},
  note = {Funding Acknowledgments: NSF 2127548, 1842042}
}
  17. Osinski, T., Rynge, M., Hong, J. K., Vahi, K., Chu, R., Sul, C., Deelman, E., & Kim, B.-D. (2022). An automated Cryo-EM computational environment on the HPC system using Pegasus WMS. 2022 IEEE/ACM Workshop on Workflows in Support of Large-Scale Science (WORKS), 60–67. https://doi.org/10.1109/WORKS56498.2022.00013 (Funding Acknowledgments: NSF 1664162) 
    @inproceedings{osinski-works-2022,
  author = {Osinski, Tomasz and Rynge, Mats and Hong, James K. and Vahi, Karan and Chu, Ruilin and Sul, Cesar and Deelman, Ewa and Kim, Byoung-Do},
  booktitle = {2022 IEEE/ACM Workshop on Workflows in Support of Large-Scale Science (WORKS)},
  title = {An automated Cryo-EM computational environment on the HPC system using Pegasus WMS},
  year = {2022},
  volume = {},
  number = {},
  pages = {60-67},
  doi = {10.1109/WORKS56498.2022.00013},
  note = {Funding Acknowledgments: NSF 1664162}
}
  18. Patel, R., Roachell, B., Caíno-Lores, S., Ketron, R., Leonard, J., Tan, N., Vahi, K., Brown, D. A., Deelman, E., & Taufer, M. (2022). Reproducibility of the First Image of a Black Hole in the Galaxy M87 From the Event Horizon Telescope Collaboration. Computing in Science & Engineering, 24(5), 42–52. https://doi.org/10.1109/MCSE.2023.3241105 (Funding Acknowledgments: NSF 2041977, 1941443, 2041901, 1664162 and 2041878) 
    @article{patel-cise-2023,
  author = {Patel, Ria and Roachell, Brandan and Caíno-Lores, Silvina and Ketron, Ross and Leonard, Jacob and Tan, Nigel and Vahi, Karan and Brown, Duncan A. and Deelman, Ewa and Taufer, Michela},
  journal = {Computing in Science & Engineering},
  title = {Reproducibility of the First Image of a Black Hole in the Galaxy M87 From the Event Horizon Telescope Collaboration},
  year = {2022},
  volume = {24},
  number = {5},
  pages = {42-52},
  doi = {10.1109/MCSE.2023.3241105},
  note = {Funding Acknowledgments: NSF 2041977, 1941443, 2041901, 1664162 and 2041878}
}
  19. Tanaka, R., Papadimitriou, G., Viswanath, S. C., Wang, C., Lyons, E., Thareja, K., Qu, C., Esquivel, A., Deelman, E., Mandal, A., Calyam, P., & Zink, M. (2022). Automating Edge-to-cloud Workflows for Science: Traversing the Edge-to-cloud Continuum with Pegasus. 2022 22nd IEEE International Symposium on Cluster, Cloud and Internet Computing (CCGrid), 826–833. https://doi.org/10.1109/CCGrid54584.2022.00098 (Funding Acknowledgments: NSF 2018074, 1664162. Best Paper Award.) 
    @inproceedings{tanaka-cloud2things-2022,
  author = {Tanaka, Ryan and Papadimitriou, George and Viswanath, Sai Charan and Wang, Cong and Lyons, Eric and Thareja, Komal and Qu, Chengyi and Esquivel, Alicia and Deelman, Ewa and Mandal, Anirban and Calyam, Prasad and Zink, Michael},
  booktitle = {2022 22nd IEEE International Symposium on Cluster, Cloud and Internet Computing (CCGrid)},
  doi = {10.1109/CCGrid54584.2022.00098},
  number = {},
  pages = {826-833},
  title = {Automating Edge-to-cloud Workflows for Science: Traversing the Edge-to-cloud Continuum with Pegasus},
  volume = {},
  year = {2022},
  note = {Funding Acknowledgments: NSF 2018074, 1664162. Best Paper Award.}
}
  20. Xin, Y., Fu, S.-W., Mandal, A., Tanaka, R., Rynge, M., Vahi, K., & Deelman, E. (2022). Data Integrity Error Localization in Networked Systems with Missing Data. ICC 2022 - IEEE International Conference on Communications, 341–346. https://doi.org/10.1109/ICC45855.2022.9838996 (Funding Acknowledgments: NSF 1839900) 
    @inproceedings{xin-icc-2022,
  author = {Xin, Yufeng and Fu, Shih-Wen and Mandal, Anirban and Tanaka, Ryan and Rynge, Mats and Vahi, Karan and Deelman, Ewa},
  booktitle = {ICC 2022 - IEEE International Conference on Communications},
  title = {Data Integrity Error Localization in Networked Systems with Missing Data},
  year = {2022},
  volume = {},
  number = {},
  pages = {341-346},
  doi = {10.1109/ICC45855.2022.9838996},
  note = {Funding Acknowledgments: NSF 1839900}
}

2021

  1. Brown, D., Vahi, K., Taufer, M., Welch, V., & Deelman, E. (2021). Reproducing GW150914: the first observation of gravitational waves from a binary black hole merger. Computing in Science & Engineering. https://doi.org/10.1109/MCSE.2021.3059232 (Funding Acknowledgments: NSF 1664162, NSF 1823405) 
    @article{brown2021reproducing,
  title = {Reproducing GW150914: the first observation of gravitational waves from a binary black hole merger},
  author = {Brown, Duncan and Vahi, Karan and Taufer, Michela and Welch, Von and Deelman, Ewa},
  journal = {Computing in Science \& Engineering},
  year = {2021},
  publisher = {IEEE},
  doi = {10.1109/MCSE.2021.3059232},
  note = {Funding Acknowledgments: NSF 1664162, NSF 1823405}
}
  2. Burkat, K., Pawlik, M., Balis, B., Malawski, M., Vahi, K., Rynge, M., da Silva, R. F., & Deelman, E. (2021). Serverless Containers – Rising Viable Approach to Scientific Workflows. 2021 IEEE 17th International Conference on EScience (EScience), 40–49. https://doi.org/10.1109/eScience51609.2021.00014 
    @inproceedings{burkat-escience-2021,
  author = {Burkat, Krzysztof and Pawlik, Maciej and Balis, Bartosz and Malawski, Maciej and Vahi, Karan and Rynge, Mats and da Silva, Rafael Ferreira and Deelman, Ewa},
  booktitle = {2021 IEEE 17th International Conference on eScience (eScience)},
  title = {Serverless Containers – Rising Viable Approach to Scientific Workflows},
  year = {2021},
  volume = {},
  number = {},
  pages = {40-49},
  doi = {10.1109/eScience51609.2021.00014}
}
  3. Casanova, H., Deelman, E., Gesing, S., Hildreth, M., Hudson, S., Koch, W., Larson, J., McDowell, M. A., Meyers, N., Navarro, J.-L., Papadimitriou, G., Tanaka, R., Taylor, I., Thain, D., Wild, S. M., Filgueira, R., & da Silva, R. F. (2021). Emerging Frameworks for Advancing Scientific Workflows Research, Development, and Education. 2021 IEEE Workshop on Workflows in Support of Large-Scale Science (WORKS), 74–80. https://doi.org/10.1109/WORKS54523.2021.00015 (Funding Acknowledgments: DOE DE-SC0012636, NSF 1664162) 
    @inproceedings{casanova-works-2021,
  author = {Casanova, Henri and Deelman, Ewa and Gesing, Sandra and Hildreth, Michael and Hudson, Stephen and Koch, William and Larson, Jeffrey and McDowell, Mary Ann and Meyers, Natalie and Navarro, John-Luke and Papadimitriou, George and Tanaka, Ryan and Taylor, Ian and Thain, Douglas and Wild, Stefan M. and Filgueira, Rosa and da Silva, Rafael Ferreira},
  booktitle = {2021 IEEE Workshop on Workflows in Support of Large-Scale Science (WORKS)},
  title = {Emerging Frameworks for Advancing Scientific Workflows Research, Development, and Education},
  year = {2021},
  volume = {},
  number = {},
  pages = {74-80},
  doi = {10.1109/WORKS54523.2021.00015},
  note = {Funding Acknowledgments: DOE DE-SC0012636, NSF 1664162}
}
  4. Casanova, H., Tanaka, R., Koch, W., & Ferreira da Silva, R. (2021). Teaching Parallel and Distributed Computing Concepts in Simulation with WRENCH. Journal of Parallel and Distributed Computing. https://doi.org/10.1016/j.jpdc.2021.05.009 (Funding Acknowledgments: NSF 1923539, NSF 1642335) 
    @article{casanova2021jpdc,
  title = {Teaching Parallel and Distributed Computing Concepts in Simulation with WRENCH},
  author = {Casanova, Henri and Tanaka, Ryan and Koch, William and Ferreira da Silva, Rafael},
  journal = {Journal of Parallel and Distributed Computing},
  volume = {},
  number = {},
  pages = {},
  doi = {10.1016/j.jpdc.2021.05.009},
  year = {2021},
  note = {Funding Acknowledgments: NSF 1923539, NSF 1642335}
}
  5. Coleman, T., Casanova, H., & Ferreira da Silva, R. (2021). WfChef: Automated Generation of Accurate Scientific Workflow Generators. 17th IEEE EScience Conference. (Funding Acknowledgments: NSF 1923539, NSF 2016619) 
    @inproceedings{coleman2021escience,
  author = {Coleman, Tain\=a and Casanova, Henri and Ferreira da Silva, Rafael},
  title = {WfChef: Automated Generation of Accurate Scientific Workflow Generators},
  booktitle = {17th IEEE eScience Conference},
  year = {2021},
  pages = {},
  doi = {},
  note = {Funding Acknowledgments: NSF 1923539, NSF 2016619}
}
  6. Coleman, T., Casanova, H., Gwartney, T., & Ferreira da Silva, R. (2021). Evaluating energy-aware scheduling algorithms for I/O-intensive scientific workflows. International Conference on Computational Science (ICCS), 183–197. https://doi.org/10.1007/978-3-030-77961-0_16 (Funding Acknowledgments: NSF 1923539, NSF 2016619) 
    @inproceedings{coleman2021iccs,
  author = {Coleman, Tain\=a and Casanova, Henri and Gwartney, Ty and Ferreira da Silva, Rafael},
  title = {Evaluating energy-aware scheduling algorithms for I/O-intensive scientific workflows},
  booktitle = {International Conference on Computational Science (ICCS)},
  year = {2021},
  pages = {183--197},
  doi = {10.1007/978-3-030-77961-0_16},
  organization = {Springer},
  note = {Funding Acknowledgments: NSF 1923539, NSF 2016619}
}
  7. Deelman, E., Ferreira da Silva, R., Vahi, K., Rynge, M., Mayani, R., Tanaka, R., Whitcup, W., & Livny, M. (2021). The Pegasus Workflow Management System: Translational Computer Science in Practice. Journal of Computational Science, 52, 101200. https://doi.org/10.1016/j.jocs.2020.101200 (Funding Acknowledgments: NSF 1664162) 
    @article{deelman2020jocs,
  title = {The Pegasus Workflow Management System: Translational Computer Science in Practice},
  author = {Deelman, Ewa and Ferreira da Silva, Rafael and Vahi, Karan and Rynge, Mats and Mayani, Rajiv and Tanaka, Ryan and Whitcup, Wendy and Livny, Miron},
  journal = {Journal of Computational Science},
  volume = {52},
  number = {},
  pages = {101200},
  year = {2021},
  doi = {10.1016/j.jocs.2020.101200},
  note = {Funding Acknowledgments: NSF 1664162}
}
  8. Deelman, E., Mandal, A., Murillo, A. P., Nabrzyski, J., Pascucci, V., Ricci, R., Baldin, I., Sons, S., Christopherson, L., Vardeman, C., Ferreira da Silva, R., Wyngaard, J., Petruzza, S., Rynge, M., Vahi, K., Whitcup, W. R., Drake, J., & Scott, E. (2021). Blueprint: Cyberinfrastructure Center of Excellence. Zenodo. https://doi.org/10.5281/zenodo.4587866 
    @article{deelman2021blueprint,
  title = {{Blueprint: Cyberinfrastructure Center of Excellence}},
  author = {Deelman, Ewa and Mandal, Anirban and Murillo, Angela P. and Nabrzyski, Jarek and Pascucci, Valerio and Ricci, Robert and Baldin, Ilya and Sons, Susan and Christopherson, Laura and Vardeman, Charles and Ferreira da Silva, Rafael and Wyngaard, Jane and Petruzza, Steve and Rynge, Mats and Vahi, Karan and Whitcup, Wendy R. and Drake, Josh and Scott, Erik},
  journal = {Zenodo},
  year = {2021},
  doi = {10.5281/zenodo.4587866}
}
  9. Do, H.-D., Hayot-Sasson, V., Ferreira da Silva, R., Steele, C., Casanova, H., & Glatard, T. (2021). Modeling the Linux page cache for accurate simulation of data-intensive applications. IEEE Cluster. (Funding Acknowledgments: NSF 1923539) 
    @inproceedings{do2021cluster,
  author = {Do, Hoang-Dung and Hayot-Sasson, Val\'erie and Ferreira da Silva, Rafael and Steele, Christopher and Casanova, Henri and Glatard, Tristan},
  title = {Modeling the Linux page cache for accurate simulation of data-intensive applications},
  booktitle = {IEEE Cluster},
  year = {2021},
  pages = {},
  doi = {},
  note = {Funding Acknowledgments: NSF 1923539}
}
  10. Do, T. M. A., Pottier, L., Caíno-Lores, S., Ferreira da Silva, R., Cuendet, M. A., Weinstein, H., Estrada, T., Taufer, M., & Deelman, E. (2021). A Lightweight Method for Evaluating In Situ Workflow Efficiency. Journal of Computational Science, 48, 101259. https://doi.org/10.1016/j.jocs.2020.101259 (Funding Acknowledgments: NSF 1741040, DOE DE-SC0012636) 
    @article{do-jocs-2021,
  title = {A Lightweight Method for Evaluating In Situ Workflow Efficiency},
  author = {Do, Tu Mai Anh and Pottier, Lo\"ic and Ca\'ino-Lores, Silvina and Ferreira da Silva, Rafael and Cuendet, Michel A. and Weinstein, Harel and Estrada, Trilce and Taufer, Michela and Deelman, Ewa},
  journal = {Journal of Computational Science},
  volume = {48},
  number = {},
  pages = {101259},
  year = {2021},
  doi = {10.1016/j.jocs.2020.101259},
  note = {Funding Acknowledgments: NSF 1741040, DOE DE-SC0012636}
}
  11. Do, T. M. A., Pottier Loı̈c, Ferreira da Silva, R., Caı́no-Lores Silvina, Taufer, M., & Deelman, E. (2021). Assessing Resource Provisioning and Allocation of Ensembles of In Situ Workflows. 50th International Conference on Parallel Processing Workshop. https://doi.org/10.1145/3458744.3474051 (Funding Acknowledgments: NSF 1741040, DOE SC0012636) 
    @inproceedings{do2021p2s2,
  author = {Do, Tu Mai Anh and Pottier, Lo\"{\i}c and Ferreira da Silva, Rafael and Ca\'{\i}no-Lores, Silvina and Taufer, Michela and Deelman, Ewa},
  title = {Assessing Resource Provisioning and Allocation of Ensembles of In Situ Workflows},
  year = {2021},
  isbn = {9781450384414},
  publisher = {Association for Computing Machinery},
  address = {New York, NY, USA},
  url = {https://doi.org/10.1145/3458744.3474051},
  doi = {10.1145/3458744.3474051},
  booktitle = {50th International Conference on Parallel Processing Workshop},
  articleno = {38},
  numpages = {10},
  keywords = {Scientific workflow, High-performance computing, In situ model, Ensemble workflow, Molecular dynamics},
  location = {Lemont, IL, USA},
  series = {ICPP Workshops '21},
  note = {Funding Acknowledgments: NSF 1741040, DOE SC0012636}
}
  12. Ferreira da Silva, R., Casanova, H., Chard, K., Altintas, I., Badia, R. M., Balis, B., Coleman, T., Coppens, F., Di Natale, F., Enders, B., Fahringer, T., Filgueira, R., Fursin, G., Garijo, D., Goble, C., Howell, D., Jha, S., Katz, D. S., Laney, D., … Wolf, M. (2021). A Community Roadmap for Scientific Workflows Research and Development. 2021 IEEE Workshop on Workflows in Support of Large-Scale Science (WORKS), 81–90. https://doi.org/10.1109/WORKS54523.2021.00016 
    @inproceedings{community2021works,
  title = {A Community Roadmap for Scientific Workflows Research and Development},
  author = {Ferreira da Silva, Rafael and Casanova, Henri and Chard, Kyle and Altintas, Ilkay and Badia, Rosa M and Balis, Bartosz and Coleman, Tain\~a and Coppens, Frederik and Di Natale, Frank and Enders, Bjoern and Fahringer, Thomas and Filgueira, Rosa and Fursin, Grigori and Garijo, Daniel and Goble, Carole and Howell, Dorran and Jha, Shantenu and Katz, Daniel S. and Laney, Daniel and Leser, Ulf and Malawski, Maciej and Mehta, Kshitij and Pottier, Lo\"ic and Ozik, Jonathan and Peterson, J. Luc and Ramakrishnan, Lavanya and Soiland-Reyes, Stian and Thain, Douglas and Wolf, Matthew},
  booktitle = {2021 IEEE Workshop on Workflows in Support of Large-Scale Science (WORKS)},
  pages = {81--90},
  year = {2021},
  doi = {10.1109/WORKS54523.2021.00016}
}
  13. Ferreira da Silva, R., Casanova, H., Chard, K., Coleman, T., Laney, D., Ahn, D., Jha, S., Howell, D., Soiland-Reys, S., Altintas, I., Thain, D., Filgueira, R., Babuji, Y., Badia, R. M., Balis, B., Caino-Lores, S., Callaghan, S., Coppens, F., Crusoe, M. R., … Wozniak, J. (2021). Workflows Community Summit: Advancing the State-of-the-art of Scientific Workflows Management Systems Research and Development. Zenodo. https://doi.org/10.5281/zenodo.4915801 
    @misc{wcs2021technical,
  author = {Ferreira da Silva, Rafael and Casanova, Henri and Chard, Kyle and Coleman, Tain\={a} and Laney, Dan and Ahn, Dong and Jha, Shantenu and Howell, Dorran and Soiland-Reys, Stian and Altintas, Ilkay and Thain, Douglas and Filgueira, Rosa and Babuji, Yadu and Badia, Rosa M. and Balis, Bartosz and Caino-Lores, Silvina and Callaghan, Scott and Coppens, Frederik and Crusoe, Michael R. and De, Kaushik and Di Natale, Frank and Do, Tu M. A. and Enders, Bjoern and Fahringer, Thomas and Fouilloux, Anne and Fursin, Grigori and Gaignard, Alban and Ganose, Alex and Garijo, Daniel and Gesing, Sandra and Goble, Carole and Hasan, Adil and Huber, Sebastiaan and Katz, Daniel S. and Leser, Ulf and Lowe, Douglas and Ludaescher, Bertram and Maheshwari, Ketan and Malawski, Maciej and Mayani, Rajiv and Mehta, Kshitij and Merzky, Andre and Munson, Todd and Ozik, Jonathan and Pottier, Lo\"{i}c and Ristov, Sashko and Roozmeh, Mehdi and Souza, Renan and Suter, Fr\'ed\'eric and Tovar, Benjamin and Turilli, Matteo and Vahi, Karan and Vidal-Torreira, Alvaro and Whitcup, Wendy and Wilde, Michael and Williams, Alan and Wolf, Matthew and Wozniak, Justin},
  title = {{Workflows Community Summit: Advancing the State-of-the-art of Scientific Workflows Management Systems Research and Development}},
  month = jun,
  year = {2021},
  publisher = {Zenodo},
  doi = {10.5281/zenodo.4915801}
}
  14. Ferreira da Silva, R., Casanova, H., Chard, K., Laney, D., Ahn, D., Jha, S., Goble, C., Ramakrishnan, L., eerson, L., Enders, B., Thain, D., Altintas, I., Babuji, Y., Badia, R., Bonazzi, V., Coleman, T., Crusoe, M., Deelman, E., Di Natale, F., … Wozniak, J. (2021). Workflows Community Summit: Bringing the Scientific Workflows Community Together. Zenodo. https://doi.org/10.5281/zenodo.4606958 
    @misc{ferreiradasilva2021wcs,
  author = {Ferreira da Silva, Rafael and Casanova, Henri and Chard, Kyle and Laney, Dan and Ahn, Dong and Jha, Shantenu and Goble, Carole and Ramakrishnan, Lavanya and eerson, Luc and Enders, Bjoern and Thain, Douglas and Altintas, Ilkay and Babuji, Yadu and Badia, Rosa and Bonazzi, Vivien and Coleman, Taina and Crusoe, Michael and Deelman, Ewa and Di Natale, Frank and Di Tommaso, Paolo and Fahringer, Thomas and Filgueira, Rosa and Fursin, Grigori and Ganose, Alex and Gruning, Bjorn and Katz, Daniel S. and Kuchar, Olga and Kupresanin, Ana and Ludascher, Bertram and Maheshwari, Ketan and Mattoso, Marta and Mehta, Kshitij and Munson, Todd and Ozik, Jonathan and Peterka, Tom and Pottier, Lo\"ic and Randles, Tim and Soiland-Reyes, Stian and Tovar, Benjamin and Turilli, Matteo and Uram, Thomas and Vahi, Karan and Wilde, Michael and Wolf, Matthew and Wozniak, Justin},
  title = {{Workflows Community Summit: Bringing the Scientific Workflows Community Together}},
  month = mar,
  year = {2021},
  publisher = {Zenodo},
  doi = {10.5281/zenodo.4606958}
}
  15. Gesing, S., Ferreira da Silva, R., Deelman, E., Hildreth, M., McDowell, M. A., Meyers, N., Taylor, I., & Tain, D. (2021). VisDict: Enhancing the Communication between Workflow Providers and User Communities via a Visual Dictionary. 2021 IEEE/ACM Workflows in Support of Large-Scale Science (WORKS). 
    @inproceedings{gesing-works-2021,
  title = {VisDict: Enhancing the Communication between Workflow Providers and User Communities via a Visual Dictionary},
  author = {Gesing, Sandra and Ferreira da Silva, Rafael and Deelman, Ewa and Hildreth, Michael and McDowell, Mary Ann and Meyers, Natalie and Taylor, Ian and Tain, Douglas},
  booktitle = {2021 IEEE/ACM Workflows in Support of Large-Scale Science (WORKS)},
  year = {2021},
  pages = {},
  doi = {}
}
  16. Gil, Y., Garijo, D., Khider, D., Knoblock, C. A., Ratnakar, V., Osorio, M., Vargas, H., Pham, M., Pujara, J., Shbita, B., Vu, B., Chiang, Y.-Y., Feldman, D., Lin, Y., Song, H., Kumar, V., Khandelwal, A., Steinbach, M., Tayal, K., … Shu, L. (2021). Artificial Intelligence for Modeling Complex Systems: Taming the Complexity of Expert Models to Improve Decision Making. ACM Transactions on Interactive Intelligent Systems, 11(2). (Funding Acknowledgments: DARPA W911NF-18-1-0027) 
    @article{gil2021tiis,
  title = {Artificial Intelligence for Modeling Complex Systems: Taming the Complexity of Expert Models to Improve Decision Making},
  author = {Gil, Yolanda and Garijo, Daniel and Khider, Deborah and Knoblock, Craig A. and Ratnakar, Varun and Osorio, Maximiliano and Vargas, Hernán and Pham, Minh and Pujara, Jay and Shbita, Basel and Vu, Binh and Chiang, Yao-Yi and Feldman, Dan and Lin, Yijun and Song, Hayley and Kumar, Vipin and Khandelwal, Ankush and Steinbach, Michael and Tayal, Kshitij and Xu, Shaoming and Pierce, Suzanne A. and Pearson, Lissa and Hardesty-Lewis, Daniel and Deelman, Ewa and Ferreira da Silva, Rafael and Mayani, Rajiv and Kemanian, Armen R. and Shi, Yuning and Leonard, Lorne and Peckham, Scott and Stoica, Maria and Cobourn, Kelly and Zhang, Zeya and Duffy, Christopher and Shu, Lele},
  journal = {ACM Transactions on Interactive Intelligent Systems},
  volume = {11},
  number = {2},
  pages = {},
  doi = {},
  year = {2021},
  note = {Funding Acknowledgments: DARPA W911NF-18-1-0027}
}
  17. Hataishi, E., Dutot, P.-F., Ferreira da Silva, R., & Casanova, H. (2021). GLUME: A Strategy for Reducing Workflow Execution Times on Batch-Scheduled Platforms. Workshop on Job Scheduling Strategies for Parallel Processing (JSSPP). (Funding Acknowledgments: NSF 1923539) 
    @inproceedings{hataishi2021jsspp,
  author = {Hataishi, Evan and Dutot, Pierre-Francois and Ferreira da Silva, Rafael and Casanova, Henri},
  title = {GLUME: A Strategy for Reducing Workflow Execution Times on Batch-Scheduled Platforms},
  booktitle = {Workshop on Job Scheduling Strategies for Parallel Processing (JSSPP)},
  year = {2021},
  pages = {},
  doi = {},
  note = {Funding Acknowledgments: NSF 1923539}
}
  18. Hayes, C., Kulkarni, C., Milman, E. D., Okunloye, O., Olshansky, A., Oruche, R., Kee, K., Moreira, P. C. S., Vardeman, C., Coleman, T., Do, T. M. A., Jain, A., Krawczuk, P., Lam, K., Nagarkar, S., Papadimitriou, G., Subramanya, S., White, R., Whitcup, W., … Deelman, E. (2021). 2021 SciTech and Friends Research Symposium. Zenodo. https://doi.org/10.5281/zenodo.4847543 
    @misc{scitech2021symposium,
  author = {Hayes, Cassandra and Kulkarni, Chaitra and Milman, Eric D. and Okunloye, Oluwabusayo and Olshansky, Alex and Oruche, Roland and Kee, Kerk and Moreira, Priscila C. S. and Vardeman, Charles and Coleman, Tain\=a and Do, Tu Mai Anh and Jain, Aditi and Krawczuk, Patrycja and Lam, Kelsie and Nagarkar, Shubham and Papadimitriou, George and Subramanya, Srujana and White, Rebecca and Whitcup, Wendy and Ferreira da Silva, Rafael and Deelman, Ewa},
  title = {{2021 SciTech and Friends Research Symposium}},
  month = may,
  year = {2021},
  publisher = {Zenodo},
  doi = {10.5281/zenodo.4847543},
  url = {https://doi.org/10.5281/zenodo.4847543}
}
  19. Ketron, R., Leonard, J., Roachell, B., Patel, R., White, R., Caíno-Lores, S., Tan, N., Miles, P., Vahi, K., Deelman, E., Brown, D., & Taufer, M. (2021). A Case Study in Scientific Reproducibility from the Event Horizon Telescope (EHT). 2021 IEEE 17th International Conference on EScience (EScience), 249–250. https://doi.org/10.1109/eScience51609.2021.00045 (Funding Acknowledgments: NSF 2041977, 2041901, 2041878) 
    @inproceedings{ketron-escience-2021,
  author = {Ketron, R. and Leonard, J. and Roachell, B. and Patel, R. and White, R. and Caíno-Lores, S. and Tan, N. and Miles, P. and Vahi, K. and Deelman, E. and Brown, D. and Taufer, M.},
  booktitle = {2021 IEEE 17th International Conference on eScience (eScience)},
  title = {A Case Study in Scientific Reproducibility from the Event Horizon Telescope (EHT)},
  year = {2021},
  volume = {},
  number = {},
  pages = {249-250},
  doi = {10.1109/eScience51609.2021.00045},
  note = {Funding Acknowledgments: NSF 2041977, 2041901, 2041878}
}
  20. Krawczuk, P., Nagarkar, S., & Deelman, E. (2021). CrisisFlow: Multimodal Representation Learning Workflow for Crisis Computing. 2021 IEEE 17th International Conference on EScience (EScience), 264–266. https://doi.org/10.1109/eScience51609.2021.00052 (Funding Acknowledgments: NSF 1664162) 
    @inproceedings{krawczuk-escience-2021,
  author = {Krawczuk, Patrycja and Nagarkar, Shubham and Deelman, Ewa},
  booktitle = {2021 IEEE 17th International Conference on eScience (eScience)},
  title = {CrisisFlow: Multimodal Representation Learning Workflow for Crisis Computing},
  year = {2021},
  volume = {},
  number = {},
  pages = {264-266},
  doi = {10.1109/eScience51609.2021.00052},
  note = {Funding Acknowledgments: NSF 1664162}
}
  21. Krawczuk, P., Papadimitriou, G., Nagarkar, S., Kiran, M., Mandal, A., & Deelman, E. (2021). Anomaly Detection in Scientific Workflows using End-to-End Execution Gantt Charts and Convolutional Neural Networks. Practice and Experience in Advanced Research Computing. https://doi.org/10.1145/3437359.3465597 (Funding Acknowledgments: DOE DESC0012636) 
    @inproceedings{krawczuk-pearc-2021,
  author = {Krawczuk, Patrycja and Papadimitriou, George and Nagarkar, Shubham and Kiran, Mariam and Mandal, Anirban and Deelman, Ewa},
  title = {Anomaly Detection in Scientific Workflows using End-to-End Execution Gantt Charts and Convolutional Neural Networks},
  year = {2021},
  isbn = {9781450382922},
  publisher = {Association for Computing Machinery},
  address = {New York, NY, USA},
  url = {http://doi.acm.org/10.1145/3437359.3465597},
  doi = {10.1145/3437359.3465597},
  booktitle = {Practice and Experience in Advanced Research Computing},
  articleno = {26},
  numpages = {5},
  location = {Boston, MA, USA},
  series = {PEARC '21},
  note = {Funding Acknowledgments: DOE DESC0012636}
}
  22. Krawczuk, P., Papadimitriou, G., Tanaka, R., Do, T. M. A., Subramany, S., Nagarkar, S., Jain, A., Lam, K., Mandal, A., Pottier, L., & Deelman, E. (2021). A Performance Characterization of Scientific Machine Learning Workflows. 2021 IEEE/ACM Workflows in Support of Large-Scale Science (WORKS), 58–65. https://doi.org/10.1109/WORKS54523.2021.00013 (Funding Acknowledgments: DOE DE-SC0012636, DE-SC0022328, NSF 1664162) 
    @inproceedings{krawczuk-works-2021,
  title = {A Performance Characterization of Scientific Machine Learning Workflows},
  author = {Krawczuk, Patrycja and Papadimitriou, George and Tanaka, Ryan and Do, Tu Mai Anh and Subramany, Srujana and Nagarkar, Shubham and Jain, Aditi and Lam, Kelsie and Mandal, Anirban and Pottier, Lo\"ic and Deelman, Ewa},
  booktitle = {2021 IEEE/ACM Workflows in Support of Large-Scale Science (WORKS)},
  year = {2021},
  pages = {58-65},
  doi = {10.1109/WORKS54523.2021.00013},
  note = {Funding Acknowledgments: DOE DE-SC0012636, DE-SC0022328, NSF 1664162}
}
  23. Lyons, E., Saplakoglu, H., Zink, M., Thareja, K., Mandal, A., Qu, C., Wang, S., Calyam, P., Papadimitriou, G., Tanaka, R., & Deelman, E. (2021). FlyNet: A Platform to Support Scientific Workflows from the Edge to the Core for UAV Applications. Proceedings of the 14th IEEE/ACM International Conference on Utility and Cloud Computing. https://doi.org/10.1145/3468737.3494098 (Funding Acknowledgments: NSF 2018074) 
    @inproceedings{lyons-ucc-2021,
  author = {Lyons, Eric and Saplakoglu, Hakan and Zink, Michael and Thareja, Komal and Mandal, Anirban and Qu, Chengyi and Wang, Songjie and Calyam, Prasad and Papadimitriou, George and Tanaka, Ryan and Deelman, Ewa},
  title = {FlyNet: A Platform to Support Scientific Workflows from the Edge to the Core for UAV Applications},
  year = {2021},
  isbn = {9781450385640},
  publisher = {Association for Computing Machinery},
  address = {New York, NY, USA},
  url = {https://doi.org/10.1145/3468737.3494098},
  doi = {10.1145/3468737.3494098},
  booktitle = {Proceedings of the 14th IEEE/ACM International Conference on Utility and Cloud Computing},
  articleno = {12},
  numpages = {10},
  location = {Leicester, United Kingdom},
  series = {UCC '21},
  note = {Funding Acknowledgments: NSF 2018074}
}
  24. Lyons, E., Seo, D.-J., Kim, S., Habibi, H., Papadimitriou, G., Tanaka, R., Deelman, E., Zink, M., & Mandal, A. (2021). Predicting Flash Floods in the Dallas-Fort Worth Metroplex Using Workflows and Cloud Computing. 2021 IEEE 17th International Conference on EScience (EScience), 259–261. https://doi.org/10.1109/eScience51609.2021.00050 (Funding Acknowledgments: NSF 1826997, 2018074, 1664162) 
    @inproceedings{lyons-escience-2021,
  author = {Lyons, Eric and Seo, Dong-Jun and Kim, Sunghee and Habibi, Hamideh and Papadimitriou, George and Tanaka, Ryan and Deelman, Ewa and Zink, Michael and Mandal, Anirban},
  booktitle = {2021 IEEE 17th International Conference on eScience (eScience)},
  title = {Predicting Flash Floods in the Dallas-Fort Worth Metroplex Using Workflows and Cloud Computing},
  year = {2021},
  volume = {},
  number = {},
  pages = {259-261},
  doi = {10.1109/eScience51609.2021.00050},
  note = {Funding Acknowledgments: NSF 1826997, 2018074, 1664162}
}
  25. Papadimitriou, G., & Deelman, E. (2021). A Lightweight GPU Monitoring Extension for Pegasus Kickstart. 2021 IEEE/ACM Workflows in Support of Large-Scale Science (WORKS). https://doi.org/10.5281/zenodo.5915106 (Funding Acknowledgments: DOE DE-SC0012636, NSF 1664162) 
    @inproceedings{papadimitriou-works-2021,
  title = {A Lightweight GPU Monitoring Extension for Pegasus Kickstart},
  author = {Papadimitriou, George and Deelman, Ewa},
  booktitle = {2021 IEEE/ACM Workflows in Support of Large-Scale Science (WORKS)},
  year = {2021},
  pages = {},
  doi = {10.5281/zenodo.5915106},
  note = {Funding Acknowledgments: DOE DE-SC0012636, NSF 1664162}
}
  26. Papadimitriou, G., Lyons, E., Wang, C., Thareja, K., Tanaka, R., Ruth, P., Rodero, I., Deelman, E., Zink, M., & Mandal, A. (2021). Fair sharing of network resources among workflow ensembles. Cluster Computing. https://doi.org/10.1007/s10586-021-03457-3 (Funding Acknowledgments: NSF 1826997) 
    @article{papadimitriou-cluster-2021,
  title = {Fair sharing of network resources among workflow ensembles},
  author = {Papadimitriou, George and Lyons, Eric and Wang, Cong and Thareja, Komal and Tanaka, Ryan and Ruth, Paul and Rodero, Ivan and Deelman, Ewa and Zink, Michael and Mandal, Anirban},
  year = {2021},
  journal = {Cluster Computing},
  issn = {1573-7543},
  url = {https://doi.org/10.1007/s10586-021-03457-3},
  doi = {10.1007/s10586-021-03457-3},
  note = {Funding Acknowledgments: NSF 1826997}
}
  27. Papadimitriou, G., Wang, C., Vahi, K., Ferreira da Silva, R., Mandal, A., Zhengchun, L., Mayani, R., Rynge, M., Kiran, M., Lynch, V. E., Kettimuthu, R., Deelman, E., Vetter, J. S., & Foster, I. (2021). End-to-End Online Performance Data Capture and Analysis for Scientific Workflows. Future Generation Computer Systems, 117, 387–400. https://doi.org/10.1016/j.future.2020.11.024 (Funding Acknowledgments: DOE DE-SC0012636. Best Paper Award and Editor’s Choice Article) 
    @article{papadimitriou-fgcs-2021,
  title = {End-to-End Online Performance Data Capture and Analysis for Scientific Workflows},
  author = {Papadimitriou, George and Wang, Cong and Vahi, Karan and Ferreira da Silva, Rafael and Mandal, Anirban and Zhengchun, Liu and Mayani, Rajiv and Rynge, Mats and Kiran, Mariam and Lynch, Vickie E. and Kettimuthu, Rajkumar and Deelman, Ewa and Vetter, Jeffrey S. and Foster, Ian},
  journal = {Future Generation Computer Systems},
  year = {2021},
  volume = {117},
  number = {},
  pages = {387-400},
  doi = {10.1016/j.future.2020.11.024},
  note = {Funding Acknowledgments: DOE DE-SC0012636. Best Paper Award and Editor's Choice Article}
}
  28. Rangan, R., Watkins, A. M., Chacon, J., Kretsch, R., Kladwang, W., Zheludev, I. N., Townley, J., Rynge, M., Thain, G., & Das, R. (2021). De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures. Nucleic Acids Research, 49(6), 3092–3108. https://doi.org/10.1093/nar/gkab119 
    @article{rangan-nucleicacids-2021,
  author = {Rangan, Ramya and Watkins, Andrew M and Chacon, Jose and Kretsch, Rachael and Kladwang, Wipapat and Zheludev, Ivan N and Townley, Jill and Rynge, Mats and Thain, Gregory and Das, Rhiju},
  title = {{De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures}},
  journal = {Nucleic Acids Research},
  volume = {49},
  number = {6},
  pages = {3092-3108},
  year = {2021},
  month = mar,
  issn = {0305-1048},
  doi = {10.1093/nar/gkab119},
  url = {https://doi.org/10.1093/nar/gkab119},
  eprint = {https://academic.oup.com/nar/article-pdf/49/6/3092/36884656/gkab119.pdf}
}
  29. Taufer, M., Deelman, E., Silva, R. F. da, Estrada, T., Hall, M., & Livny, M. (2021). A Roadmap to Robust Science for High-throughput Applications: The Developers’ Perspective. 2021 IEEE International Conference on Cluster Computing (CLUSTER), 807–808. https://doi.org/10.1109/Cluster48925.2021.00068 (Funding Acknowledgments: NSF 2028881, 2028923, 2028930, 2028955, 2028956) 
    @inproceedings{taufer-cluster-2021,
  author = {Taufer, M. and Deelman, E. and Silva, R. Ferreira da and Estrada, T. and Hall, M. and Livny, M.},
  booktitle = {2021 IEEE International Conference on Cluster Computing (CLUSTER)},
  title = {A Roadmap to Robust Science for High-throughput Applications: The Developers’ Perspective},
  year = {2021},
  volume = {},
  number = {},
  pages = {807-808},
  doi = {10.1109/Cluster48925.2021.00068},
  note = {Funding Acknowledgments: NSF 2028881, 2028923, 2028930, 2028955, 2028956}
}
  30. Taufer, M., Deelman, E., da Silva, R. F., Estrada, T., & Hall, M. (2021). A Roadmap to Robust Science for High-throughput Applications: The Scientists’ Perspective. 2021 IEEE 17th International Conference on EScience (EScience), 247–248. https://doi.org/10.1109/eScience51609.2021.00044 (Funding Acknowledgments: NSF 2028881, 2028923, 2028930, 2028955, 2028956) 
    @inproceedings{taufer-escience-2021,
  author = {Taufer, M. and Deelman, E. and da Silva, R. Ferreira and Estrada, T. and Hall, M.},
  booktitle = {2021 IEEE 17th International Conference on eScience (eScience)},
  title = {A Roadmap to Robust Science for High-throughput Applications: The Scientists’ Perspective},
  year = {2021},
  volume = {},
  number = {},
  pages = {247-248},
  doi = {10.1109/eScience51609.2021.00044},
  note = {Funding Acknowledgments: NSF 2028881, 2028923, 2028930, 2028955, 2028956}
}
  31. Tu, H., Papadimitriou, G., Kiran, M., Wang, C., Mandal, A., Deelman, E., & Menzies, T. (2021). Mining Workflows for Anomalous Data Transfers. 2021 2021 IEEE/ACM 18th International Conference on Mining Software Repositories (MSR) (MSR), 1–12. https://doi.org/10.1109/MSR52588.2021.00013 (Funding Acknowledgments: NSF 1826574, NSF 1931425, DOE DE-SC0012636) 
    @inproceedings{ken2021msr,
  author = {Tu, H. and Papadimitriou, G. and Kiran, M. and Wang, C. and Mandal, A. and Deelman, E. and Menzies, T.},
  booktitle = {2021 2021 IEEE/ACM 18th International Conference on Mining Software Repositories (MSR) (MSR)},
  title = {Mining Workflows for Anomalous Data Transfers},
  year = {2021},
  volume = {},
  issn = {},
  pages = {1-12},
  keywords = {scientific workflow, tcp signatures, anomaly detection, hyper-parameter tuning, sequential optimization},
  doi = {10.1109/MSR52588.2021.00013},
  url = {https://doi.ieeecomputersociety.org/10.1109/MSR52588.2021.00013},
  publisher = {IEEE Computer Society},
  address = {Los Alamitos, CA, USA},
  month = may,
  note = {Funding Acknowledgments: NSF 1826574, NSF 1931425, DOE DE-SC0012636}
}
  32. Xin, Y., Fu, S.-W., Mandal, A., Baldin, I., Tanaka, R., Rynge, M., Vahi, K., Deelman, E., Abhinit, I., & Von, W. (2021). Root Cause Analysis of Data Integrity Errors in Networked Systems with Incomplete Information. 2021 International Conference on Information and Communication Technology Convergence (ICTC), 735–740. https://doi.org/10.1109/ICTC52510.2021.9621124 
    @inproceedings{xin-ictc-2021,
  author = {Xin, Yufeng and Fu, Shih-Wen and Mandal, Anirban and Baldin, Ilya and Tanaka, Ryan and Rynge, Mats and Vahi, Karan and Deelman, Ewa and Abhinit, Ishan and Von, Welch},
  booktitle = {2021 International Conference on Information and Communication Technology Convergence (ICTC)},
  title = {Root Cause Analysis of Data Integrity Errors in Networked Systems with Incomplete Information},
  year = {2021},
  volume = {},
  number = {},
  pages = {735-740},
  doi = {10.1109/ICTC52510.2021.9621124}
}

2020

  1. Adams, J. C., Back, G., Bala, P., Bane, M. K., Cameron, K., Casanova, H., Ellis, M., Ferreira da Silva, R., Jethwani, G., Koch, W., Lee, T., & Zhu, T. (2020). Lightning Talks of EduHPC 2020. 2020 IEEE/ACM Workshop on Education for High-Performance Computing (EduHPC), 59–64. https://doi.org/10.1109/EduHPC51895.2020.00013 (Funding Acknowledgments: NSF 1923539) 
    @inproceedings{adams2020eduhpc,
  author = {Adams, Joel C. and Back, Godmar and Bala, Piotr and Bane, Michael K. and Cameron, Kirk and Casanova, Henri and Ellis, Margaret and Ferreira da Silva, Rafael and Jethwani, Gautam and Koch, William and Lee, Tabitha and Zhu, Tongyu},
  title = {Lightning Talks of EduHPC 2020},
  booktitle = {2020 IEEE/ACM Workshop on Education for High-Performance Computing (EduHPC)},
  pages = {59--64},
  year = {2020},
  doi = {10.1109/EduHPC51895.2020.00013},
  note = {Funding Acknowledgments: NSF 1923539}
}
  2. Casanova, H., Ferreira da Silva, R., Gonzalez-Escribano, A., Koch, W., Torres, Y., & Bunde, D. P. (2020). Peachy Parallel Assignments (EduHPC 2020). 2020 IEEE/ACM Workshop on Education for High-Performance Computing (EduHPC), 53–58. https://doi.org/10.1109/EduHPC51895.2020.00012 (Funding Acknowledgments: NSF 1923539) 
    @inproceedings{casanova2020eduhpc,
  title = {Peachy Parallel Assignments (EduHPC 2020)},
  author = {Casanova, Henri and Ferreira da Silva, Rafael and Gonzalez-Escribano, Arturo and Koch, William and Torres, Yuri and Bunde, David P.},
  booktitle = {2020 IEEE/ACM Workshop on Education for High-Performance Computing (EduHPC)},
  pages = {53--58},
  year = {2020},
  doi = {10.1109/EduHPC51895.2020.00012},
  note = {Funding Acknowledgments: NSF 1923539}
}
  3. Casanova, H., Ferreira da Silva, R., Tanaka, R., Pandey, S., Jethwani, G., Koch, W., Albrecht, S., Oeth, J., & Suter, F. (2020). Developing Accurate and Scalable Simulators of Production Workflow Management Systems with WRENCH. Future Generation Computer Systems, 112, 162–175. https://doi.org/10.1016/j.future.2020.05.030 (Funding Acknowledgments: NSF 1642335, NSF 1923539) 
    @article{casanova2020fgcs,
  title = {Developing Accurate and Scalable Simulators of Production Workflow Management Systems with WRENCH},
  author = {Casanova, Henri and Ferreira da Silva, Rafael and Tanaka, Ryan and Pandey, Suraj and Jethwani, Gautam and Koch, William and Albrecht, Spencer and Oeth, James and Suter, Fr\'{e}d\'{e}ric},
  journal = {Future Generation Computer Systems},
  volume = {112},
  number = {},
  pages = {162--175},
  year = {2020},
  doi = {10.1016/j.future.2020.05.030},
  note = {Funding Acknowledgments: NSF 1642335, NSF 1923539}
}
  4. Do, T. M. A., Pottier, L., Thomas, S., Ferreira da Silva, R., Cuendet, M. A., Weinstein, H., Estrada, T., Taufer, M., & Deelman, E. (2020). A Novel Metric to Evaluate In Situ Workflows. International Conference on Computational Science (ICCS), 538–553. https://doi.org/10.1007/978-3-030-50371-0_40 (Funding Acknowledgments: NSF 1741040) 
    @inproceedings{do2020iccs,
  author = {Do, Tu Mai Anh and Pottier, Lo\"ic and Thomas, Stephen and Ferreira da Silva, Rafael and Cuendet, Michel A. and Weinstein, Harel and Estrada, Trilce and Taufer, Michela and Deelman, Ewa},
  title = {A Novel Metric to Evaluate In Situ Workflows},
  booktitle = {International Conference on Computational Science (ICCS)},
  year = {2020},
  pages = {538--553},
  doi = {10.1007/978-3-030-50371-0_40},
  note = {Funding Acknowledgments: NSF 1741040}
}
  5. Ferreira da Silva, R., Casanova, H., Orgerie, A.-C., Tanaka, R., Deelman, E., & Suter, F. (2020). Characterizing, Modeling, and Accurately Simulating Power and Energy Consumption of I/O-intensive Scientific Workflows. Journal of Computational Science, 44, 101157. https://doi.org/10.1016/j.jocs.2020.101157 (Funding Acknowledgments: NSF 1642335, NSF 1923539, NSF 1664162, DOE DE-SC0012636) 
    @article{ferreiradasilva2020jocs,
  title = {Characterizing, Modeling, and Accurately Simulating Power and Energy Consumption of I/O-intensive Scientific Workflows},
  author = {Ferreira da Silva, Rafael and Casanova, Henri and Orgerie, Anne-C\'{e}cile and Tanaka, Ryan and Deelman, Ewa and Suter, Fr\'{e}d\'{e}ric},
  journal = {Journal of Computational Science},
  volume = {44},
  number = {},
  pages = {101157},
  year = {2020},
  doi = {10.1016/j.jocs.2020.101157},
  note = {Funding Acknowledgments: NSF 1642335, NSF 1923539, NSF 1664162, DOE DE-SC0012636}
}
  6. Ferreira da Silva, R., Pottier, L., Coleman, T., Deelman, E., & Casanova, H. (2020). WorkflowHub: Community Framework for Enabling Scientific Workflow Research and Development. 2020 IEEE/ACM Workflows in Support of Large-Scale Science (WORKS), 49–56. https://doi.org/10.1109/WORKS51914.2020.00012 (Funding Acknowledgments: NSF 2016619, DOE DE-SC0012636, NSF 1664162, NSF 1923539) 
    @inproceedings{ferreiradasilva2020works,
  title = {WorkflowHub: Community Framework for Enabling Scientific Workflow Research and Development},
  author = {Ferreira da Silva, Rafael and Pottier, Lo\"ic and Coleman, Tain\=a and Deelman, Ewa and Casanova, Henri},
  booktitle = {2020 IEEE/ACM Workflows in Support of Large-Scale Science (WORKS)},
  year = {2020},
  pages = {49--56},
  doi = {10.1109/WORKS51914.2020.00012},
  note = {Funding Acknowledgments: NSF 2016619, DOE DE-SC0012636, NSF 1664162, NSF 1923539}
}
  7. Kiran, M., Wang, C., Papadimitriou, G., Mandal, A., & Deelman, E. (2020). Detecting Anomalous Packets in Network Transfers: Investigations using PCA, Autoencoder and Isolation Forest in TCP. Machine Learning. https://doi.org/10.1007/s10994-020-05870-y (Funding Acknowledgments: DOE DESC0012636) 
    @article{kiran-ml-2020,
  author = {Kiran, Mariam and Wang, Cong and Papadimitriou, George and Mandal, Anirban and Deelman, Ewa},
  title = {Detecting Anomalous Packets in Network Transfers: Investigations using PCA, Autoencoder and Isolation Forest in TCP},
  journal = {Machine Learning},
  year = {2020},
  volume = {},
  number = {},
  pages = {},
  issn = {1573-0565},
  doi = {10.1007/s10994-020-05870-y},
  url = {https://doi.org/10.1007/s10994-020-05870-y},
  note = {Funding Acknowledgments: DOE DESC0012636}
}
  8. Lyons, E., Westbrook, D., Grote, A., Papadimitriou, G., Thareja, K., Wang, C., Zink, M., Deelman, E., Mandal, A., & Ruth, P. (2020). An On-Demand Weather Avoidance System for Small Aircraft Flight Path Routing. In F. Darema, E. Blasch, S. Ravela, & A. Aved (Eds.), Dynamic Data Driven Application Systems (pp. 311–319). Springer International Publishing. https://doi.org/10.1007/978-3-030-61725-7_36 (Funding Acknowledgments: NSF 1826997, 2018074) 
    @inproceedings{lyons-dddas-2020,
  author = {Lyons, Eric and Westbrook, David and Grote, Andrew and Papadimitriou, George and Thareja, Komal and Wang, Cong and Zink, Michael and Deelman, Ewa and Mandal, Anirban and Ruth, Paul},
  editor = {Darema, Frederica and Blasch, Erik and Ravela, Sai and Aved, Alex},
  title = {An On-Demand Weather Avoidance System for Small Aircraft Flight Path Routing},
  booktitle = {Dynamic Data Driven Application Systems},
  year = {2020},
  publisher = {Springer International Publishing},
  address = {Cham},
  pages = {311--319},
  isbn = {978-3-030-61725-7},
  doi = {10.1007/978-3-030-61725-7_36},
  note = {Funding Acknowledgments: NSF 1826997, 2018074}
}
  9. Lyons, E., Zink, M., Mandal, A., Wang, C., Ruth, P., Radhakrishnan, C., Papadimitriou, G., Deelman, E., Thareja, K., & Rodero, I. (2020). DyNamo: Scalable Weather Workflow Processing in the Academic MultiCloud. 100th American Meteorological Society Annual Meeting. (Funding Acknowledgments: NSF 1826997) 
    @article{lyons-ams100-2020,
  title = {DyNamo: Scalable Weather Workflow Processing in the Academic MultiCloud},
  author = {Lyons, Eric and Zink, Michael and Mandal, Anirban and Wang, Cong and Ruth, Paul and Radhakrishnan, Chandrasekar and Papadimitriou, George and Deelman, Ewa and Thareja, Komal and Rodero, Ivan},
  journal = {100th American Meteorological Society Annual Meeting},
  volume = {},
  number = {},
  pages = {},
  year = {2020},
  doi = {},
  note = {Funding Acknowledgments: NSF 1826997}
}
  10. Papadimitriou, G., Lyons, E., Wang, C., Thareja, K., Tanaka, R., Ruth, P., Villalobos, J. J., Rodero, I., Deelman, E., Zink, M., & Mandal, A. (2020). Application Aware Software Defined Flows of Workflow Ensembles. 2020 IEEE/ACM Innovating the Network for Data-Intensive Science (INDIS), 10–21. https://doi.org/10.1109/INDIS51933.2020.00007 (Funding Acknowledgments: NSF 1826997) 
    @inproceedings{papadimitriou-indis-2020,
  title = {Application Aware Software Defined Flows of Workflow Ensembles},
  author = {Papadimitriou, George and Lyons, Eric and Wang, Cong and Thareja, Komal and Tanaka, Ryan and Ruth, Paul and Villalobos, J.J. and Rodero, Ivan and Deelman, Ewa and Zink, Michael and Mandal, Anirban},
  booktitle = {2020 IEEE/ACM Innovating the Network for Data-Intensive Science (INDIS)},
  year = {2020},
  volume = {},
  number = {},
  pages = {10-21},
  doi = {10.1109/INDIS51933.2020.00007},
  note = {Funding Acknowledgments: NSF 1826997}
}
  11. Papadimitriou, G., Vahi, K., Kincl, J., Anantharaj, V., Deelman, E., & Wells, J. (2020). Workflow Submit Nodes as a Service on Leadership Class Systems. Proceedings of the Practice and Experience in Advanced Research Computing. https://doi.org/10.1145/3311790.3396671 (Funding Acknowledgments: DOE DESC0012636. Best Student Paper Award in Advanced Research Computing Environments – Systems and System Software Track.) 
    @inproceedings{papadimitriou-pearc-2020,
  author = {Papadimitriou, George and Vahi, Karan and Kincl, Jason and Anantharaj, Valentine and Deelman, Ewa and Wells, Jack},
  title = {Workflow Submit Nodes as a Service on Leadership Class Systems},
  year = {2020},
  isbn = {978-1-4503-6689-2/20/07},
  publisher = {Association for Computing Machinery},
  address = {New York, NY, USA},
  url = {http://doi.acm.org/10.1145/3311790.3396671},
  doi = {10.1145/3311790.3396671},
  booktitle = {Proceedings of the Practice and Experience in Advanced Research Computing},
  articleno = {},
  numpages = {},
  location = {Portland, OR, USA},
  series = {PEARC '20},
  note = {Funding Acknowledgments: DOE DESC0012636. Best Student Paper Award in Advanced Research Computing Environments – Systems and System Software Track.}
}
  12. Pottier, L., Ferreira da Silva, R., Casanova, H., & Deelman, E. (2020). Modeling the Performance of Scientific Workflow Executions on HPC Platforms with Burst Buffers. 2020 IEEE International Conference on Cluster Computing (CLUSTER), 92–103. https://doi.org/10.1109/CLUSTER49012.2020.00019 (Funding Acknowledgments: DOE DE-SC0012636, NSF 1664162, NSF 1741040, NSF 1923539, NSF 1923621) 
    @inproceedings{pottier2020cluster,
  author = {Pottier, Lo\"ic and Ferreira da Silva, Rafael and Casanova, Henri and Deelman, Ewa},
  title = {Modeling the Performance of Scientific Workflow Executions on HPC Platforms with Burst Buffers},
  booktitle = {2020 IEEE International Conference on Cluster Computing (CLUSTER)},
  year = {2020},
  pages = {92--103},
  doi = {10.1109/CLUSTER49012.2020.00019},
  note = {Funding Acknowledgments: DOE DE-SC0012636, NSF 1664162, NSF 1741040, NSF 1923539, NSF 1923621}
}
  13. Versluis, L., Mathá, R., Talluri, S., Hegeman, T., Prodan, R., Deelman, E., & Iosup, A. (2020). The Workflow Trace Archive: Open-Access Data from Public and Private Computing Infrastructures. IEEE Transactions on Parallel and Distributed Systems, 31(9), 2170–2184. https://doi.org/10.1109/TPDS.2020.2984821 (Funding Acknowledgments: NSF 1664162) 
    @article{versluis-tpds-2020,
  author = {Versluis, Laurens and Mathá, Roland and Talluri, Sacheendra and Hegeman, Tim and Prodan, Radu and Deelman, Ewa and Iosup, Alexandru},
  title = {The Workflow Trace Archive: Open-Access Data from Public and Private Computing Infrastructures},
  journal = {IEEE Transactions on Parallel and Distributed Systems},
  year = {2020},
  volume = {31},
  number = {9},
  doi = {10.1109/TPDS.2020.2984821},
  pages = {2170-2184},
  note = {Funding Acknowledgments: NSF 1664162}
}
  14. Wang, C., Papadimitriou, G., Kiran, M., Mandal, A., & Deelman, E. (2020). Identifying Execution Anomalies for Data Intensive Workflows Using Lightweight ML Techniques. 2020 IEEE High Performance Extreme Computing Conference (HPEC), 1–7. https://doi.org/10.1109/HPEC43674.2020.9286139 (Funding Acknowledgments: DOE DESC0012636) 
    @inproceedings{wang-hpec-2020,
  title = {Identifying Execution Anomalies for Data Intensive Workflows Using Lightweight ML Techniques},
  author = {Wang, Cong and Papadimitriou, George and Kiran, Mariam and Mandal, Anirban and Deelman, Ewa},
  booktitle = {2020 IEEE High Performance Extreme Computing Conference (HPEC)},
  year = {2020},
  volume = {},
  number = {},
  pages = {1-7},
  doi = {10.1109/HPEC43674.2020.9286139},
  note = {Funding Acknowledgments: DOE DESC0012636}
}
  15. Vahi, K., Goldstein, D., Papadimitriou, G., Nugent, P., & Deelman, E. (2020). Gearing the DECam Analysis Pipeline for Multi-Messenger Astronomy Using Pegasus Workflows. In R. Pizzo, E. R. Deul, J. D. Mol, J. de Plaa, & H. Verkouter (Eds.), Astronomical Data Analysis Software and Systems XXIX (Vol. 527, p. 631). (Funding Acknowledgments: NSF 1664162, DOE DESC0012636) 
    @inproceedings{vahi-adass-2020,
  author = {{Vahi}, K. and {Goldstein}, D. and {Papadimitriou}, G. and {Nugent}, P. and {Deelman}, E.},
  title = {{Gearing the DECam Analysis Pipeline for Multi-Messenger Astronomy Using Pegasus Workflows}},
  booktitle = {Astronomical Data Analysis Software and Systems XXIX},
  year = {2020},
  editor = {{Pizzo}, R. and {Deul}, E.~R. and {Mol}, J.~D. and {de Plaa}, J. and {Verkouter}, H.},
  series = {Astronomical Society of the Pacific Conference Series},
  volume = {527},
  month = jan,
  pages = {631},
  adsurl = {https://ui.adsabs.harvard.edu/abs/2020ASPC..527..631V},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System},
  note = {Funding Acknowledgments: NSF 1664162, DOE DESC0012636}
}

2019

  1. Bogol, S., Brenner, P., Brinckman, A., Deelman, E., Ferreira da Silva, R., Gupta, S., Nabrzyski, J., Park, S., Perez, D., Rynge, M., Taylor, I., Vahi, K., Werf, M. V., Sarah, R., & Wyngaard, S. (2019). A Secure Gateway for Enabling ASIC Design Collaborations. 11th International Workshop on Science Gateways (IWSG 2019). (Funding Acknowledgments: DARPA HR0011-16-C-0043) 
    @inproceedings{bogol-iwsg-2019,
  title = {A Secure Gateway for Enabling ASIC Design Collaborations},
  author = {Bogol, Steve and Brenner, Paul and Brinckman, Adam and Deelman, Ewa and Ferreira da Silva, Rafael and Gupta, Sandeep and Nabrzyski, Jarek and Park, Soowang and Perez, Damian and Rynge, Mats and Taylor, Ian and Vahi, Karan and Werf, Matt Vander and Sarah, Rucker and Wyngaard, Sebastian},
  booktitle = {11th International Workshop on Science Gateways (IWSG 2019)},
  year = {2019},
  pages = {},
  doi = {},
  note = {Funding Acknowledgments: DARPA HR0011-16-C-0043}
}
  2. Brinckman, A., Deelman, E., Gupta, S., Nabrzyski, J., Park, S., Ferreira da Silva, R., Taylor, I. J., & Vahi, K. (2019). Collaborative Circuit Designs using the CRAFT Repository. Future Generation Computer Systems, 94, 841–853. https://doi.org/10.1016/j.future.2018.01.018 (Funding Acknowledgments: DARPA HR0011-16-C-0043) 
    @article{brinckman-fgcs-2018,
  title = {Collaborative Circuit Designs using the CRAFT Repository},
  author = {Brinckman, Adam and Deelman, Ewa and Gupta, Sandeep and Nabrzyski, Jarek and Park, Soowang and Ferreira da Silva, Rafael and Taylor, Ian J. and Vahi, Karan},
  journal = {Future Generation Computer Systems},
  volume = {94},
  number = {},
  pages = {841--853},
  year = {2019},
  doi = {10.1016/j.future.2018.01.018},
  note = {Funding Acknowledgments: DARPA HR0011-16-C-0043}
}
  3. Chang, P., Allen, G., Anderson, W., Bianco, F. B., Bloom, J. S., Brady, P. R., Brazier, A., Cenko, S. B., Couch, S. M., DeYoung, T., Deelman, E., Etienne, Z. B., Foley, R. J., Fox, D. B., Golkhou, V. Z., Grant, D. R., Hanna, C., Holley-Bockelmann, K., Howell, D. A., … Zhang, Z. (2019). Cyberinfrastructure Requirements to Enhance Multi-messenger Astrophysics. https://arxiv.org/abs/1903.04590 
    @misc{chang-astro2020-2019,
  author = {Chang, Philip and Allen, Gabrielle and Anderson, Warren and Bianco, Federica B. and Bloom, Joshua S. and Brady, Patrick R. and Brazier, Adam and Cenko, S. Bradley and Couch, Sean M. and DeYoung, Tyce and Deelman, Ewa and Etienne, Zachariah B and Foley, Ryan J. and Fox, Derek B and Golkhou, V. Zach and Grant, Darren R and Hanna, Chad and Holley-Bockelmann, Kelly and Howell, D. Andrew and Huerta, E. A. and Johnson, Margaret W. G. and Juric, Mario and Kaplan, David L. and Katz, Daniel S. and Keivani, Azadeh and Kerzendorf, Wolfgang and Kopper, Claudio and Lam, Michael T. and Lehner, Luis and Marka, Zsuzsa and Marka, Szabolcs and Nabrzyski, Jarek and Narayan, Gautham and O'Shea, Brian W. and Petravick, Donald and Quick, Rob and Street, Rachel A. and Taboada, Ignacio and Timmes, Frank and Turk, Matthew J. and Weltman, Amanda and Zhang, Zhao},
  title = {Cyberinfrastructure Requirements to Enhance Multi-messenger Astrophysics},
  year = {2019},
  eprint = {arXiv:1903.04590},
  url = {https://arxiv.org/abs/1903.04590}
}
  4. Chapp, D., Rorabaugh, D., Brown, D. A., Deelman, E., Vahi, K., Welch, V., & Taufer, M. (2019). Applicability Study of the PRIMAD Model to LIGO Gravitational Wave Search Workflows. Proceedings of the 2nd International Workshop on Practical Reproducible Evaluation of Computer Systems (P-RECS’19), 1–6. https://doi.org/10.1145/3322790.3330591 
    @inproceedings{chap2019precs,
  author = {Chapp, Dylan and Rorabaugh, Danny and Brown, Duncan A. and Deelman, Ewa and Vahi, Karan and Welch, Von and Taufer, Michela},
  title = {Applicability Study of the PRIMAD Model to LIGO Gravitational Wave Search Workflows},
  year = {2019},
  doi = {10.1145/3322790.3330591},
  booktitle = {Proceedings of the 2nd International Workshop on Practical Reproducible Evaluation of Computer Systems (P-RECS'19)},
  pages = {1–6}
}
  5. Deelman, E., Mandal, A., Jiang, M., & Sakellariou, R. (2019). The role of machine learning in scientific workflows. The International Journal of High Performance Computing Applications. https://doi.org/10.1177/1094342019852127 (Funding Acknowledgments: LLNL-ABS-755833 DE-AC52-07NA27344, DOE DESC0012636, NSF 1839900, LLNL-JRNL-765200) 
    @article{deelman-ijhpca-2019,
  title = {The role of machine learning in scientific workflows},
  author = {Deelman, Ewa and Mandal, Anirban and Jiang, Ming and Sakellariou, Rizos},
  journal = {The International Journal of High Performance Computing Applications},
  volume = {},
  number = {},
  pages = {},
  year = {2019},
  doi = {10.1177/1094342019852127},
  note = {Funding Acknowledgments: LLNL-ABS-755833 DE-AC52-07NA27344, DOE DESC0012636, NSF 1839900, LLNL-JRNL-765200}
}
  6. Deelman, E., Mandal, A., Pascucci, V., Sons, S., Wyngaard, J., Vardeman II, C. F., Petruzza, S., Baldin, I., Christopherson, L., Mitchell, R., Pottier, L., Rynge, M., Scott, E., Vahi, K., Kogank, M., Mann, J. A., Gulbransen, T., Allen, D., Barlow, D., … Stone, S. (2019). Cyberinfrastructure Center of Excellence Pilot: Connecting Large Facilities Cyberinfrastructure. 15th International Conference on EScience (EScience). (Funding Acknowledgments: NSF 1842042) 
    @inproceedings{deelman-escience-2019,
  title = {Cyberinfrastructure Center of Excellence Pilot: Connecting Large Facilities Cyberinfrastructure},
  author = {Deelman, Ewa and Mandal, Anirban and Pascucci, Valerio and Sons, Susan and Wyngaard, Jane and Vardeman II, Charles F and Petruzza, Steve and Baldin, Ilya and Christopherson, Laura and Mitchell, Ryan and Pottier, Lo\"ic and Rynge, Mats and Scott, Erik and Vahi, Karan and Kogank, Marina and Mann, Jasmine A and Gulbransen, Tom and Allen, Daniel and Barlow, David and Bonarrigo, Santiago and Clark, Chris and Goldman, Leslie and Goulden, Tristan and Harvey, Phil and Hulsander, David and Jacob, Steve and Laney, Christine and Lobo-Padilla, Ivan and Sampson, Jeremey and Staarmann, John and Stone, Steve},
  booktitle = {15th International Conference on eScience (eScience)},
  year = {2019},
  location = {San Diego, CA, USA},
  pages = {},
  doi = {},
  note = {Funding Acknowledgments: NSF 1842042}
}
  7. Deelman, E., Vahi, K., Rynge, M., Mayani, R., Ferreira da Silva, R., Papadimitriou, G., & Livny, M. (2019). The Evolution of the Pegasus Workflow Management Software. Computing in Science Engineering, 21(4), 22–36. https://doi.org/10.1109/MCSE.2019.2919690 (Funding Acknowledgments: NSF 1664162, NSF 1148515, DOE DESC0012636, NSF 1642053) 
    @article{deelman-cise-2019,
  title = {The Evolution of the Pegasus Workflow Management Software},
  author = {Deelman, Ewa and Vahi, Karan and Rynge, Mats and Mayani, Rajiv and Ferreira da Silva, Rafael and Papadimitriou, George and Livny, Miron},
  journal = {Computing in Science Engineering},
  volume = {21},
  number = {4},
  pages = {22--36},
  year = {2019},
  doi = {10.1109/MCSE.2019.2919690},
  note = {Funding Acknowledgments: NSF 1664162, NSF 1148515, DOE DESC0012636, NSF 1642053}
}
  8. Edwards, R., Abeysinghe, E., Pierce, M., & Rynge, M. (2019). Search SRA Gateway for Metagenomics Data. Gateways 2019. 
    @inproceedings{edwards-gateways-2019,
  title = {Search SRA Gateway for Metagenomics Data},
  author = {Edwards, Robert and Abeysinghe, Eroma and Pierce, Marlon and Rynge, Mats},
  booktitle = {Gateways 2019},
  year = {2019},
  pages = {},
  doi = {}
}
  9. Ferreira da Silva, R., Callaghan, S., Do, T. M. A., Papadimitriou, G., & Deelman, E. (2019). Measuring the Impact of Burst Buffers on Data-Intensive Scientific Workflows. Future Generation Computer Systems, 101, 208–220. https://doi.org/10.1016/j.future.2019.06.016 (Funding Acknowledgments: DOE DESC0012636, NSF 1664162, NSF 1741040) 
    @article{ferreiradasilva-fgcs-bb-2019,
  title = {Measuring the Impact of Burst Buffers on Data-Intensive Scientific Workflows},
  author = {Ferreira da Silva, Rafael and Callaghan, Scott and Do, Tu Mai Anh and Papadimitriou, George and Deelman, Ewa},
  journal = {Future Generation Computer Systems},
  volume = {101},
  number = {},
  pages = {208--220},
  year = {2019},
  doi = {10.1016/j.future.2019.06.016},
  note = {Funding Acknowledgments: DOE DESC0012636, NSF 1664162, NSF 1741040}
}
  10. Ferreira da Silva, R., Casanova, H., Tanaka, R., & Suter, F. (2019). Bridging Concepts and Practice in eScience via Simulation-driven Engineering. Workshop on Bridging from Concepts to Data and Computation for EScience (BC2DC’19), 15th International Conference on EScience (EScience), 609–614. https://doi.org/10.1109/eScience.2019.00084 (Funding Acknowledgments: NSF 1642335, NSF 1923539) 
    @inproceedings{ferreiradasilva2019escience,
  title = {Bridging Concepts and Practice in eScience via Simulation-driven Engineering},
  author = {Ferreira da Silva, Rafael and Casanova, Henri and Tanaka, Ryan and Suter, Frederic},
  booktitle = {Workshop on Bridging from Concepts to Data and Computation for eScience (BC2DC'19), 15th International Conference on eScience (eScience)},
  year = {2019},
  pages = {609--614},
  doi = {10.1109/eScience.2019.00084},
  note = {Funding Acknowledgments: NSF 1642335, NSF 1923539}
}
  11. Ferreira da Silva, R., Filgueira, R., Deelman, E., Pairo-Castineira, E., Overton, I. M., & Atkinson, M. (2019). Using Simple PID-inspired Controllers for Online Resilient Resource Management of Distributed Scientific Workflows. Future Generation Computer Systems, 95, 615–628. https://doi.org/10.1016/j.future.2019.01.015 (Funding Acknowledgments: DOE DE-SC0012636) 
    @article{ferreiradasilva-fgcs-2019,
  title = {Using Simple PID-inspired Controllers for Online Resilient Resource Management of Distributed Scientific Workflows},
  author = {Ferreira da Silva, Rafael and Filgueira, Rosa and Deelman, Ewa and Pairo-Castineira, Erola and Overton, Ian Michael and Atkinson, Malcolm},
  journal = {Future Generation Computer Systems},
  volume = {95},
  number = {},
  pages = {615-628},
  year = {2019},
  doi = {10.1016/j.future.2019.01.015},
  note = {Funding Acknowledgments: DOE DE-SC0012636}
}
  12. Ferreira da Silva, R., Mayani, R., Shi, Y., Kemanian, A. R., Rynge, M., & Deelman, E. (2019). Empowering Agroecosystem Modeling with HTC Scientific Workflows: The Cycles Model Use Case. First International Workshop on Big Data Tools, Methods, and Use Cases for Innovative Scientific Discovery (BTSD), 4545–4552. https://doi.org/10.1109/BigData47090.2019.9006107 (Funding Acknowledgments: DARPA W911NF-18-1-0027, NSF 1664162) 
    @inproceedings{ferreiradasilva2019btsd,
  title = {Empowering Agroecosystem Modeling with HTC Scientific Workflows: The Cycles Model Use Case},
  author = {Ferreira da Silva, Rafael and Mayani, Rajiv and Shi, Yuning and Kemanian, Armen R. and Rynge, Mats and Deelman, Ewa},
  booktitle = {First International Workshop on Big Data Tools, Methods, and Use Cases for Innovative Scientific Discovery (BTSD)},
  year = {2019},
  pages = {4545--4552},
  doi = {10.1109/BigData47090.2019.9006107},
  note = {Funding Acknowledgments: DARPA W911NF-18-1-0027, NSF 1664162}
}
  13. Ferreira da Silva, R., Orgerie, A.-C., Casanova, H., Tanaka, R., Deelman, E., & Suter, F. (2019). Accurately Simulating Energy Consumption of I/O-intensive Scientific Workflows. Computational Science – ICCS 2019, 138–152. https://doi.org/10.1007/978-3-030-22734-0_11 (Funding Acknowledgments: NSF 1642335, NSF 1664162, DOE DE-SC0012636) 
    @inproceedings{ferreiradasilva-iccs-2019,
  author = {Ferreira da Silva, Rafael and Orgerie, Anne-C\'{e}cile and Casanova, Henri and Tanaka, Ryan and Deelman, Ewa and Suter, Fr\'{e}d\'{e}ric},
  title = {Accurately Simulating Energy Consumption of I/O-intensive Scientific Workflows},
  booktitle = {Computational Science -- ICCS 2019},
  year = {2019},
  pages = {138--152},
  publisher = {Springer International Publishing},
  doi = {10.1007/978-3-030-22734-0_11},
  note = {Funding Acknowledgments: NSF 1642335, NSF 1664162, DOE DE-SC0012636}
}
  14. Garijo, D., Khider, D., Ratnakar, V., Gil, Y., Deelman, E., Ferreira da Silva, R., Knoblock, C., Chiang, Y.-Y., Pham, M., Pujara, J., Vu, B., Feldman, D., Mayani, R., Cobourn, K., Duffy, C., Kemanian, A., Shu, L., Kumar, V., Khandelwal, A., … Pierce, S. (2019). An Intelligent Interface for Integrating Climate, Hydrology, Agriculture, and Socioeconomic Models. ACM 24th International Conference on Intelligent User Interfaces (IUI’19), 111–112. https://doi.org/10.1145/3308557.3308711 (Funding Acknowledgments: DARPA W911NF-18-1-0027) 
    @inproceedings{garijo-iui-2019,
  author = {Garijo, Daniel and Khider, Deborah and Ratnakar, Varun and Gil, Yolanda and Deelman, Ewa and Ferreira da Silva, Rafael and Knoblock, Craig and Chiang, Yao-Yi and Pham, Minh and Pujara, Jay and Vu, Binh and Feldman, Dan and Mayani, Rajiv and Cobourn, Kelly and Duffy, Chris and Kemanian, Armen and Shu, Lele and Kumar, Vipin and Khandelwal, Ankush and Tayal, Kshitij and Peckham, Scott and Stoica, Maria and Dabrowski, Anna and Hardesty-Lewis, Daniel and Pierce, Suzanne},
  title = {An Intelligent Interface for Integrating Climate, Hydrology, Agriculture, and Socioeconomic Models},
  booktitle = {ACM 24th International Conference on Intelligent User Interfaces (IUI'19)},
  year = {2019},
  pages = {111--112},
  doi = {10.1145/3308557.3308711},
  note = {Funding Acknowledgments: DARPA W911NF-18-1-0027}
}
  15. Lyons, E., Papadimitriou, G., Wang, C., Thareja, K., Ruth, P., Villalobos, J. J., Rodero, I., Deelman, E., Zink, M., & Mandal, A. (2019). Toward a Dynamic Network-centric Distributed Cloud Platform for Scientific Workflows: A Case Study for Adaptive Weather Sensing. 15th International Conference on EScience (EScience), 67–76. https://doi.org/10.1109/eScience.2019.00015 (Funding Acknowledgments: NSF 1826997) 
    @inproceedings{lyons-escience-2019,
  title = {Toward a Dynamic Network-centric Distributed Cloud Platform for Scientific Workflows: A Case Study for Adaptive Weather Sensing},
  author = {Lyons, Eric and Papadimitriou, George and Wang, Cong and Thareja, Komal and Ruth, Paul and Villalobos, J.J. and Rodero, Ivan and Deelman, Ewa and Zink, Michael and Mandal, Anirban},
  booktitle = {15th International Conference on eScience (eScience)},
  year = {2019},
  location = {San Diego, CA, USA},
  pages = {67--76},
  doi = {10.1109/eScience.2019.00015},
  note = {Funding Acknowledgments: NSF 1826997}
}
  16. Mitchell, R., Pottier, L., Jacobs, S., Ferreira da Silva, R., Rynge, M., Vahi, K., & Deelman, E. (2019). Exploration of Workflow Management Systems Emerging Features from Users Perspectives. First International Workshop on Big Data Tools, Methods, and Use Cases for Innovative Scientific Discovery (BTSD), 4537–4544. https://doi.org/10.1109/BigData47090.2019.9005494 (Funding Acknowledgments: NSF 1842042) 
    @inproceedings{mitchell2019btsd,
  title = {Exploration of Workflow Management Systems Emerging Features from Users Perspectives},
  author = {Mitchell, Ryan and Pottier, Lo\"ic and Jacobs, Steve and Ferreira da Silva, Rafael and Rynge, Mats and Vahi, Karan and Deelman, Ewa},
  booktitle = {First International Workshop on Big Data Tools, Methods, and Use Cases for Innovative Scientific Discovery (BTSD)},
  year = {2019},
  pages = {4537--4544},
  doi = {10.1109/BigData47090.2019.9005494},
  note = {Funding Acknowledgments: NSF 1842042}
}
  17. Papadimitriou, G., Kiran, M., Wang, C., Mandal, A., & Deelman, E. (2019). Training Classifiers to Identify TCP Signatures in Scientific Workflows. 2019 IEEE/ACM Innovating the Network for Data-Intensive Science (INDIS), 61–68. https://doi.org/10.1109/INDIS49552.2019.00012 (Funding Acknowledgments: DOE DESC0012636) 
    @inproceedings{papadimitriou-indis-2019,
  title = {Training Classifiers to Identify TCP Signatures in Scientific Workflows},
  author = {Papadimitriou, George and Kiran, Mariam and Wang, Cong and Mandal, Anirban and Deelman, Ewa},
  booktitle = {2019 IEEE/ACM Innovating the Network for Data-Intensive Science (INDIS)},
  year = {2019},
  location = {Denver, CO, USA},
  pages = {61-68},
  doi = {10.1109/INDIS49552.2019.00012},
  month = nov,
  note = {Funding Acknowledgments: DOE DESC0012636}
}
  18. Pendergrass, S. A., Buyske, S., Jeff, J. M., Frase, A., Dudek, S., Bradford, Y., Ambite, J. L., Avery, C. L., Buzkova, P., Deelman, E., Fesinmeyer, M. D., Haiman, C., Heiss, G., Hindorff, L. A., Hsu, C. N., Jackson, R. D., Lin, Y., Le Marchand, L., Matise, T. C., … Crawford, D. C. (2019). A phenome-wide association study (PheWAS) in the Population Architecture using Genomics and Epidemiology (PAGE) study reveals potential pleiotropy in African Americans. PLoS ONE, 14(12), e0226771. (Funding Acknowledgments: NIH U01HG004801 (Coordinating Center)) 
    @article{pmid31891604,
  author = {Pendergrass, S. A. and Buyske, S. and Jeff, J. M. and Frase, A. and Dudek, S. and Bradford, Y. and Ambite, J. L. and Avery, C. L. and Buzkova, P. and Deelman, E. and Fesinmeyer, M. D. and Haiman, C. and Heiss, G. and Hindorff, L. A. and Hsu, C. N. and Jackson, R. D. and Lin, Y. and Le Marchand, L. and Matise, T. C. and Monroe, K. R. and Moreland, L. and North, K. E. and Park, S. L. and Reiner, A. and Wallace, R. and Wilkens, L. R. and Kooperberg, C. and Ritchie, M. D. and Crawford, D. C.},
  title = {A phenome-wide association study (PheWAS) in the Population Architecture using Genomics and Epidemiology (PAGE) study reveals potential pleiotropy in African Americans},
  journal = {PLoS ONE},
  year = {2019},
  volume = {14},
  number = {12},
  pages = {e0226771},
  note = {Funding Acknowledgments: NIH U01HG004801 (Coordinating Center)}
}
  19. Pendergrass, S. A., Buyske, S., Jeff, J. M., Frase, A., Dudek, S., Bradford, Y., Ambite, J.-L., Avery, C. L., Buzkova, P., Deelman, E., & others. (2019). A phenome-wide association study (PheWAS) in the Population Architecture using Genomics and Epidemiology (PAGE) study reveals potential pleiotropy in African Americans. PloS One, 14(12). https://doi.org/10.1371/journal.pone.0226771 
    @article{pendergrass2019phenome,
  title = {A phenome-wide association study (PheWAS) in the Population Architecture using Genomics and Epidemiology (PAGE) study reveals potential pleiotropy in African Americans},
  author = {Pendergrass, Sarah A and Buyske, Steven and Jeff, Janina M and Frase, Alex and Dudek, Scott and Bradford, Yuki and Ambite, Jose-Luis and Avery, Christy L and Buzkova, Petra and Deelman, Ewa and others},
  journal = {PloS one},
  volume = {14},
  number = {12},
  year = {2019},
  publisher = {Public Library of Science},
  doi = {10.1371/journal.pone.0226771}
}
  20. Rodero, I., Qin, Y., Valls, J., Simonet, A., Villalobos, J. J., Parashar, M., Youn, C., Wang, C., Thareja, K., Ruth, P., Papadimitriou, G., Lyons, E., & Zink, M. (2019). Enabling Data Streaming-based Science Gateway through Federated Cyberinfrastructure. Gateways 2019. (Funding Acknowledgments: NSF 1835692, NSF 1745246, NSF 1826997) 
    @inproceedings{rodero-gateways-2019,
  title = {Enabling Data Streaming-based Science Gateway through Federated Cyberinfrastructure},
  author = {Rodero, Ivan and Qin, Yubo and Valls, Jesus and Simonet, Anthony and Villalobos, J.J. and Parashar, Manish and Youn, Chooban and Wang, Cong and Thareja, Komal and Ruth, Paul and Papadimitriou, George and Lyons, Eric and Zink, Michael},
  booktitle = {Gateways 2019},
  year = {2019},
  location = {San Diego, CA, USA},
  pages = {},
  doi = {},
  note = {Funding Acknowledgments: NSF 1835692, NSF 1745246, NSF 1826997}
}
  21. Rynge, M., Vahi, K., Deelman, E., Mandal, A., Baldin, I., Bhide, O., Heiland, R., Welch, V., Hill, R., Poehlman, W. L., & Feltus, F. A. (2019). Integrity Protection for Scientific Workflow Data: Motivation and Initial Experiences. Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (Learning), 17:1–17:8. https://doi.org/10.1145/3332186.3332222 (Funding Acknowledgments: NSF 1642070, NSF 1642053, NSF 1642090. Best Paper in Advanced Research Computing Software and Applications Track. The Phil Andrews Most Transformative Contribution Award.) 
    @inproceedings{rynge-pearc-2019,
  author = {Rynge, Mats and Vahi, Karan and Deelman, Ewa and Mandal, Anirban and Baldin, Ilya and Bhide, Omkar and Heiland, Randy and Welch, Von and Hill, Raquel and Poehlman, William L. and Feltus, F. Alex},
  title = {Integrity Protection for Scientific Workflow Data: Motivation and Initial Experiences},
  booktitle = {Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (Learning)},
  series = {PEARC '19},
  year = {2019},
  isbn = {978-1-4503-7227-5},
  location = {Chicago, IL, USA},
  pages = {17:1--17:8},
  articleno = {17},
  numpages = {8},
  url = {http://doi.acm.org/10.1145/3332186.3332222},
  doi = {10.1145/3332186.3332222},
  acmid = {3332222},
  publisher = {ACM},
  address = {New York, NY, USA},
  note = {Funding Acknowledgments: NSF 1642070, NSF 1642053, NSF 1642090. Best Paper in Advanced Research Computing Software and Applications Track. The Phil Andrews Most Transformative Contribution Award.}
}
  22. Tanaka, R., Casanova, H., & Ferreira da Silva, R. (2019). Teaching Parallel and Distributed Computing Concepts in Simulation with WRENCH. Workshop on Education for High-Performance Computing (EduHPC), 1–9. https://doi.org/10.1109/EduHPC49559.2019.00006 (Funding Acknowledgments: NSF 1642335, NSF 1923539) 
    @inproceedings{tanaka2019eduhpc,
  title = {Teaching Parallel and Distributed Computing Concepts in Simulation with WRENCH},
  author = {Tanaka, Ryan and Casanova, Henri and Ferreira da Silva, Rafael},
  booktitle = {Workshop on Education for High-Performance Computing (EduHPC)},
  year = {2019},
  volume = {},
  number = {},
  pages = {1-9},
  doi = {10.1109/EduHPC49559.2019.00006},
  note = {Funding Acknowledgments: NSF 1642335, NSF 1923539}
}
  23. Thomas, S., Wyatt, M., Do, T. M. A., Pottier, L., Ferreira da Silva, R., Weinstein, H., Cuendet, M. A., Estrada, T., Deelman, E., & Taufer, M. (2019). Characterization of In Situ and In Transit Analytics of Molecular Dynamics Simulations for Next-generation Supercomputers. 15th International Conference on EScience (EScience), 188–198. https://doi.org/10.1109/eScience.2019.00027 (Funding Acknowledgments: NSF 1741040) 
    @inproceedings{thomas-escience-2019,
  title = {Characterization of In Situ and In Transit Analytics of Molecular Dynamics Simulations for Next-generation Supercomputers},
  author = {Thomas, Stephen and Wyatt, Michael and Do, Tu Mai Anh and Pottier, Lo\"ic and Ferreira da Silva, Rafael and Weinstein, Harel and Cuendet, Michel A. and Estrada, Trilce and Deelman, Ewa and Taufer, Michela},
  booktitle = {15th International Conference on eScience (eScience)},
  year = {2019},
  pages = {188--198},
  doi = {10.1109/eScience.2019.00027},
  note = {Funding Acknowledgments: NSF 1741040}
}
  24. Vahi, K., Rynge, M., Papadimitriou, G., Brown, D., Mayani, R., Ferreira da Silva, R., Deelman, E., Mandal, A., Lyons, E., & Zink, M. (2019). Custom Execution Environments with Containers in Pegasus-enabled Scientific Workflows. 15th International Conference on EScience (EScience), 281–290. https://doi.org/10.1109/eScience.2019.00039 (Funding Acknowledgments: NSF 1664162, NSF 1826997, NSF 1443047) 
    @inproceedings{vahi-escience-2019,
  title = {Custom Execution Environments with Containers in Pegasus-enabled Scientific Workflows},
  author = {Vahi, Karan and Rynge, Mats and Papadimitriou, George and Brown, Duncan and Mayani, Rajiv and Ferreira da Silva, Rafael and Deelman, Ewa and Mandal, Anirban and Lyons, Eric and Zink, Michael},
  booktitle = {15th International Conference on eScience (eScience)},
  year = {2019},
  location = {San Diego, CA, USA},
  pages = {281--290},
  doi = {10.1109/eScience.2019.00039},
  note = {Funding Acknowledgments: NSF 1664162, NSF 1826997, NSF 1443047}
}
  25. Vahi, K., Wang, M. H., Chang, C., Dodelson, S., Rynge, M., & Deelman, E. (2019). Workflows using Pegasus: Enabling Dark Energy Survey Pipelines. Astronomical Data Analysis Software and Systems XXVIII, 523, 689–692. (Funding Acknowledgments: NSF 1664162) 
    @article{2018-vahi-adass-weak-leansing,
  title = {Workflows using Pegasus: Enabling Dark Energy Survey Pipelines},
  author = {Vahi, Karan and Wang, Michael H. and Chang, Chihway and Dodelson, Scott and Rynge, Mats and Deelman, Ewa},
  journal = {Astronomical Data Analysis Software and Systems XXVIII},
  volume = {523},
  year = {2019},
  pages = {689--692},
  note = {Funding Acknowledgments: NSF 1664162}
}
  26. Weitzel, D., Zvada, M., Vukotic, I., Gardner, R. W., Bockelman, B., Rynge, M., Hernandez, E. F., Lin, B., & Selmeci, M. (2019). StashCache: A Distributed Caching Federation for the Open Science Grid. CoRR, abs/1905.06911. http://arxiv.org/abs/1905.06911 
    @article{DBLP:journals/corr/abs-1905-06911,
  author = {Weitzel, Derek and Zvada, Mari{\'{a}}n and Vukotic, Ilija and Gardner, Robert W. and Bockelman, Brian and Rynge, Mats and Hernandez, Edgar Fajardo and Lin, Brian and Selmeci, Matyas},
  title = {StashCache: {A} Distributed Caching Federation for the Open Science
   Grid},
  journal = {CoRR},
  volume = {abs/1905.06911},
  year = {2019},
  url = {http://arxiv.org/abs/1905.06911},
  archiveprefix = {arXiv},
  eprint = {1905.06911},
  timestamp = {Tue, 28 May 2019 12:48:08 +0200},
  biburl = {https://dblp.org/rec/bib/journals/corr/abs-1905-06911},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
  27. Wojcik, G. L., Graff, M., Nishimura, K. K., Tao, R., Haessler, J., Gignoux, C. R., Highland, H. M., Patel, Y. M., Sorokin, E. P., Avery, C. L., Belbin, G. M., Bien, S. A., Cheng, I., Cullina, S., Hodonsky, C. J., Hu, Y., Huckins, L. M., Jeff, J., Justice, A. E., … Carlson, C. S. (2019). Genetic analyses of diverse populations improves discovery for complex traits. Nature, 570, 514–518. https://doi.org/10.1038/s41586-019-1310-4 
    @article{wojcik2019genetic,
  title = {Genetic analyses of diverse populations improves discovery for complex traits},
  author = {Wojcik, Genevieve L and Graff, Mariaelisa and Nishimura, Katherine K and Tao, Ran and Haessler, Jeffrey and Gignoux, Christopher R and Highland, Heather M and Patel, Yesha M and Sorokin, Elena P and Avery, Christy L and Belbin, Gillian M. and Bien, Stephanie A. and Cheng, Iona and Cullina, Sinead and Hodonsky, Chani J. and Hu, Yao and Huckins, Laura M. and Jeff, Janina and Justice, Anne E. and Kocarnik, Jonathan M. and Lim, Unhee and Lin, Bridget M. and Lu, Yingchang and Nelson, Sarah C. and Park, Sung-Shim L. and Poisner, Hannah and Preuss, Michael H. and Richard, Melissa A. and Schurmann, Claudia and Setiawan, Veronica W. and Sockell, Alexandra and Vahi, Karan and Verbanck, Marie and Vishnu, Abhishek and Walker, Ryan W. and Young, Kristin L. and Zubair, Niha and Acuña-Alonso, Victor and Ambite, Jose Luis and Barnes, Kathleen C. and Boerwinkle, Eric and Bottinger, Erwin P. and Bustamante, Carlos D. and Caberto, Christian and Canizales-Quinteros, Samuel and Conomos, Matthew P. and Deelman, Ewa and Do, Ron and Doheny, Kimberly and Fernández-Rhodes, Lindsay and Fornage, Myriam and Hailu, Benyam and Heiss, Gerardo and Henn, Brenna M. and Hindorff, Lucia A. and Jackson, Rebecca D. and Laurie, Cecelia A. and Laurie, Cathy C. and Li, Yuqing and Lin, Dan-Yu and Moreno-Estrada, Andres and Nadkarni, Girish and Norman, Paul J. and Pooler, Loreall C. and Reiner, Alexander P. and Romm, Jane and Sabatti, Chiara and Sandoval, Karla and Sheng, Xin and Stahl, Eli A. and Stram, Daniel O. and Thornton, Timothy A. and Wassel, Christina L. and Wilkens, Lynne R. and Winkler, Cheryl A. and Yoneyama, Sachi and Buyske, Steven and Haiman, Christopher A. and Kooperberg, Charles and Marchand, Le and Loos, Ruth J. F. and Matise, Tara C. and North, Kari E. and Peters, Ulrike and Kenny, Eimear E. and Carlson, Christopher S.},
  journal = {Nature},
  volume = {570},
  pages = {514--518},
  year = {2019},
  publisher = {Nature Publishing Group},
  doi = {10.1038/s41586-019-1310-4}
}

2018

  1. Bhide, O., Hill, R., Vahi, K., Rynge, M., & Velch, V. (2018). Combating Workflow Failures with Integrity-based Checkpoints and Blockchain. 6th International Workshop on Distributed Storage and Blockchain Technologies for Big Data. (Funding Acknowledgments: NSF 1642070, 1642053, and 1642090) 
    @inproceedings{2108-bhide-workflows-blockchain,
  title = {Combating Workflow Failures with Integrity-based Checkpoints and Blockchain},
  author = {Bhide, Omkar and Hill, Raquel and Vahi, Karan and Rynge, Mats and Velch, Von},
  booktitle = {6th International Workshop on Distributed Storage and Blockchain Technologies for Big Data},
  year = {2018},
  note = {Funding Acknowledgments: NSF 1642070, 1642053, and 1642090}
}
  2. Casanova, H., Pandey, S., Oeth, J., Tanaka, R., Suter, F., & Ferreira da Silva, R. (2018). WRENCH: A Framework for Simulating Workflow Management Systems. 13th Workshop on Workflows in Support of Large-Scale Science (WORKS’18), 74–85. https://doi.org/10.1109/WORKS.2018.00013 (Funding Acknowledgments: NSF 1642335) 
    @inproceedings{casanova-works-2018,
  title = {WRENCH: A Framework for Simulating Workflow Management Systems},
  author = {Casanova, Henri and Pandey, Suraj and Oeth, James and Tanaka, Ryan and Suter, Frederic and Ferreira da Silva, Rafael},
  booktitle = {13th Workshop on Workflows in Support of Large-Scale Science (WORKS'18)},
  year = {2018},
  pages = {74--85},
  doi = {10.1109/WORKS.2018.00013},
  note = {Funding Acknowledgments: NSF 1642335}
}
  3. Deelman, E., Peterka, T., Altintas, I., Carothers, C. D., van Dam, K. K., Moreland, K., Parashar, M., Ramakrishnan, L., Taufer, M., & Vetter, J. (2018). The future of scientific workflows. The International Journal of High Performance Computing Applications, 32(1), 159–175. https://doi.org/10.1177/1094342017704893 
    @article{deelman-ijhpca-2017,
  author = {Deelman, Ewa and Peterka, Tom and Altintas, Ilkay and Carothers, Christopher D and van Dam, Kerstin Kleese and Moreland, Kenneth and Parashar, Manish and Ramakrishnan, Lavanya and Taufer, Michela and Vetter, Jeffrey},
  title = {The future of scientific workflows},
  journal = {The International Journal of High Performance Computing Applications},
  volume = {32},
  number = {1},
  pages = {159--175},
  year = {2018},
  doi = {10.1177/1094342017704893}
}
  4. Do, T. M. A., Jiang, M., Gallagher, B., Chu, A., Harrison, C., Vahi, K., & Deelman, E. (2018). Enabling Data Analytics Workflows using Node-Local Storage. The International Conference for High Performance Computing, Networking, Storage, and Analysis (SC18), Poster. (Funding Acknowledgments: LLNL-ABS-755833 DE-AC52-07NA27344, NSF 1741040) 
    @inproceedings{do-sc-18,
  title = {Enabling Data Analytics Workflows using Node-Local Storage},
  author = {Do, Tu Mai Anh and Jiang, Ming and Gallagher, Brian and Chu, Albert and Harrison, Cyrus and Vahi, Karan and Deelman, Ewa},
  booktitle = {The International Conference for High Performance Computing, Networking, Storage, and Analysis (SC18), Poster},
  year = {2018},
  note = {Funding Acknowledgments: LLNL-ABS-755833 DE-AC52-07NA27344, NSF 1741040}
}
  5. Estrada, T., Benson, J., Carrillo-Cabada, H., Razavi, A., Cuendet, M., Weinstein, H., Deelman, E., & Taufer, M. (2018). Graphic Encoding of Macromolecules for Efficient High-Throughput Analysis. 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, 315–324. https://doi.org/10.1145/3233547.3233607 (Funding Acknowledgments: NSF 1741040) 
    @inproceedings{estrada-graphic-2018,
  author = {Estrada, Trilce and Benson, Jeremy and Carrillo-Cabada, Hector and Razavi, Asghar and Cuendet, Michel and Weinstein, Harel and Deelman, Ewa and Taufer, Michela},
  year = {2018},
  month = aug,
  pages = {315-324},
  title = {Graphic Encoding of Macromolecules for Efficient High-Throughput Analysis},
  booktitle = {2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics},
  doi = {10.1145/3233547.3233607},
  note = {Funding Acknowledgments: NSF 1741040}
}
  6. Ferreira da Silva, R., Garijo, D., Peckham, S., Gil, Y., Deelman, E., & Ratnakar, V. (2018). Towards Model Integration via Abductive Workflow Composition and Multi-Method Scalable Model Execution. 9th International Congress on Environmental Modelling and Software. (Funding Acknowledgments: DARPA W911NF-18-1-0027) 
    @inproceedings{ferreiradasilva-iemss-2018,
  title = {Towards Model Integration via Abductive Workflow Composition and Multi-Method Scalable Model Execution},
  author = {Ferreira da Silva, Rafael and Garijo, Daniel and Peckham, Scott and Gil, Yolanda and Deelman, Ewa and Ratnakar, Varun},
  booktitle = {9th International Congress on Environmental Modelling and Software},
  year = {2018},
  pages = {},
  doi = {},
  note = {Funding Acknowledgments: DARPA W911NF-18-1-0027}
}
  7. Filgueira, R., Ferreira da Silva, R., Deelman, E., Christodoulou, V., & Krause, A. (2018). IoT-Hub: New IoT data-platform for Virtual Research Environments. 10th International Workshop on Science Gateways (IWSG 2018). (Funding Acknowledgments: DOE DE-SC0012636) 
    @inproceedings{filgueira-iwsg-2018,
  title = {IoT-Hub: New IoT data-platform for Virtual Research Environments},
  author = {Filgueira, Rosa and Ferreira da Silva, Rafael and Deelman, Ewa and Christodoulou, Vyron and Krause, Amrey},
  booktitle = {10th International Workshop on Science Gateways (IWSG 2018)},
  year = {2018},
  pages = {},
  doi = {},
  note = {Funding Acknowledgments: DOE DE-SC0012636}
}
  8. Gil, Y., Cobourn, K., Deelman, E., Duffy, C., Ferreira da Silva, R., Kemanian, A., Knoblock, C., Kumar, V., Peckham, S., Carvalho, L., Chiang, Y.-Y., Garijo, D., Khider, D., Khandelwal, A., Pahm, M., Pujara, J., Ratnakar, V., Stoica, M., & Vu, B. (2018). MINT: Model Integration Through Knowledge-Powered Data and Process Composition. 9th International Congress on Environmental Modelling and Software. (Funding Acknowledgments: DARPA W911NF-18-1-0027) 
    @inproceedings{gil-iemss-2018,
  title = {MINT: Model Integration Through Knowledge-Powered Data and Process Composition},
  author = {Gil, Yolanda and Cobourn, Kelly and Deelman, Ewa and Duffy, Chris and Ferreira da Silva, Rafael and Kemanian, Armen and Knoblock, Craig and Kumar, Vipin and Peckham, Scott and Carvalho, Lucas and Chiang, Yao-Yi and Garijo, Daniel and Khider, Deborah and Khandelwal, Ankush and Pahm, Minh and Pujara, Jay and Ratnakar, Varun and Stoica, Maria and Vu, Binh},
  booktitle = {9th International Congress on Environmental Modelling and Software},
  year = {2018},
  pages = {},
  doi = {},
  note = {Funding Acknowledgments: DARPA W911NF-18-1-0027}
}
  9. Jordan, T. H., Callaghan, S., Graves, R. W., Wang, F., Milner, K. R., Goulet, C. A., Maechling, P. J., Olsen, K. B., Cui, Y., Juve, G., Vahi, K., Yu, J., Deelman, E., & Gill, D. (2018). CyberShake Models of Seismic Hazards in Southern and Central California. Seismological Research Letters, 89(2B), 875–876. 
    @article{jordan-srl-2018,
  title = {CyberShake Models of Seismic Hazards in Southern and Central California},
  author = {Jordan, T. H. and Callaghan, S. and Graves, R. W. and Wang, F. and Milner, K. R. and Goulet, C. A. and Maechling, P. J. and Olsen, K. B. and Cui, Y. and Juve, G. and Vahi, K. and Yu, J. and Deelman, E. and Gill, D.},
  journal = {Seismological Research Letters},
  volume = {89},
  number = {2B},
  pages = {875--876},
  year = {2018},
  doi = {}
}
  10. Jordan, T. H., Callaghan, S., Graves, R. W., Wang, F., Milner, K. R., Goulet, C. A., Maechling, P. J., Olsen, K. B., Cui, Y., Juve, G., Vahi, K., Yu, J., Deelman, E., & Gill, D. (2018). CyberShake Models of Seismic Hazards in Southern and Central California. 11th National Conference in Earthquake Engineering. 
    @inproceedings{jordan-11ncee-2018,
  title = {CyberShake Models of Seismic Hazards in Southern and Central California},
  author = {Jordan, T. H. and Callaghan, S. and Graves, R. W. and Wang, F. and Milner, K. R. and Goulet, C. A. and Maechling, P. J. and Olsen, K. B. and Cui, Y. and Juve, G. and Vahi, K. and Yu, J. and Deelman, E. and Gill, D.},
  booktitle = {11th National Conference in Earthquake Engineering},
  year = {2018},
  pages = {},
  doi = {}
}
  11. Levi, K., Rynge, M., Abeysinghe, E., & Edwards, R. A. (2018). Searching the Sequence Read Archive Using Jetstream and Wrangler. Proceedings of the Practice and Experience on Advanced Research Computing, 50:1–50:7. https://doi.org/10.1145/3219104.3229278 
    @inproceedings{levi-pearc18-2018,
  author = {Levi, Kyle and Rynge, Mats and Abeysinghe, Eroma and Edwards, Robert A.},
  title = {Searching the Sequence Read Archive Using Jetstream and Wrangler},
  booktitle = {Proceedings of the Practice and Experience on Advanced Research Computing},
  series = {PEARC '18},
  year = {2018},
  isbn = {978-1-4503-6446-1},
  location = {Pittsburgh, PA, USA},
  pages = {50:1--50:7},
  articleno = {50},
  numpages = {7},
  url = {http://doi.acm.org/10.1145/3219104.3229278},
  doi = {10.1145/3219104.3229278},
  acmid = {3229278},
  publisher = {ACM},
  keywords = {Apache Airavata, Bacteriophage, Credential Store, Jetstream, Metagenomics, Metagenomics Discovery Challenge, SRA, SRA Gateway, SciGaP, Search SRA, Sequence Read Archive, Wrangler}
}
  12. Pandey, S., Vahi, K., Ferreira da Silva, R., Deelman, E., Jian, M., Harrison, C., Chu, A., & Casanova, H. (2018). Event-Based Triggering and Management of Scientific Workflow Ensembles. http://sighpc.ipsj.or.jp/HPCAsia2018/poster/post102s2-file1.pdf (Poster presented at the HPC Asia 2018: Tokyo, Japan) 
    @misc{suraj-hpc-asia18-event-triggers,
  author = {Pandey, Suraj and Vahi, Karan and Ferreira da Silva, Rafael and Deelman, Ewa and Jian, Ming and Harrison, Cyrus and Chu, Al and Casanova, Henri},
  title = {Event-Based Triggering and Management of Scientific Workflow Ensembles},
  year = {2018},
  url = {http://sighpc.ipsj.or.jp/HPCAsia2018/poster/post102s2-file1.pdf},
  note = {Poster presented at the HPC Asia 2018: Tokyo, Japan}
}
  13. Thapa, S., Gardner, R. W., Herner, K., Hufnagel, D., Lesny, D., & Rynge, M. (2018). Homogenizing OSG and XSEDE: Providing Access to XSEDE Allocations Through OSG Infrastructure. Proceedings of the Practice and Experience on Advanced Research Computing, 15:1–15:7. https://doi.org/10.1145/3219104.3219157 
    @inproceedings{thapa-pearc18-2018,
  author = {Thapa, Suchandra and Gardner, Robert W. and Herner, Kenneth and Hufnagel, Dirk and Lesny, David and Rynge, Mats},
  title = {Homogenizing OSG and XSEDE: Providing Access to XSEDE Allocations Through OSG Infrastructure},
  booktitle = {Proceedings of the Practice and Experience on Advanced Research Computing},
  series = {PEARC '18},
  year = {2018},
  isbn = {978-1-4503-6446-1},
  location = {Pittsburgh, PA, USA},
  pages = {15:1--15:7},
  articleno = {15},
  numpages = {7},
  url = {http://doi.acm.org/10.1145/3219104.3219157},
  doi = {10.1145/3219104.3219157},
  acmid = {3219157},
  publisher = {ACM},
  keywords = {ATLAS, Bridges, CMS, CVMFS, OSG, PSC, Stampede2, TACC, XSEDE, distributed data access}
}
  14. Tovar, B., Ferreira da Silva, R., Juve, G., Deelman, E., Allcock, W., Thain, D., & Livny, M. (2018). A Job Sizing Strategy for High-Throughput Scientific Workflows. IEEE Transactions on Parallel and Distributed Systems, 29(2), 240–253. https://doi.org/10.1109/TPDS.2017.2762310 (Funding Acknowledgments: DOE ER26110) 
    @article{tovar-tpds-2017,
  title = {A Job Sizing Strategy for High-Throughput Scientific Workflows},
  author = {Tovar, Benjamin and Ferreira da Silva, Rafael and Juve, Gideon and Deelman, Ewa and Allcock, William and Thain, Douglas and Livny, Miron},
  journal = {IEEE Transactions on Parallel and Distributed Systems},
  volume = {29},
  number = {2},
  pages = {240--253},
  year = {2018},
  doi = {10.1109/TPDS.2017.2762310},
  note = {Funding Acknowledgments: DOE ER26110}
}

2017

  1. Abbott, B. P., Abbott, R., Abbott, T. D., Acernese, F., Ackley, K., Adams, C., Adams, T., Addesso, P., Adhikari, R. X., Adya, V. B., & others. (2017). Upper limits on gravitational waves from Scorpius X-1 from a model-based cross-correlation search in Advanced LIGO data. The Astrophysical Journal, 847(1), 47. 
    @article{abbott2017upper,
  title = {Upper limits on gravitational waves from Scorpius X-1 from a model-based cross-correlation search in Advanced LIGO data},
  author = {Abbott, BP and Abbott, R and Abbott, TD and Acernese, F and Ackley, K and Adams, C and Adams, T and Addesso, P and Adhikari, RX and Adya, VB and others},
  journal = {The Astrophysical Journal},
  volume = {847},
  number = {1},
  pages = {47},
  year = {2017},
  publisher = {IOP Publishing}
}
  2. Abbott, B. P., Abbott, R., Abbott, T. D., Acernese, F., Ackley, K., Adams, C., Adams, T., Addesso, P., Adhikari, R. X., Adya, V. B., & others. (2017). First low-frequency Einstein@ Home all-sky search for continuous gravitational waves in Advanced LIGO data. Physical Review D, 96(12), 122004. 
    @article{abbott2017first,
  title = {First low-frequency Einstein@ Home all-sky search for continuous gravitational waves in Advanced LIGO data},
  author = {Abbott, Benjamin P and Abbott, R and Abbott, TD and Acernese, F and Ackley, K and Adams, C and Adams, T and Addesso, P and Adhikari, RX and Adya, VB and others},
  journal = {Physical Review D},
  volume = {96},
  number = {12},
  pages = {122004},
  year = {2017},
  publisher = {American Physical Society}
}
  3. Abbott, B. P., Abbott, R., Abbott, T. D., Acernese, F., Ackley, K., Adams, C., Adams, T., Addesso, P., Adhikari, R. X., Adya, V. B., & others. (2017). Search for gravitational waves from Scorpius X-1 in the first Advanced LIGO observing run with a hidden Markov model. Physical Review D, 95(12), 122003. 
    @article{abbott2017search,
  title = {Search for gravitational waves from Scorpius X-1 in the first Advanced LIGO observing run with a hidden Markov model},
  author = {Abbott, Benjamin P and Abbott, R and Abbott, TD and Acernese, F and Ackley, K and Adams, C and Adams, T and Addesso, P and Adhikari, RX and Adya, VB and others},
  journal = {Physical Review D},
  volume = {95},
  number = {12},
  pages = {122003},
  year = {2017},
  publisher = {American Physical Society}
}
  4. Abbott, B. P., Abbott, R., Abbott, T. D., Acernese, F., Ackley, K., Adams, C., Adams, T., Addesso, P., Adhikari, R. X., Adya, V. B., & others. (2017). Search for intermediate mass black hole binaries in the first observing run of Advanced LIGO. Physical Review D, 96(2), 022001. 
    @article{abbott2017searci,
  title = {Search for intermediate mass black hole binaries in the first observing run of Advanced LIGO},
  author = {Abbott, Benjamin P and Abbott, R and Abbott, TD and Acernese, F and Ackley, K and Adams, C and Adams, T and Addesso, P and Adhikari, RX and Adya, VB and others},
  journal = {Physical Review D},
  volume = {96},
  number = {2},
  pages = {022001},
  year = {2017},
  publisher = {American Physical Society}
}
  5. Abbott, B. P., Abbott, R., Abbott, T. D., Acernese, F., Ackley, K., Adams, C., Adams, T., Addesso, P., Adhikari, R. X., Adya, V. B., & others. (2017). All-sky search for periodic gravitational waves in the O1 LIGO data. Physical Review D, 96(6), 062002. 
    @article{abbott2017all,
  title = {All-sky search for periodic gravitational waves in the O1 LIGO data},
  author = {Abbott, Benjamin P and Abbott, Rich and Abbott, TD and Acernese, Fausto and Ackley, Kendall and Adams, Carl and Adams, Thomas and Addesso, Paolo and Adhikari, RX and Adya, VB and others},
  journal = {Physical Review D},
  volume = {96},
  number = {6},
  pages = {062002},
  year = {2017},
  publisher = {American Physical Society}
}
  6. Callaghan, S., Juve, G., Vahi, K., Maechling, P. J., Jordan, T. H., & Deelman, E. (2017). rvGAHP - Push-based Job Submission using Reverse SSH Connections. 12th Workshop on Workflows in Support of Large-Scale Science (WORKS’17). (Funding Acknowledgments: NSF 1664162 and 1443047) 
    @inproceedings{callaghan-works-2017,
  title = {{rvGAHP} - Push-based Job Submission using Reverse SSH Connections},
  author = {Callaghan, Scott and Juve, Gideon and Vahi, Karan and Maechling, Philip J. and Jordan, Thomas H. and Deelman, Ewa},
  booktitle = {12th Workshop on Workflows in Support of Large-Scale Science (WORKS'17)},
  year = {2017},
  pages = {},
  doi = {},
  note = {Funding Acknowledgments: NSF 1664162 and 1443047}
}
  7. Deelman, E., Carothers, C., Mandal, A., Tierney, B., Vetter, J. S., Baldin, I., Castillo, C., Juve, G., Krol, D., Lynch, V., Mayer, B., Meredith, J., Proffen, T., Ruth, P., & Ferreira da Silva, R. (2017). PANORAMA: An Approach to Performance Modeling and Diagnosis of Extreme Scale Workflows. International Journal of High Performance Computing Applications, 31(1), 4–18. https://doi.org/10.1177/1094342015594515 (Funding Acknowledgments: DOE DE-SC0012636) 
    @article{deelman-hpc-2015,
  title = {{PANORAMA}: An Approach to Performance Modeling and Diagnosis of Extreme Scale Workflows},
  journal = {International Journal of High Performance Computing Applications},
  volume = {31},
  number = {1},
  pages = {4--18},
  year = {2017},
  author = {Deelman, Ewa and Carothers, Christopher and Mandal, Anirban and Tierney, Brian and Vetter, Jeffrey S. and Baldin, Ilya and Castillo, Claris and Juve, Gideon and Krol, Dariusz and Lynch, Vickie and Mayer, Ben and Meredith, Jeremy and Proffen, Thomas and Ruth, Paul and Ferreira da Silva, Rafael},
  note = {Funding Acknowledgments: DOE DE-SC0012636},
  doi = {10.1177/1094342015594515},
  url = {http://dx.doi.org/10.1177/1094342015594515}
}
  8. Ferreira da Silva, R., Callaghan, S., & Deelman, E. (2017). On the Use of Burst Buffers for Accelerating Data-Intensive Scientific Workflows. 12th Workshop on Workflows in Support of Large-Scale Science (WORKS’17). https://doi.org/10.1145/3150994.3151000 (Funding Acknowledgments: DOE DE-SC0012636, NSF 1664162) 
    @inproceedings{ferreiradasilva-works-2017,
  title = {On the Use of Burst Buffers for Accelerating Data-Intensive Scientific Workflows},
  author = {Ferreira da Silva, Rafael and Callaghan, Scott and Deelman, Ewa},
  booktitle = {12th Workshop on Workflows in Support of Large-Scale Science (WORKS'17)},
  year = {2017},
  pages = {},
  doi = {10.1145/3150994.3151000},
  note = {Funding Acknowledgments: DOE DE-SC0012636, NSF 1664162}
}
  9. Ferreira da Silva, R., Filgueira, R., Pietri, I., Jiang, M., Sakellariou, R., & Deelman, E. (2017). A Characterization of Workflow Management Systems for Extreme-Scale Applications. Future Generation Computer Systems, 75, 228–238. https://doi.org/10.1016/j.future.2017.02.026 (Funding Acknowledgments: DOE DE-SC0012636, DE-AC52-07NA27344) 
    @article{ferreiradasilva-fgcs-2017,
  title = {A Characterization of Workflow Management Systems for Extreme-Scale Applications},
  author = {Ferreira da Silva, Rafael and Filgueira, Rosa and Pietri, Ilia and Jiang, Ming and Sakellariou, Rizos and Deelman, Ewa},
  journal = {Future Generation Computer Systems},
  volume = {75},
  number = {},
  pages = {228--238},
  year = {2017},
  doi = {10.1016/j.future.2017.02.026},
  note = {Funding Acknowledgments: DOE DE-SC0012636, DE-AC52-07NA27344}
}
  10. Gil, Y., Garijo, D., Ratnakar, V., Mayani, R., Adusumilli, R., Boyce, H., Srivastava, A., & Mallick, P. (2017). Towards Continuous Scientific Data Analysis and Hypothesis Evolution. Thirty-First AAAI Conference on Artificial Intelligence, 4406–4414. () 
    @inproceedings{gil-aaai-2017,
  title = {Towards Continuous Scientific Data Analysis and Hypothesis Evolution},
  author = {Gil, Yolanda and Garijo, Daniel and Ratnakar, Varun and Mayani, Rajiv and Adusumilli, Ravali and Boyce, Hunter and Srivastava, Arunima and Mallick, Parag},
  booktitle = {Thirty-First AAAI Conference on Artificial Intelligence},
  year = {2017},
  pages = {4406--4414},
  doi = {},
  note = {}
}
  11. Jayatilaka, B., Levshina, T., Sehgal, C., Gardner, R., Rynge, M., & Wurthwein, F. (2017). The OSG Open Facility: an on-ramp for opportunistic scientific computing. Journal of Physics: Conference Series, 898(8), 082048. http://stacks.iop.org/1742-6596/898/i=8/a=082048 
    @article{jayatilaka-physics-2017,
  author = {Jayatilaka, B and Levshina, T and Sehgal, C and Gardner, R and Rynge, M and Wurthwein, F},
  title = {The OSG Open Facility: an on-ramp for opportunistic scientific computing},
  journal = {Journal of Physics: Conference Series},
  volume = {898},
  number = {8},
  pages = {082048},
  url = {http://stacks.iop.org/1742-6596/898/i=8/a=082048},
  year = {2017}
}
  12. Lynch, V., Calvo, J. B., Deelman, E., Ferreira da Silva, R., Goswami, M., Hui, Y., Lingerfelt, E., & Vetter, J. (2017). Distributed Workflows for Modeling Experimental Data. 2017 IEEE High Performance Extreme Computing Conference (HPEC’17). https://doi.org/10.1109/HPEC.2017.8091071 (Funding Acknowledgments: DOE DE-SC0012636) 
    @inproceedings{lynch-hpec-2017,
  title = {Distributed Workflows for Modeling Experimental Data},
  author = {Lynch, Vickie and Calvo, Jose Borreguero and Deelman, Ewa and Ferreira da Silva, Rafael and Goswami, Monojoy and Hui, Yawei and Lingerfelt, Eric and Vetter, Jeffrey},
  booktitle = {2017 IEEE High Performance Extreme Computing Conference (HPEC'17)},
  year = {2017},
  pages = {},
  doi = {10.1109/HPEC.2017.8091071},
  note = {Funding Acknowledgments: DOE DE-SC0012636}
}
  13. Mandal, A., Ruth, P., Baldin, I., Ferreira da Silva, R., & Deelman, E. (2017). Toward Prioritization of Data Flows for Scientific Workflows Using Virtual Software Defined Exchanges. First International Workshop on Workflow Science (WoWS 2017), 566–575. https://doi.org/10.1109/eScience.2017.92 (Funding Acknowledgments: DOE DE-SC0012636) 
    @inproceedings{mandal-wows-2017,
  title = {Toward Prioritization of Data Flows for Scientific Workflows Using Virtual Software Defined Exchanges},
  author = {Mandal, Anirban and Ruth, Paul and Baldin, Ilya and Ferreira da Silva, Rafael and Deelman, Ewa},
  booktitle = {First International Workshop on Workflow Science (WoWS 2017)},
  year = {2017},
  pages = {566--575},
  doi = {10.1109/eScience.2017.92},
  note = {Funding Acknowledgments: DOE DE-SC0012636}
}
  14. Poehlman, W. L., Rynge, M., Balamurugan, D., Mills, N., & Feltus, F. A. (2017). OSG-KINC: High-throughput gene co-expression network construction using the open science grid. 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 1827–1831. https://doi.org/10.1109/BIBM.2017.8217938 
    @inproceedings{poehlman-ieee-bibm-2017,
  author = {Poehlman, W. L. and Rynge, M. and Balamurugan, D. and Mills, N. and Feltus, F. A.},
  booktitle = {2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)},
  title = {OSG-KINC: High-throughput gene co-expression network construction using the open science grid},
  year = {2017},
  volume = {},
  number = {},
  pages = {1827-1831},
  keywords = {Biological information theory;Correlation;Gene expression;Genomics;RNA;Software},
  doi = {10.1109/BIBM.2017.8217938},
  issn = {},
  month = nov
}
  15. Santana-Perez, I., Ferreira da Silva, R., Rynge, M., Deelman, E., Perez-Hernandez, M. S., & Corcho, O. (2017). Reproducibility of Execution Environments in Computational Science Using Semantics and Clouds. Future Generation Computer Systems, 67, 354–367. https://doi.org/10.1016/j.future.2015.12.017 (Funding Acknowledgments: NSF ACI SI2-SSI 1148515, NSF FutureGrid 0910812) 
    @article{santanaperez-fgcs-2016,
  title = {Reproducibility of Execution Environments in Computational Science Using Semantics and Clouds},
  author = {Santana-Perez, Idafen and Ferreira da Silva, Rafael and Rynge, Mats and Deelman, Ewa and Perez-Hernandez, Maria S. and Corcho, Oscar},
  journal = {Future Generation Computer Systems},
  volume = {67},
  pages = {354--367},
  year = {2017},
  doi = {10.1016/j.future.2015.12.017},
  note = {Funding Acknowledgments: NSF ACI SI2-SSI 1148515, NSF FutureGrid 0910812},
  url = {http://dx.doi.org/10.1016/j.future.2015.12.017}
}
  16. Scientific, L. I. G. O., Abbott, B. P., Abbott, R., Abbott, T. D., Acernese, F., Ackley, K., Adams, C., Adams, T., Addesso, P., Adhikari, R. X., & others. (2017). GW170104: observation of a 50-solar-mass binary black hole coalescence at redshift 0.2. Physical Review Letters, 118(22), 221101. 
    @article{scientific2017gw170104,
  title = {GW170104: observation of a 50-solar-mass binary black hole coalescence at redshift 0.2},
  author = {Scientific, LIGO and Abbott, BP and Abbott, R and Abbott, TD and Acernese, F and Ackley, K and Adams, C and Adams, T and Addesso, P and Adhikari, RX and others},
  journal = {Physical Review Letters},
  volume = {118},
  number = {22},
  pages = {221101},
  year = {2017},
  publisher = {American Physical Society}
}
  17. Taylor, I. J., Brinckman, A., Deelman, E., Ferreira da Silva, R., Gupta, S., Nabrzyski, J., Park, S., & Vahi, K. (2017). Accelerating Circuit Realization via a Collaborative Gateway of Innovations. 9th International Workshop on Science Gateways (IWSG 2017). (Funding Acknowledgments: DARPA HR0011-16-C-0043) 
    @inproceedings{taylor-iwsg-2017,
  title = {Accelerating Circuit Realization via a Collaborative Gateway of Innovations},
  author = {Taylor, Ian J. and Brinckman, Adam and Deelman, Ewa and Ferreira da Silva, Rafael and Gupta, Sandeep and Nabrzyski, Jarek and Park, Soowang and Vahi, Karan},
  booktitle = {9th International Workshop on Science Gateways (IWSG 2017)},
  year = {2017},
  pages = {},
  doi = {},
  note = {Funding Acknowledgments: DARPA HR0011-16-C-0043}
}

2016

  1. Chen, W., Ferreira da Silva, R., Deelman, E., & Fahringer, T. (2016). Dynamic and Fault-Tolerant Clustering for Scientific Workflows. IEEE Transactions on Cloud Computing, 4(1), 49–62. https://doi.org/10.1109/TCC.2015.2427200 (Funding Acknowledgments: NSF IIS-0905032, NSF ACI SI2-SSI 1148515, and NSF FutureGrid 0910812) 
    @article{chen-tcc-2015,
  title = {Dynamic and Fault-Tolerant Clustering for Scientific Workflows},
  journal = {{IEEE} Transactions on Cloud Computing},
  volume = {4},
  number = {1},
  pages = {49--62},
  year = {2016},
  author = {Chen, Weiwei and Ferreira da Silva, Rafael and Deelman, Ewa and Fahringer, Thomas},
  note = {Funding Acknowledgments: NSF IIS-0905032, NSF ACI SI2-SSI 1148515, and NSF FutureGrid 0910812},
  doi = {10.1109/TCC.2015.2427200},
  url = {http://pegasus.isi.edu/publications/2015/chen-tcc-2015.pdf}
}
  2. Deelman, E., Vahi, K., Rynge, M., Juve, G., Mayani, R., & Ferreira da Silva, R. (2016). Pegasus in the Cloud: Science Automation through Workflow Technologies. IEEE Internet Computing, 20(1), 70–76. https://doi.org/10.1109/MIC.2016.15 (Funding Acknowledgments: NSF ACI SI2-SSI 1148515, NSF ACI 1245926, NSF FutureGrid 0910812, NHGRI 1U01 HG006531-01) 
    @article{deelman-ic-2016,
  title = {Pegasus in the Cloud: Science Automation through Workflow Technologies},
  author = {Deelman, Ewa and Vahi, Karan and Rynge, Mats and Juve, Gideon and Mayani, Rajiv and Ferreira da Silva, Rafael},
  journal = {IEEE Internet Computing},
  volume = {20},
  number = {1},
  pages = {70--76},
  year = {2016},
  note = {Funding Acknowledgments: NSF ACI SI2-SSI 1148515, NSF ACI 1245926, NSF FutureGrid 0910812, NHGRI 1U01 HG006531-01},
  url = {http://dx.doi.org/10.1109/MIC.2016.15},
  doi = {10.1109/MIC.2016.15}
}
  3. Ferreira da Silva, R., Deelman, E., Filgueira, R., Vahi, K., Rynge, M., Mayani, R., & Mayer, B. (2016). Automating Environmental Computing Applications with Scientific Workflows. Environmental Computing Workshop (ECW’16), IEEE 12th International Conference on e-Science, 400–406. https://doi.org/10.1109/eScience.2016.7870926 (Funding Acknowledgments: DOE DESC0012636, NSF ACI SI2-SSI 1148515) 
    @inproceedings{ferreiradasilva-ecw-2016,
  author = {Ferreira da Silva, Rafael and Deelman, Ewa and Filgueira, Rosa and Vahi, Karan and Rynge, Mats and Mayani, Rajiv and Mayer, Benjamin},
  title = {Automating Environmental Computing Applications with Scientific Workflows},
  year = {2016},
  note = {Funding Acknowledgments: DOE DESC0012636, NSF ACI SI2-SSI 1148515},
  booktitle = {Environmental Computing Workshop (ECW'16), IEEE 12th International Conference on e-Science},
  doi = {10.1109/eScience.2016.7870926},
  pages = {400--406}
}
  4. Ferreira da Silva, R., Filgueira, R., Deelman, E., Pairo-Castineira, E., Overton, I. M., & Atkinson, M. (2016). Using Simple PID Controllers to Prevent and Mitigate Faults in Scientific Workflows. 11th Workflows in Support of Large-Scale Science (WORKS’16), 15–24. (Funding Acknowledgments: DOE DE-SC0012636) 
    @inproceedings{ferreiradasilva-works-2016,
  author = {Ferreira da Silva, Rafael and Filgueira, Rosa and Deelman, Ewa and Pairo-Castineira, Erola and Overton, Ian Michael and Atkinson, Malcolm},
  title = {Using Simple PID Controllers to Prevent and Mitigate Faults in Scientific Workflows},
  booktitle = {11th Workflows in Support of Large-Scale Science (WORKS'16)},
  year = {2016},
  pages = {15--24},
  note = {Funding Acknowledgments: DOE DE-SC0012636}
}
  5. Filgueira, R., Ferreira da Silva, R., Krause, A., Deelman, E., & Atkinson, M. (2016). Asterism: Pegasus and dispel4py hybrid workflows for data-intensive science. 7th International Workshop on Data-Intensive Computing in the Clouds (DataCloud’16), 1–8. https://doi.org/10.1109/DataCloud.2016.004 (Funding Acknowledgments: NSF ACI SI2-SSI 1148515) 
    @inproceedings{filgueira-datacloud-2016,
  author = {Filgueira, Rosa and Ferreira da Silva, Rafael and Krause, Amrey and Deelman, Ewa and Atkinson, Malcolm},
  title = {Asterism: Pegasus and dispel4py hybrid workflows for data-intensive science},
  booktitle = {7th International Workshop on Data-Intensive Computing in the Clouds (DataCloud'16)},
  year = {2016},
  doi = {10.1109/DataCloud.2016.004},
  pages = {1--8},
  note = {Funding Acknowledgments: NSF ACI SI2-SSI 1148515}
}
  6. Gaikwad, P., Mandal, A., Ruth, P., Juve, G., Krol, D., & Deelman, E. (2016). Anomaly Detection for Scientific Workflow Applications on Networked Clouds. IEEE 2016 International Conference on High Performance Computing & Simulation (HPCS 2016). https://doi.org/10.1109/HPCSim.2016.7568396 (Funding Acknowledgments: DOE DE-SC0012636) 
    @inproceedings{gaikwad-intercloud-2016,
  author = {Gaikwad, Prathamesh and Mandal, Anirban and Ruth, Paul and Juve, Gideon and Krol, Dariusz and Deelman, Ewa},
  title = {Anomaly Detection for Scientific Workflow Applications on Networked Clouds},
  booktitle = {IEEE 2016 International Conference on High Performance Computing & Simulation (HPCS 2016)},
  year = {2016},
  note = {Funding Acknowledgments: DOE DE-SC0012636},
  doi = {10.1109/HPCSim.2016.7568396}
}
  7. Krol, D., Ferreira da Silva, R., Deelman, E., & Lynch, V. E. (2016). Workflow Performance Profiles: Development and Analysis. In Euro-Par 2016: Parallel Processing Workshops (pp. 108–120). https://doi.org/10.1007/978-3-319-58943-5_9 (Funding Acknowledgments: DOE DE-SC0012636) 
    @incollection{krol-heteropar-2016,
  author = {Krol, Dariusz and Ferreira da Silva, Rafael and Deelman, Ewa and Lynch, Vickie E.},
  title = {Workflow Performance Profiles: Development and Analysis},
  year = {2016},
  note = {Funding Acknowledgments: DOE DE-SC0012636},
  booktitle = {Euro-Par 2016: Parallel Processing Workshops},
  doi = {10.1007/978-3-319-58943-5_9},
  pages = {108--120}
}
  8. Krol, D., Kitowski, J., Ferreira da Silva, R., Juve, G., Vahi, K., Rynge, M., & Deelman, E. (2016). Science Automation in Practice: Performance Data Farming in Workflows. 21st IEEE International Conference on Emerging Technologies and Factory Automation (ETFA). https://doi.org/10.1109/ETFA.2016.7733677 (Funding Acknowledgments: DOE DE-SC0012636) 
    @inproceedings{krol-etfa-2016,
  author = {Krol, Dariusz and Kitowski, Jacek and Ferreira da Silva, Rafael and Juve, Gideon and Vahi, Karan and Rynge, Mats and Deelman, Ewa},
  title = {Science Automation in Practice: Performance Data Farming in Workflows},
  booktitle = {21st IEEE International Conference on Emerging Technologies and Factory Automation (ETFA)},
  year = {2016},
  note = {Funding Acknowledgments: DOE DE-SC0012636},
  doi = {10.1109/ETFA.2016.7733677}
}
  9. Liu, Y., Khan, S. M., Wang, J., Rynge, M., Zhang, Y., Zeng, S., Chen, S., Maldonado dos Santos, J. V., Valliyodan, B., Calyam, P. P., Merchant, N., Nguyen, H. T., Xu, D., & Joshi, T. (2016). PGen: large-scale genomic variations analysis workflow and browser in SoyKB. BMC Bioinformatics, 17(13), 337. https://doi.org/10.1186/s12859-016-1227-y 
    @article{Liu2016,
  author = {Liu, Yang and Khan, Saad M. and Wang, Juexin and Rynge, Mats and Zhang, Yuanxun and Zeng, Shuai and Chen, Shiyuan and Maldonado dos Santos, Joao V. and Valliyodan, Babu and Calyam, Prasad P. and Merchant, Nirav and Nguyen, Henry T. and Xu, Dong and Joshi, Trupti},
  title = {PGen: large-scale genomic variations analysis workflow and browser in SoyKB},
  journal = {BMC Bioinformatics},
  year = {2016},
  volume = {17},
  number = {13},
  pages = {337},
  issn = {1471-2105},
  doi = {10.1186/s12859-016-1227-y},
  url = {http://dx.doi.org/10.1186/s12859-016-1227-y}
}
  10. Mandal, A., Ruth, P., Baldin, I., Krol, D., Juve, G., Mayani, R., Ferreira da Silva, R., Deelman, E., Meredith, J., Vetter, J., Lynch, V., Mayer, B., Wynne III, J., Blanco, M., Carothers, C., LaPre, J., & Tierney, B. (2016). Toward an End-to-end Framework for Modeling, Monitoring, and Anomaly Detection for Scientific Workflows. Workshop on Large-Scale Parallel Processing (LSPP 2016), 1370–1379. https://doi.org/10.1109/IPDPSW.2016.202 (Funding Acknowledgments: DOE DE-SC0012636) 
    @inproceedings{mandal-lspp-2016,
  author = {Mandal, Anirban and Ruth, Paul and Baldin, Ilya and Krol, Dariusz and Juve, Gideon and Mayani, Rajiv and Ferreira da Silva, Rafael and Deelman, Ewa and Meredith, Jeremy and Vetter, Jeffrey and Lynch, Vickie and Mayer, Ben and Wynne III, James and Blanco, Mark and Carothers, Chris and LaPre, Justin and Tierney, Brian},
  title = {Toward an End-to-end Framework for Modeling, Monitoring, and Anomaly Detection for Scientific Workflows},
  booktitle = {{Workshop on Large-Scale Parallel Processing (LSPP 2016)}},
  year = {2016},
  note = {Funding Acknowledgments: DOE DE-SC0012636},
  url = {http://pegasus.isi.edu/publications/2016/mandal-lspp-2016.pdf},
  doi = {10.1109/IPDPSW.2016.202},
  pages = {1370--1379}
}
  11. Nawaz, H., Juve, G., Ferreira da Silva, R., & Deelman, E. (2016). Performance Analysis of an I/O-Intensive Workflow executing on Google Cloud and Amazon Web Services. 18th Workshop on Advances in Parallel and Distributed Computational Models (APDCM), 535–544. https://doi.org/10.1109/IPDPSW.2016.90 (Funding Acknowledgments: DOE DE-SC0012636) 
    @inproceedings{nawaz-apdcm-2016,
  author = {Nawaz, Hassan and Juve, Gideon and Ferreira da Silva, Rafael and Deelman, Ewa},
  title = {Performance Analysis of an I/O-Intensive Workflow executing on Google Cloud and Amazon Web Services},
  booktitle = {{18th Workshop on Advances in Parallel and Distributed Computational Models (APDCM)}},
  year = {2016},
  note = {Funding Acknowledgments: DOE DE-SC0012636},
  url = {http://pegasus.isi.edu/publications/2016/nawaz-apdcm-2016.pdf},
  doi = {10.1109/IPDPSW.2016.90},
  pages = {535--544}
}
  12. Poehlman, W. L., Rynge, M., Branton, C., Balamurugan, D., & Feltus, F. A. (2016). OSG-GEM: Gene Expression Matrix Construction Using the Open Science Grid. Bioinformatics and Biology Insights, 10, 133–141. https://doi.org/10.4137/BBI.S38193 
    @article{10.4137/BBI.S38193,
  author = {Poehlman, William L. and Rynge, Mats and Branton, Chris and Balamurugan, D. and Feltus, Frank A.},
  journal = {Bioinformatics and Biology Insights},
  publisher = {Libertas Academica},
  title = {OSG-GEM: Gene Expression Matrix Construction Using the Open Science Grid},
  year = {2016},
  month = aug,
  volume = {10},
  url = {http://www.la-press.com/osg-gem-gene-expression-matrix-construction-using-the-open-science-gri-article-a5814},
  pages = {133--141},
  doi = {10.4137/BBI.S38193}
}
  13. Schlagkamp, S., Ferreira da Silva, R., Allcock, W., Deelman, E., & Schwiegelshohn, U. (2016). Consecutive Job Submission Behavior at Mira Supercomputer. 25th ACM International Symposium on High-Performance Parallel and Distributed Computing (HPDC). https://doi.org/10.1145/2907294.2907314 (Funding Acknowledgments: DOE ER26110, DOE DE-SC0012636) 
    @inproceedings{schlagkamp-hpdc-2016,
  author = {Schlagkamp, Stephan and Ferreira da Silva, Rafael and Allcock, William and Deelman, Ewa and Schwiegelshohn, Uwe},
  title = {Consecutive Job Submission Behavior at Mira Supercomputer},
  booktitle = {{25th ACM International Symposium on High-Performance Parallel and Distributed Computing (HPDC)}},
  year = {2016},
  note = {Funding Acknowledgments: DOE ER26110, DOE DE-SC0012636},
  url = {http://pegasus.isi.edu/publications/2016/schlagkamp-hpdc-2016.pdf},
  doi = {10.1145/2907294.2907314}
}
  14. Schlagkamp, S., Ferreira da Silva, R., Deelman, E., & Schwiegelshohn, U. (2016). Understanding User Behavior: from HPC to HTC. International Conference on Computational Science (ICCS). https://doi.org/10.1016/j.procs.2016.05.397 (Funding Acknowledgments: DOE ER26110, DOE DE-SC0012636) 
    @inproceedings{schlagkamp-iccs-2016,
  author = {Schlagkamp, Stephan and Ferreira da Silva, Rafael and Deelman, Ewa and Schwiegelshohn, Uwe},
  title = {Understanding User Behavior: from HPC to HTC},
  booktitle = {{International Conference on Computational Science (ICCS)}},
  year = {2016},
  note = {Funding Acknowledgments: DOE ER26110, DOE DE-SC0012636},
  url = {http://pegasus.isi.edu/publications/2016/schlagkamp-iccs-2016.pdf},
  doi = {10.1016/j.procs.2016.05.397}
}
  15. Stodden, V., McNutt, M., Balley, D. H., Deelman, E., Gil, Y., Hanson, B., Heroux, M. A., Ioannidis, J. P. A., & Taufer. (2016). Enhancing reproducibility for computational methods. Science, 354(6317), 1240–1241. https://doi.org/10.1126/science.aah6168 
    @article{stodden-science-2016,
  author = {Stodden, Victoria and McNutt, Marcia and Balley, David H. and Deelman, Ewa and Gil, Yolanda and Hanson, Brooks and Heroux, Michael A. and Ioannidis, John P.A. and Taufer},
  title = {Enhancing reproducibility for computational methods},
  journal = {Science},
  year = {2016},
  volume = {354},
  number = {6317},
  pages = {1240--1241},
  doi = {10.1126/science.aah6168},
  url = {http://science.sciencemag.org/content/354/6317/1240.full},
  publisher = {American Association for the Advancement of Science},
  issn = {0036-8075}
}
  16. Swetnam, T. L., Pelletier, J. D., Rasmussen, C., Callahan, N. R., Merchant, N., Lyons, E., Rynge, M., Liu, Y., Nandigam, V., & Crosby, C. (2016). Scaling GIS Analysis Tasks from the Desktop to the Cloud Utilizing Contemporary Distributed Computing and Data Management Approaches: A Case Study of Project-based Learning and Cyberinfrastructure Concepts. XSEDE16 Conference on Diversity, Big Data, and Science at Scale, 21:1–21:6. https://doi.org/10.1145/2949550.2949573 
    @inproceedings{Swetnam:2016:SGA:2949550.2949573,
  author = {Swetnam, T. L. and Pelletier, J. D. and Rasmussen, C. and Callahan, N. R. and Merchant, N. and Lyons, E. and Rynge, M. and Liu, Y. and Nandigam, V. and Crosby, C.},
  title = {Scaling GIS Analysis Tasks from the Desktop to the Cloud Utilizing Contemporary Distributed Computing and Data Management Approaches: A Case Study of Project-based Learning and Cyberinfrastructure Concepts},
  booktitle = {XSEDE16 Conference on Diversity, Big Data, and Science at Scale},
  series = {XSEDE16},
  year = {2016},
  isbn = {978-1-4503-4755-6},
  location = {Miami, USA},
  pages = {21:1--21:6},
  articleno = {21},
  numpages = {6},
  url = {http://doi.acm.org/10.1145/2949550.2949573},
  doi = {10.1145/2949550.2949573},
  acmid = {2949573},
  publisher = {ACM},
  keywords = {CyberGIS, GDAL, GRASS, Makeflow, Work Queue}
}

2015

  1. Bryk, P., Malawski, M., Juve, G., & Deelman, E. (2015). Storage-aware Algorithms for Scheduling of Workflow Ensembles in Clouds. Journal of Grid Computing, 14(2), 359–378. https://doi.org/10.1007/s10723-015-9355-6 (Funding Acknowledgments: DOE ER26110) 
    @article{bryk-jgc-2015,
  author = {Bryk, Piotr and Malawski, Maciej and Juve, Gideon and Deelman, Ewa},
  title = {Storage-aware Algorithms for Scheduling of Workflow Ensembles in Clouds},
  journal = {Journal of Grid Computing},
  volume = {14},
  number = {2},
  pages = {359--378},
  year = {2015},
  note = {Funding Acknowledgments: DOE ER26110},
  doi = {10.1007/s10723-015-9355-6},
  url = {http://link.springer.com/article/10.1007%2Fs10723-015-9355-6}
}
  2. Chen, W., Ferreira da Silva, R., Deelman, E., & Sakellariou, R. (2015). Using Imbalance Metrics to Optimize Task Clustering in Scientific Workflow Executions. Future Generation Computer Systems, 46, 69–84. https://doi.org/10.1016/j.future.2014.09.014 (Funding Acknowledgments: NSF IIS-0905032 and NSF FutureGrid 0910812) 
    @article{chen-fgcs-2014,
  author = {Chen, Weiwei and Ferreira da Silva, Rafael and Deelman, Ewa and Sakellariou, Rizos},
  url = {http://pegasus.isi.edu/publications/2014/2014-fgcs-chen.pdf},
  title = {Using Imbalance Metrics to Optimize Task Clustering in Scientific Workflow Executions},
  journal = {Future Generation Computer Systems},
  volume = {46},
  pages = {69--84},
  year = {2015},
  note = {Funding Acknowledgments: NSF IIS-0905032 and NSF FutureGrid 0910812},
  doi = {10.1016/j.future.2014.09.014}
}
  3. Deelman, E., Carothers, C., Mandal, A., Tierney, B., Vetter, J. S., Baldin, I., Castillo, C., Juve, G., Krol, D., Lynch, V., Mayer, B., Meredith, J., Proffen, T., Ruth, P., & Ferreira da Silva, R. (2015). Panorama: Modeling The Performance of Scientific Workflows. Workshop on Modeling and Simulation of Systems and Applications (ModSim 2015). http://pegasus.isi.edu/publications/2015/deelman-modsim-2015.pdf (Funding Acknowledgments: DOE DE-SC0012636) 
    @inproceedings{deelman-modsim-2015,
  title = {Panorama: Modeling The Performance of Scientific Workflows},
  booktitle = {Workshop on Modeling and Simulation of Systems and Applications ({ModSim} 2015)},
  year = {2015},
  author = {Deelman, Ewa and Carothers, Christopher and Mandal, Anirban and Tierney, Brian and Vetter, Jeffrey S. and Baldin, Ilya and Castillo, Claris and Juve, Gideon and Krol, Dariusz and Lynch, Vickie and Mayer, Ben and Meredith, Jeremy and Proffen, Thomas and Ruth, Paul and Ferreira da Silva, Rafael},
  note = {Funding Acknowledgments: DOE DE-SC0012636},
  url = {http://pegasus.isi.edu/publications/2015/deelman-modsim-2015.pdf}
}
  4. Deelman, E., Vahi, K., Juve, G., Rynge, M., Callaghan, S., Maechling, P. J., Mayani, R., Chen, W., Ferreira da Silva, R., Livny, M., & Wenger, K. (2015). Pegasus: a Workflow Management System for Science Automation. Future Generation Computer Systems, 46, 17–35. https://doi.org/10.1016/j.future.2014.10.008 (Funding Acknowledgments: NSF ACI SDCI 0722019, NSF ACI SI2-SSI 1148515 and NSF OCI-1053575) 
    @article{deelman-fgcs-2015,
  author = {Deelman, Ewa and Vahi, Karan and Juve, Gideon and Rynge, Mats and Callaghan, Scott and Maechling, Philip J and Mayani, Rajiv and Chen, Weiwei and Ferreira da Silva, Rafael and Livny, Miron and Wenger, Kent},
  url = {http://pegasus.isi.edu/publications/2014/2014-fgcs-deelman.pdf},
  title = {Pegasus: a Workflow Management System for Science Automation},
  journal = {Future Generation Computer Systems},
  volume = {46},
  pages = {17--35},
  year = {2015},
  note = {Funding Acknowledgments: NSF ACI SDCI 0722019, NSF ACI SI2-SSI 1148515 and NSF OCI-1053575},
  doi = {10.1016/j.future.2014.10.008}
}
  5. Ferreira da Silva, R., Juve, G., Rynge, M., Deelman, E., & Livny, M. (2015). Online Task Resource Consumption Prediction for Scientific Workflows. Parallel Processing Letters, 25(3). https://doi.org/10.1142/S0129626415410030 (Funding Acknowledgments: DOE ER26110) 
    @article{ferreiradasilva-ppl-2015,
  title = {Online Task Resource Consumption Prediction for Scientific Workflows},
  author = {Ferreira da Silva, Rafael and Juve, Gideon and Rynge, Mats and Deelman, Ewa and Livny, Miron},
  journal = {Parallel Processing Letters},
  volume = {25},
  number = {3},
  year = {2015},
  note = {Funding Acknowledgments: DOE ER26110},
  doi = {10.1142/S0129626415410030},
  url = {http://www.worldscientific.com/doi/abs/10.1142/S0129626415410030}
}
  6. Ferreira da Silva, R., Rynge, M., Juve, G., Sfiligoi, I., Deelman, E., Letts, J., Wurthwein, F., & Livny, M. (2015). Characterizing a High Throughput Computing Workload: The Compact Muon Solenoid (CMS) Experiment at LHC. Procedia Computer Science, International Conference On Computational Science, ICCS 2015 Computational Science at the Gates of Nature, 51, 39–48. https://doi.org/10.1016/j.procs.2015.05.190 (Funding Acknowledgments: DOE ER26110) 
    @article{ferreiradasilva2015iccs,
  author = {Ferreira da Silva, Rafael and Rynge, Mats and Juve, Gideon and Sfiligoi, Igor and Deelman, Ewa and Letts, James and Wurthwein, Frank and Livny, Miron},
  title = {Characterizing a High Throughput Computing Workload: The Compact Muon Solenoid ({CMS}) Experiment at {LHC}},
  year = {2015},
  journal = {Procedia Computer Science, International Conference On Computational Science, ICCS 2015 Computational Science at the Gates of Nature},
  pages = {39--48},
  volume = {51},
  doi = {10.1016/j.procs.2015.05.190},
  note = {Funding Acknowledgments: DOE ER26110},
  url = {http://pegasus.isi.edu/publications/2015/FerreiradaSilva-ICCS-2015.pdf}
}
  7. Glatard, T., Ferreira da Silva, R., Boujelben, N., Adalat, R., Beck, N., Rioux, P., Rousseau, M.-E., Deelman, E., & Evans, A. C. (2015). Boutiques: an application-sharing system based on Linux containers. NeuroInformatics 2015. https://doi.org/10.3389/conf.fnins.2015.91.00012 
    @inproceedings{glatard-neuroinformatics-2016,
  author = {Glatard, Tristan and Ferreira da Silva, Rafael and Boujelben, Nouha and Adalat, Reza and Beck, Natacha and Rioux, Pierre and Rousseau, Marc-Etienne and Deelman, Ewa and Evans, Alan C.},
  url = {http://dx.doi.org/10.3389/conf.fnins.2015.91.00012},
  doi = {10.3389/conf.fnins.2015.91.00012},
  title = {Boutiques: an application-sharing system based on Linux containers},
  booktitle = {NeuroInformatics 2015},
  year = {2015}
}
  8. Glatard, T., Lewis, L. B., Ferreira da Silva, R., Adalat, R., Beck, N., Lepage, C., Rioux, P., Rousseau, M.-E., Sherif, T., Deelman, E., Khalili-Mahani, N., & Evans, A. C. (2015). Reproducibility of neuroimaging analyses across operating systems. Frontiers in Neuroinformatics, 9(12). https://doi.org/10.3389/fninf.2015.00012 (Funding Acknowledgments: NSF ACI SI2-SSI 1148515) 
    @article{glatard-neuroinformatics-2015,
  title = {Reproducibility of neuroimaging analyses across operating systems},
  journal = {Frontiers in Neuroinformatics},
  volume = {9},
  number = {12},
  pages = {},
  year = {2015},
  doi = {10.3389/fninf.2015.00012},
  author = {Glatard, Tristan and Lewis, Lindsay Burke and Ferreira da Silva, Rafael and Adalat, Reza and Beck, Natacha and Lepage, Claude and Rioux, Pierre and Rousseau, Marc-Etienne and Sherif, Tarek and Deelman, Ewa and Khalili-Mahani, Najmeh and Evans, Alan Charles},
  note = {Funding Acknowledgments: NSF ACI SI2-SSI 1148515},
  url = {http://journal.frontiersin.org/article/10.3389/fninf.2015.00012/abstract}
}
  9. Howison, J., Deelman, E., McLennan, M. J., Ferreira da Silva, R., & Herbsleb, J. D. (2015). Understanding the scientific software ecosystem and its impact: Current and future measures. Research Evaluation, 24(4), 454–470. https://doi.org/10.1093/reseval/rvv014 (Funding Acknowledgments: NSF ACI SI2-SSI 1148515) 
    @article{howison-reseval-2015,
  author = {Howison, James and Deelman, Ewa and McLennan, Michael J. and Ferreira da Silva, Rafael and Herbsleb, James D.},
  title = {Understanding the scientific software ecosystem and its impact: Current and future measures},
  journal = {Research Evaluation},
  year = {2015},
  volume = {24},
  number = {4},
  pages = {454--470},
  doi = {10.1093/reseval/rvv014},
  note = {Funding Acknowledgments: NSF ACI SI2-SSI 1148515},
  url = {http://rev.oxfordjournals.org/content/early/2015/07/26/reseval.rvv014}
}
  10. Juve, G., Tovar, B., Ferreira da Silva, R., Krol, D., Thain, D., Deelman, E., Allcock, W., & Livny, M. (2015). Practical Resource Monitoring for Robust High Throughput Computing. Workshop on Monitoring and Analysis for High Performance Computing Systems Plus Applications. https://doi.org/10.1109/CLUSTER.2015.115 (Funding Acknowledgments: DOE ER26110, DOE DE-SC0012636) 
    @inproceedings{juve-hpcmaspa-2015,
  author = {Juve, Gideon and Tovar, Benjamin and Ferreira da Silva, Rafael and Krol, Dariusz and Thain, Douglas and Deelman, Ewa and Allcock, William and Livny, Miron},
  title = {Practical Resource Monitoring for Robust High Throughput Computing},
  booktitle = {Workshop on Monitoring and Analysis for High Performance Computing Systems Plus Applications},
  year = {2015},
  url = {http://pegasus.isi.edu/publications/2015/juve-hpcmaspa-2015.pdf},
  note = {Funding Acknowledgments: DOE ER26110, DOE DE-SC0012636},
  doi = {10.1109/CLUSTER.2015.115}
}
  11. Malawski, M., Figiela, K., Bubak, M., Deelman, E., & Nabrzyski, J. (2015). Scheduling Multilevel Deadline-Constrained Scientific Workflows on Clouds Based on Cost Optimization. Scientific Programming, 2015, 1–13. https://doi.org/10.1155/2015/680271 (Funding Acknowledgments: NSF ACI SI2-SSI 1148515, DOE ER26110) 
    @article{malawski2015scientificprogramming,
  author = {Malawski, Maciej and Figiela, Kamil and Bubak, Marian and Deelman, Ewa and Nabrzyski, Jarek},
  title = {Scheduling Multilevel Deadline-Constrained Scientific Workflows on Clouds Based on Cost Optimization},
  journal = {Scientific Programming},
  volume = {2015},
  pages = {1--13},
  doi = {10.1155/2015/680271},
  year = {2015},
  url = {http://pegasus.isi.edu/publications/2015/2015-scientific-programming-multilevel.pdf},
  note = {Funding Acknowledgments: NSF ACI SI2-SSI 1148515, DOE ER26110}
}
  12. Malawski, M., Juve, G., Deelman, E., & Nabrzyski, J. (2015). Algorithms for Cost- and Deadline-Constrained Provisioning for Scientific Workflow Ensembles in IaaS Clouds. Future Generation Computer Systems, 48, 1–18. https://doi.org/10.1016/j.future.2015.01.004 (Funding Acknowledgments: DOE ER26110, NSF ACI SI2-SSI 1148515) 
    @article{malawski2015fgcs,
  author = {Malawski, Maciej and Juve, Gideon and Deelman, Ewa and Nabrzyski, Jarek},
  title = {Algorithms for Cost- and Deadline-Constrained Provisioning for Scientific Workflow Ensembles in IaaS Clouds},
  journal = {Future Generation Computer Systems},
  volume = {48},
  year = {2015},
  pages = {1--18},
  url = {http://pegasus.isi.edu/publications/2015/2015-fgcs-malawski.pdf},
  doi = {10.1016/j.future.2015.01.004},
  note = {Funding Acknowledgments: DOE ER26110, NSF ACI SI2-SSI 1148515}
}
  13. Mandal, A., Ruth, P., Baldin, I., Xin, Y., Castillo, C., Juve, G., Rynge, M., Deelman, E., & Chase, J. (2015). Adapting Scientific Workflows on Networked Clouds Using Proactive Introspection. IEEE/ACM Utility and Cloud Computing (UCC). https://doi.org/10.1109/UCC.2015.32 (Funding Acknowledgments: NSF CC-NIE ADAMANT project (NSF ACI 1245926), DoE DROPS project (ASCR DE-SC0005286), DoE SciDAC SUPER project (DE-FG02-11ER26050/DE-SC0006925), NSF SDCI Missing Link project (NSF ACI 1032573), and the NSF GENI project (GENI Project Office Award #1872)) 
    @inproceedings{mandal-ucc-2015,
  author = {Mandal, Anirban and Ruth, Paul and Baldin, Ilya and Xin, Yufeng and Castillo, Claris and Juve, Gideon and Rynge, Mats and Deelman, Ewa and Chase, Jeff},
  title = {Adapting Scientific Workflows on Networked Clouds Using Proactive Introspection},
  booktitle = {{IEEE/ACM Utility and Cloud Computing (UCC)}},
  year = {2015},
  note = {Funding Acknowledgments: NSF CC-NIE ADAMANT project (NSF ACI 1245926), DoE DROPS project (ASCR DE-SC0005286), DoE SciDAC SUPER project (DE-FG02-11ER26050/DE-SC0006925), NSF SDCI Missing Link project (NSF ACI 1032573), and the NSF GENI project (GENI Project Office Award #1872)},
  doi = {10.1109/UCC.2015.32}
}
  14. Mayer, B., Worley, P., Ferreira da Silva, R., & Gaddis, A. (2015). Climate Science Performance, Data and Productivity on Titan. Cray User Group Conference. http://pegasus.isi.edu/publications/2015/mayer-cug-2015.pdf (Funding Acknowledgments: DOE DE-SC0012636) 
    @inproceedings{mayer-cug-2015,
  title = {Climate Science Performance, Data and Productivity on Titan},
  author = {Mayer, Benjamin and Worley, Patrick and Ferreira da Silva, Rafael and Gaddis, Abigail},
  booktitle = {Cray User Group Conference},
  year = {2015},
  url = {http://pegasus.isi.edu/publications/2015/mayer-cug-2015.pdf},
  note = {Funding Acknowledgments: DOE DE-SC0012636}
}
  15. Oda, R., Cordeiro, D., Ferreira da Silva, R., Deelman, E., & Braghetto, K. (2015). The Case for Resource Sharing in Scientific Workflow Executions. XVI Simposio Em Sistemas Computacionais De Alto Desempenho (WSCAD). http://pegasus.isi.edu/publications/2015/oda-wscad-2015.pdf (Funding Acknowledgments: NSF ACI SI2-SSI 1148515) 
    @inproceedings{oda-wscad-2015,
  title = {The Case for Resource Sharing in Scientific Workflow Executions},
  booktitle = {XVI Simposio em Sistemas Computacionais de Alto Desempenho (WSCAD)},
  year = {2015},
  author = {Oda, Ricardo and Cordeiro, Daniel and Ferreira da Silva, Rafael and Deelman, Ewa and Braghetto, Kelly},
  note = {Funding Acknowledgments: NSF ACI SI2-SSI 1148515},
  url = {http://pegasus.isi.edu/publications/2015/oda-wscad-2015.pdf}
}
  16. Quick, R., Hayashi, S., Meroueh, S., Rynge, M., Teige, S., Wang, B., & Xu, D. (2015). Building a Chemical-Protein Interactome on the Open Science Grid. Proceedings of Science, International Symposium on Grids and Clouds (ISGC) 2015. http://pegasus.isi.edu/publications/2015/ISGC2015_024.pdf 
    @article{osg-splinter-2015,
  author = {Quick, Rob and Hayashi, Soichi and Meroueh, Samy and Rynge, Mats and Teige, Scott and Wang, Bo and Xu, David},
  title = {Building a Chemical-Protein Interactome on the Open Science Grid},
  journal = {Proceedings of Science, International Symposium on Grids and Clouds (ISGC) 2015},
  year = {2015},
  url = {http://pegasus.isi.edu/publications/2015/ISGC2015_024.pdf}
}

2014

  1. Ferreira da Silva, R., Chen, W., Juve, G., Vahi, K., & Deelman, E. (2014). Community Resources for Enabling Research in Distributed Scientific Workflows. 10th IEEE International Conference on e-Science (EScience 2014). https://doi.org/10.1109/eScience.2014.44 (Funding Acknowledgments: OCI SI2-SSI program grant #1148515, DOE contract for dv/dt ER26110) 
    @inproceedings{silva2014community,
  author = {Ferreira da Silva, Rafael and Chen, Weiwei and Juve, Gideon and Vahi, Karan and Deelman, Ewa},
  url = {http://pegasus.isi.edu/publications/2014/2014-escience.pdf},
  title = {Community Resources for Enabling Research in Distributed Scientific Workflows},
  booktitle = {10th IEEE International Conference on e-Science (eScience 2014)},
  year = {2014},
  note = {Funding Acknowledgments: OCI SI2-SSI program grant #1148515, DOE contract for dv/dt ER26110},
  doi = {10.1109/eScience.2014.44}
}
  2. Ferreira da Silva, R., Fahringer, T., Durillo, J. J., & Deelman, E. (2014). A Unified Approach for Modeling and Optimization of Energy, Makespan and Reliability for Scientific Workflows on Large-Scale Computing Infrastructures. Workshop on Modeling and Simulation of Systems and Applications (MODSIM). http://pegasus.isi.edu/publications/2014/2014-modsim.pdf (Funding Acknowledgments: DOE contract for dv/dt ER26110).) 
    @inproceedings{silva2014modsim,
  author = {Ferreira da Silva, Rafael and Fahringer, Thomas and Durillo, Juan J. and Deelman, Ewa},
  url = {http://pegasus.isi.edu/publications/2014/2014-modsim.pdf},
  title = {A Unified Approach for Modeling and Optimization of Energy, Makespan and Reliability for Scientific Workflows on Large-Scale Computing Infrastructures},
  booktitle = {Workshop on Modeling and Simulation of Systems and Applications (MODSIM)},
  year = {2014},
  note = {Funding Acknowledgments: DOE contract for dv/dt ER26110).}
}
  3. Glatard, T., Lewis, L. B., Ferreira da Silva, R., Rousseau, M.-E., Lepage, C., Rioux, P., Mahani, N., Deelman, E., & Evans, A. C. (2014). Extending provenance information in CBRAIN to address reproducibility issues across computing platforms. NeuroInformatics 2014. http://pegasus.isi.edu/publications/2014/2014-neuroinformatics.pdf 
    @inproceedings{glatard2014provenance,
  author = {Glatard, Tristan and Lewis, Lindsay B and Ferreira da Silva, Rafael and Rousseau, Marc-Etienne and Lepage, Claude and Rioux, Pierre and Mahani, Najmeh and Deelman, Ewa and Evans, Alan C},
  url = {http://pegasus.isi.edu/publications/2014/2014-neuroinformatics.pdf},
  title = {Extending provenance information in CBRAIN to address reproducibility issues across computing platforms},
  booktitle = {NeuroInformatics 2014},
  year = {2014}
}
  4. Juve, G., Tovar, B., Ferreira da Silva, R., Robinson, C., Thain, D., Deelman, E., Allcock, W., & Livny, M. (2014). Practical Resource Monitoring for Robust High Throughput Computing (Technical Report 14-950; Number Technical Report 14-950). University of Southern California. http://pegasus.isi.edu/publications/2014/2014-dvdtreport.pdf (Funding Acknowledgments: DOE contract for dv/dt ER26110) 
    @techreport{juve2014monitoring,
  author = {Juve, Gideon and Tovar, Benjamin and Ferreira da Silva, Rafael and Robinson, Casey and Thain, Douglas and Deelman, Ewa and Allcock, William and Livny, Miron},
  url = {http://pegasus.isi.edu/publications/2014/2014-dvdtreport.pdf},
  title = {Practical Resource Monitoring for Robust High Throughput Computing},
  institution = {University of Southern California},
  number = {Technical Report 14-950},
  year = {2014},
  note = {Funding Acknowledgments: DOE contract for dv/dt ER26110}
}
  5. Malawski, M., Figiela, K., Bubak, M., Deelman, E., & Nabrzyski, J. (2014). Cost Optimization of Execution of Multi-level Deadline-Constrained Scientific Workflows on Clouds. Parallel Processing and Applied Mathematics, 251–260. https://doi.org/10.1007/978-3-642-55224-3_24 (Funding Acknowledgments: OCI SI2-SSI program grant #1148515) 
    @article{malawski2014optimization,
  author = {Malawski, Maciej and Figiela, Kamil and Bubak, Marian and Deelman, Ewa and Nabrzyski, Jarek},
  url = {http://dx.doi.org/10.1007/978-3-642-55224-3_24},
  doi = {10.1007/978-3-642-55224-3_24},
  title = {Cost Optimization of Execution of Multi-level Deadline-Constrained Scientific Workflows on Clouds},
  journal = {Parallel Processing and Applied Mathematics},
  pages = {251-260},
  publisher = {Springer Berlin Heidelberg},
  year = {2014},
  note = {Funding Acknowledgments: OCI SI2-SSI program grant #1148515}
}
  6. McLennan, M., Clark, S., Deelman, E., Rynge, M., Vahi, K., McKenna, F., Kearney, D., & Song, C. (2014). HUBzero and Pegasus: integrating scientific workflows into science gateways. Concurrency and Computation: Practice and Experience. https://doi.org/10.1002/cpe.3257 (Funding Acknowledgments: OCI SI2-SSI program grant #1148515, OCI SDCI program grant #0722019) 
    @article{mclennan2014hubzero,
  author = {McLennan, Michael and Clark, Steven and Deelman, Ewa and Rynge, Mats and Vahi, Karan and McKenna, Frank and Kearney, Derrick and Song, Carol},
  url = {http://dx.doi.org/10.1002/cpe.3257},
  doi = {10.1002/cpe.3257},
  title = {HUBzero and Pegasus: integrating scientific workflows into science gateways},
  journal = {Concurrency and Computation: Practice and Experience},
  year = {2014},
  note = {Funding Acknowledgments: OCI SI2-SSI program grant #1148515, OCI SDCI program grant #0722019}
}
  7. Pietri, I., Juve, G., Deelman, E., & Sakellariou, R. (2014). A Performance Model to Estimate Execution Time of Scientific Workflows on the Cloud. 9th Workshop on Workflows in Support of Large-Scale Science (WORKS). https://doi.org/10.1109/WORKS.2014.12 (Funding Acknowledgments: DOE contract for dv/dt ER26110) 
    @inproceedings{pietri2014estimate,
  author = {Pietri, Ilia and Juve, Gideon and Deelman, Ewa and Sakellariou, Rizos},
  url = {http://pegasus.isi.edu/publications/2014/pietri-works14.pdf},
  title = {A Performance Model to Estimate Execution Time of Scientific Workflows on the Cloud},
  booktitle = {9th Workshop on Workflows in Support of Large-Scale Science (WORKS)},
  year = {2014},
  note = {Funding Acknowledgments: DOE contract for dv/dt ER26110},
  doi = {10.1109/WORKS.2014.12}
}
  8. Santana-Perez, I., Ferreira da Silva, R., Rynge, M., Deelman, E., Perez-Hernandez, M. S., & Corcho, O. (2014). A Semantic-Based Approach to Attain Reproducibility of Computational Environments in Scientific Workflows: A Case Study. 1st International Workshop on Reproducibility in Parallel Computing (REPPAR), in Conjunction with Euro-Par 2014. http://pegasus.isi.edu/publications/2014/2014-reppar.pdf (Funding Acknowledgments: NSF FutureGrid 0910812) 
    @inproceedings{santanaperez2014semantic,
  author = {Santana-Perez, Idafen and Ferreira da Silva, Rafael and Rynge, Mats and Deelman, Ewa and Perez-Hernandez, Maria S. and Corcho, Oscar},
  url = {http://pegasus.isi.edu/publications/2014/2014-reppar.pdf},
  title = {A Semantic-Based Approach to Attain Reproducibility of Computational Environments in Scientific Workflows: A Case Study},
  booktitle = {1st International Workshop on Reproducibility in Parallel Computing (REPPAR), in conjunction with Euro-Par 2014},
  year = {2014},
  note = {Funding Acknowledgments: NSF FutureGrid 0910812}
}
  9. Santana-Perez, I., Ferreira da Silva, R., Rynge, M., Deelman, E., Perez-Hernandez, M. S., & Corcho, O. (2014). Leveraging Semantics to Improve Reproducibility in Scientific Workflows. The Reproducibility at XSEDE Workshop. http://pegasus.isi.edu/publications/2014/2014-xsede.pdf (Funding Acknowledgments: NSF FutureGrid 0910812) 
    @inproceedings{santanaperez2014reproducibility,
  author = {Santana-Perez, Idafen and Ferreira da Silva, Rafael and Rynge, Mats and Deelman, Ewa and Perez-Hernandez, Maria S. and Corcho, Oscar},
  url = {http://pegasus.isi.edu/publications/2014/2014-xsede.pdf},
  title = {Leveraging Semantics to Improve Reproducibility in Scientific Workflows},
  booktitle = {The reproducibility at XSEDE workshop},
  year = {2014},
  note = {Funding Acknowledgments: NSF FutureGrid 0910812}
}
  10. Srinivasan, S., Juve, G., Ferreira da Silva, R., Vahi, K., & Deelman, E. (2014). A Cleanup Algorithm for Implementing Storage Constraints in Scientific Workflow Executions. 9th Workshop on Workflows in Support of Large-Scale Science (WORKS). https://doi.org/10.1109/WORKS.2014.8 (Funding Acknowledgments: OCI SI2-SSI program grant #1148515) 
    @inproceedings{srinivasan2014cleanup,
  author = {Srinivasan, Sudarshan and Juve, Gideon and Ferreira da Silva, Rafael and Vahi, Karan and Deelman, Ewa},
  title = {A Cleanup Algorithm for Implementing Storage Constraints in Scientific Workflow Executions},
  booktitle = {9th Workshop on Workflows in Support of Large-Scale Science (WORKS)},
  year = {2014},
  note = {Funding Acknowledgments: OCI SI2-SSI program grant #1148515},
  url = {http://pegasus.isi.edu/publications/2014/2014-works.pdf},
  doi = {10.1109/WORKS.2014.8}
}

2013

  1. Azarnoosh, S., Rynge, M., Juve, G., Nieć, E. D. M., Malawski, M., & Ferreira da Silva, R. (2013). Introducing PRECIP: An API for Managing Repeatable Experiments in the Cloud. Workshop on Cloud Computing for Research Collaborations (CRC). http://pegasus.isi.edu/publications/2013/precip-cloudcom-2013.pdf (Funding Acknowledgments: National Science Foundation under Grant No. 0910812 and AWS Educational Grant) 
    @inproceedings{azarnoosh2013precip,
  author = {Azarnoosh, Sepideh and Rynge, Mats and Juve, Gideon and Nieć, Ewa Deelman Michal and Malawski, Maciej and Ferreira da Silva, Rafael},
  url = {http://pegasus.isi.edu/publications/2013/precip-cloudcom-2013.pdf},
  title = {Introducing PRECIP: An API for Managing Repeatable Experiments in the Cloud},
  booktitle = {Workshop on Cloud Computing for Research Collaborations (CRC)},
  year = {2013},
  note = {Funding Acknowledgments: National Science Foundation under Grant No. 0910812 and AWS Educational Grant}
}
  2. Berriman, G. B., Juve, G., Vöckler, J.-S., Deelman, E., & Rynge, M. (2013). The Application of Cloud Computing to Scientific Workflows: A Study of Cost and Performance. Proceedings of the Royal Society A, 371(1983). http://rsta.royalsocietypublishing.org/content/371/1983/20120066.abstract (Funding Acknowledgments: NSF OCI-0910812, NSF OCI-0943725, NASA NCC5-626, and Amazon Educational Grant) 
    @article{berriman2013royal,
  author = {Berriman, G. Bruce and Juve, Gideon and Vöckler, Jens-S. and Deelman, Ewa and Rynge, Mats},
  url = {http://rsta.royalsocietypublishing.org/content/371/1983/20120066.abstract},
  title = {The Application of Cloud Computing to Scientific Workflows: A Study of Cost and Performance},
  journal = {Proceedings of the Royal Society A},
  volume = {371},
  number = {1983},
  month = jan,
  year = {2013},
  note = {Funding Acknowledgments: NSF OCI-0910812, NSF OCI-0943725, NASA NCC5-626, and Amazon Educational Grant}
}
  3. Chen, W., Deelman, E., & Sakellariou, R. (2013). Imbalance Optimization in Scientific Workflows. International Conference on Supercomputing (ICS 2013). (Funding Acknowledgments: NSF IIS-0905032 and NSF FutureGrid 0910812) 
    @inproceedings{chen2013imbalance,
  author = {Chen, Weiwei and Deelman, Ewa and Sakellariou, Rizos},
  title = {Imbalance Optimization in Scientific Workflows},
  booktitle = {International Conference on Supercomputing (ICS 2013)},
  year = {2013},
  note = {Funding Acknowledgments: NSF IIS-0905032 and NSF FutureGrid 0910812}
}
  4. Chen, W., Ferreira da Silva, R., Deelman, E., & Sakellariou, R. (2013). Balanced Task Clustering in Scientific Workflows. 9th IEEE International Conference on e-Science (EScience 2013). http://pegasus.isi.edu/publications/2013/chen-clustering-escience2013.pdf (Funding Acknowledgments: NSF IIS-0905032 and NSF FutureGrid 0910812) 
    @inproceedings{chen2013balanced,
  author = {Chen, Weiwei and Ferreira da Silva, Rafael and Deelman, Ewa and Sakellariou, Rizos},
  url = {http://pegasus.isi.edu/publications/2013/chen-clustering-escience2013.pdf},
  title = {Balanced Task Clustering in Scientific Workflows},
  booktitle = {9th IEEE International Conference on e-Science (eScience 2013)},
  year = {2013},
  note = {Funding Acknowledgments: NSF IIS-0905032 and NSF FutureGrid 0910812}
}
  5. Deelman, E., Juve, G., Malawski, M., & Nabrzyski, J. (2013). Hosted Science: Managing Computational Workloads in the Cloud. Parallel Processing Letters, 23(2). http://www.worldscientific.com/doi/pdf/10.1142/S0129626413400045 (Funding: NSF OCI-0943725 and OCI-1148515) 
    @article{deelman2013hosted,
  author = {Deelman, Ewa and Juve, Gideon and Malawski, Maciej and Nabrzyski, Jarek},
  url = {http://www.worldscientific.com/doi/pdf/10.1142/S0129626413400045},
  title = {Hosted Science: Managing Computational Workloads in the Cloud},
  journal = {Parallel Processing Letters},
  volume = {23},
  number = {2},
  month = jun,
  year = {2013},
  note = {Funding: NSF OCI-0943725 and OCI-1148515}
}
  6. Ferreira da Silva, R., Juve, G., Deelman, E., Glatard, T., Desprez, F., Thain, D., Tovar, B., & Livny, M. (2013). Toward Fine-Grained Online Task Characteristics Estimation in Scientific Workflows. 8th Workshop On Workflows in Support of Large-Scale Science (WORKS). http://pegasus.isi.edu/publications/2013/ferreira-da-silva-task-estimation-works2013.pdf (Funding Acknowledgments: DOE contract for dv/dt ER26110, EC FP7 Program under grant agreement 312579 ER-flow) 
    @inproceedings{silva2013estimation,
  author = {Ferreira da Silva, Rafael and Juve, Gideon and Deelman, Ewa and Glatard, Tristan and Desprez, Frederic and Thain, Douglas and Tovar, Benjamín and Livny, Miron},
  url = {http://pegasus.isi.edu/publications/2013/ferreira-da-silva-task-estimation-works2013.pdf},
  title = {Toward Fine-Grained Online Task Characteristics Estimation in Scientific Workflows},
  booktitle = {8th Workshop On Workflows in Support of Large-Scale Science (WORKS)},
  year = {2013},
  note = {Funding Acknowledgments: DOE contract for dv/dt ER26110, EC FP7 Program under grant agreement 312579 ER-flow}
}
  7. Juve, G., Chervenak, A., Deelman, E., Bharathi, S., Mehta, G., & Vahi, K. (2013). Characterizing and Profiling Scientific Workflows. Future Generation Computer Systems, 29(3), 682–692. http://pegasus.isi.edu/publications/2013/JuveG-Characterizing.pdf 
    @article{juve2013characterizing,
  author = {Juve, Gideon and Chervenak, Ann and Deelman, Ewa and Bharathi, Shishir and Mehta, Gaurang and Vahi, Karan},
  url = {http://pegasus.isi.edu/publications/2013/JuveG-Characterizing.pdf},
  title = {Characterizing and Profiling Scientific Workflows},
  journal = {Future Generation Computer Systems},
  volume = {29},
  number = {3},
  pages = {682-692},
  month = mar,
  year = {2013}
}
  8. Juve, G., Rynge, M., Deelman, E., Vöckler, J.-S., & Berriman, G. B. (2013). Comparing FutureGrid, Amazon EC2, and Open Science Grid for Scientific Workflows. Computing in Science and Engineering, 15(4), 20–29. http://pegasus.isi.edu/publications/2013/JuveG-Comparing.pdf (Funding: NSF OCI-0943725 and OCI-0910812, Amazon Web Services Educational Grant).) 
    @article{juve2013comparing,
  author = {Juve, Gideon and Rynge, Mats and Deelman, Ewa and Vöckler, Jens-S. and Berriman, G. Bruce},
  url = {http://pegasus.isi.edu/publications/2013/JuveG-Comparing.pdf},
  title = {Comparing FutureGrid, Amazon EC2, and Open Science Grid for Scientific Workflows},
  journal = {Computing in Science and Engineering},
  volume = {15},
  number = {4},
  pages = {20-29},
  year = {2013},
  note = {Funding: NSF OCI-0943725 and OCI-0910812, Amazon Web Services Educational Grant).}
}
  9. Mandal, A., Ruth, P., Baldin, I., Xin, Y., Castillo, C., Rynge, M., & Deelman, E. (2013). Evaluating I/O Aware Network Management for Scientific Workflows on Networked Clouds. The 3rd International Workshop on Network-Aware Data Management, in Conjunction with SC13. http://pegasus.isi.edu/publications/2013/io-aware-network-management-ndm2013.pdf (Funding Acknowledgments: NSF CC-NIE ADAMANT project (NSF ACI 1245926), DoE DROPS project (ASCR DE-SC0005286), DoE SciDAC SUPER project (DE-FG02-11ER26050/DE-SC0006925), NSF SDCI Missing Link project (NSF ACI 1032573), and the NSF GENI project (GENI Project Office Award #1872)) 
    @inproceedings{mandal2013io,
  author = {Mandal, Anirban and Ruth, Paul and Baldin, Ilya and Xin, Yufeng and Castillo, Claris and Rynge, Mats and Deelman, Ewa},
  url = {http://pegasus.isi.edu/publications/2013/io-aware-network-management-ndm2013.pdf},
  title = {Evaluating I/O Aware Network Management for Scientific Workflows on Networked Clouds},
  booktitle = {The 3rd International Workshop on Network-aware Data Management, in conjunction with SC13},
  year = {2013},
  note = {Funding Acknowledgments: NSF CC-NIE ADAMANT project (NSF ACI 1245926), DoE DROPS project (ASCR DE-SC0005286), DoE SciDAC SUPER project (DE-FG02-11ER26050/DE-SC0006925), NSF SDCI Missing Link project (NSF ACI 1032573), and the NSF GENI project (GENI Project Office Award #1872)}
}
  10. McLennan, M., Clark, S., McKenna, F., Deelman, E., Rynge, M., Vahi, K., Kearney, D., & Song, C. (2013). Bringing Scientific Workflow to the Masses via Pegasus and HUBzero. Proceedings of the 5th International Workshop on Science Gateways. http://pegasus.isi.edu/publications/2013/McLennan_Pegasus_Hubzero.pdf (Funding Acknowledgments: NSF grants CBET-0941302, CMMI-0927178, OCI-1148515, and OCI-0943705) 
    @inproceedings{mclennan2013masses,
  author = {McLennan, Michael and Clark, Steve and McKenna, Frank and Deelman, Ewa and Rynge, Mats and Vahi, Karan and Kearney, Derrick and Song, Carol},
  url = {http://pegasus.isi.edu/publications/2013/McLennan_Pegasus_Hubzero.pdf},
  title = {Bringing Scientific Workflow to the Masses via Pegasus and HUBzero},
  booktitle = {Proceedings of the 5th International Workshop on Science Gateways},
  year = {2013},
  note = {Funding Acknowledgments: NSF grants CBET-0941302, CMMI-0927178, OCI-1148515, and OCI-0943705}
}
  11. Pietri, I., Malawski, M., Juve, G., Deelman, E., Nabrzyski, J., & Sakellariou, R. (2013). Energy-Constrained Provisioning for Scientific Workflow Ensembles. IEEE International Conference on Cloud and Green Computing (CGC13). http://pegasus.isi.edu/publications/2013/PietriI-Energy.pdf 
    @inproceedings{pietri2013energy,
  author = {Pietri, Ilia and Malawski, Maciej and Juve, Gideon and Deelman, Ewa and Nabrzyski, Jarek and Sakellariou, Rizos},
  url = {http://pegasus.isi.edu/publications/2013/PietriI-Energy.pdf},
  title = {Energy-Constrained Provisioning for Scientific Workflow Ensembles},
  booktitle = {IEEE International Conference on Cloud and Green Computing (CGC13)},
  year = {2013}
}
  12. Rynge, M., Juve, G., Kinney, J., Good, J., Berriman, G. B., Merrihew, A., & Deelman, E. (2013). Producing an Infrared Multiwavelength Galactic Plane Atlas using Montage, Pegasus and Amazon Web Services. 23rd Annual Astronomical Data Analysis Software and Systems (ADASS) Conference. http://pegasus.isi.edu/publications/2013/rynge-montage-pegasus-amazon-adass2013.pdf (Funding Acknowledgments: OCI SI2-SSI program grant #1148515) 
    @inproceedings{rynge2013adass,
  author = {Rynge, Mats and Juve, Gideon and Kinney, Jamie and Good, John and Berriman, G. Bruce and Merrihew, Ann and Deelman, Ewa},
  url = {http://pegasus.isi.edu/publications/2013/rynge-montage-pegasus-amazon-adass2013.pdf},
  title = {Producing an Infrared Multiwavelength Galactic Plane Atlas using Montage, Pegasus and Amazon Web Services},
  booktitle = {23rd Annual Astronomical Data Analysis Software and Systems (ADASS) Conference},
  year = {2013},
  note = {Funding Acknowledgments: OCI SI2-SSI program grant #1148515}
}
  13. Vahi, K., Harvey, I., Samak, T., Gunter, D., Evans, K., Rogers, D., Taylor, I., Goode, M., Silva, F., Al-Shakarchi, E., Mehta, G., & andrew Jones, E. D. (2013). A Case Study into Using Common Real-Time Workflow Monitoring Infrastructure for Scientific Workflows. Journal of Grid Computing, 11(3), 381–406. http://link.springer.com/article/10.1007%2Fs10723-013-9265-4 (Funding Acknowledgments: NSF grant OCI-0943705) 
    @article{vahi2013jgc,
  author = {Vahi, Karan and Harvey, Ian and Samak, Taghrid and Gunter, Daniel and Evans, Kieran and Rogers, David and Taylor, Ian and Goode, Monte and Silva, Fabio and Al-Shakarchi, Eddie and Mehta, Gaurang and andrew Jones, Ewa Deelman},
  url = {http://link.springer.com/article/10.1007%2Fs10723-013-9265-4},
  title = {A Case Study into Using Common Real-Time Workflow Monitoring Infrastructure for Scientific Workflows},
  journal = {Journal of Grid Computing},
  volume = {11},
  number = {3},
  pages = {381-406},
  year = {2013},
  note = {Funding Acknowledgments: NSF grant OCI-0943705}
}
  14. Vahi, K., Rynge, M., Juve, G., Mayani, R., & Deelman, E. (2013). Rethinking Data Management for Big Data Scientific Workflows. Workshop on Big Data and Science: Infrastructure and Services. http://pegasus.isi.edu/publications/2013/Vahi-PegasusLite-IEEE-BigData-2013.pdf (Funding Acknowledgments: OCI SDCI program grant #0722019 and OCI SI2-SSI program grant #1148515) 
    @inproceedings{vahi2013rethinking,
  author = {Vahi, Karan and Rynge, Mats and Juve, Gideon and Mayani, Rajiv and Deelman, Ewa},
  url = {http://pegasus.isi.edu/publications/2013/Vahi-PegasusLite-IEEE-BigData-2013.pdf},
  title = {Rethinking Data Management for Big Data Scientific Workflows},
  booktitle = {Workshop on Big Data and Science: Infrastructure and Services},
  year = {2013},
  note = {Funding Acknowledgments: OCI SDCI program grant #0722019 and OCI SI2-SSI program grant #1148515}
}

2012

  1. Agarwal, R., Juve, G., & Deelman, E. (2012). Peer-to-Peer Data Sharing for Scientific Workflows on Amazon EC2. 7th Workshop on Workflows in Support of Large-Scale Science (WORKS12). http://pegasus.isi.edu/publications/2012/Agarwal-WORKS-2012.pdf (Funding Acknowledgments: NSF OCI-0943725, Viterbi-India Program) ) 
    @inproceedings{agarwal2012p2p,
  author = {Agarwal, Rohit and Juve, Gideon and Deelman, Ewa},
  url = {http://pegasus.isi.edu/publications/2012/Agarwal-WORKS-2012.pdf},
  title = {Peer-to-Peer Data Sharing for Scientific Workflows on Amazon EC2},
  booktitle = {7th Workshop on Workflows in Support of Large-Scale Science (WORKS12)},
  year = {2012},
  note = {Funding Acknowledgments: NSF OCI-0943725, Viterbi-India Program)  }
}
  2. Berriman, G. B., Brinkworth, C., Gelino, D., Wittman, D. K., Deelman, E., Juve, G., Rynge, M., & Kinney, J. (2012). A Tale Of 160 Scientists, Three Applications, A Workshop and A Cloud. Astronomical Data Analysis Software and Systems XXII. 
    @inproceedings{berriman2012sagan,
  author = {Berriman, G. Bruce and Brinkworth, Carolyn and Gelino, Dawn and Wittman, Dennis K. and Deelman, Ewa and Juve, Gideon and Rynge, Mats and Kinney, Jamie},
  title = {A Tale Of 160 Scientists, Three Applications, A Workshop and A Cloud},
  booktitle = {Astronomical Data Analysis Software and Systems XXII},
  year = {2012}
}
  3. Chen, W., & Deelman, E. (2012). WorkflowSim: A Toolkit for Simulating Scientific Workflows in Distributed Environments. The 8th IEEE International Conference on EScience 2012 (EScience 2012). http://pegasus.isi.edu/publications/2012/WChen-WorkflowSim-eScience12.pdf (Funding Acknowledgments: NSF IIS-0905032) 
    @inproceedings{chen2012workflowsim,
  author = {Chen, Weiwei and Deelman, Ewa},
  url = {http://pegasus.isi.edu/publications/2012/WChen-WorkflowSim-eScience12.pdf},
  title = {WorkflowSim: A Toolkit for Simulating Scientific Workflows in Distributed Environments},
  booktitle = {The 8th IEEE International Conference on eScience 2012 (eScience 2012)},
  year = {2012},
  note = {Funding Acknowledgments: NSF IIS-0905032}
}
  4. Chen, W., & Deelman, E. (2012). Fault Tolerant Clustering in Scientific Workflows. IEEE 6th International Workshop on Scientific Workflows (SWF 2012) in Conjunction with IEEE 8th World Congress on Services (SERVICES 2012). http://pegasus.isi.edu/publications/2012/WChen-FTC-Services12.pdf (Funding Acknowledgments: NSF IIS-0905032) 
    @inproceedings{chen2012tolerant,
  author = {Chen, Weiwei and Deelman, Ewa},
  url = {http://pegasus.isi.edu/publications/2012/WChen-FTC-Services12.pdf},
  title = {Fault Tolerant Clustering in Scientific Workflows},
  booktitle = {IEEE 6th International Workshop on Scientific Workflows (SWF 2012) in conjunction with IEEE 8th World Congress on Services (SERVICES 2012)},
  year = {2012},
  note = {Funding Acknowledgments: NSF IIS-0905032}
}
  5. Chen, W., & Deelman, E. (2012). Integration of Workflow Partitioning and Resource Provisioning. The 12th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid 2012), Doctoral Symposium. http://pegasus.isi.edu/publications/2012/WChen-Integration-CCGrid12.pdf (Funding Acknowledgments: NSF IIS-0905032) ) 
    @inproceedings{chen2012partitioning,
  author = {Chen, Weiwei and Deelman, Ewa},
  url = {http://pegasus.isi.edu/publications/2012/WChen-Integration-CCGrid12.pdf},
  title = {Integration of Workflow Partitioning and Resource Provisioning},
  booktitle = {The 12th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid 2012), Doctoral Symposium},
  year = {2012},
  note = {Funding Acknowledgments: NSF IIS-0905032)  }
}
  6. Chervenak, A. L., Smith, D. E., Chen, W., & Deelman, E. (2012). Integrating Policy with Scientific Workflow Management for Data-Intensive Applications. The 7th Workshop on Workflows in Support of Large-Scale Science (WORKS12). http://pegasus.isi.edu/publications/2012/WChen-PDPS-WORKS12.pdf (Funding Acknowledgments: NSF IIS-0905032 and FutureGrid 0910812) 
    @inproceedings{chervenak2012policy,
  author = {Chervenak, Ann L. and Smith, David E. and Chen, Weiwei and Deelman, Ewa},
  url = {http://pegasus.isi.edu/publications/2012/WChen-PDPS-WORKS12.pdf},
  title = {Integrating Policy with Scientific Workflow Management for Data-Intensive Applications},
  booktitle = {The 7th Workshop on Workflows in Support of Large-Scale Science (WORKS12)},
  year = {2012},
  note = {Funding Acknowledgments: NSF IIS-0905032 and FutureGrid 0910812}
}
  7. Deelman, E., Juve, G., & Berriman, G. B. (2012). Using Clouds for Science, Is it Just Kicking the Can Down The Road? 2nd International Conference on Cloud Computing and Services Science (CLOSER 2012). http://pegasus.isi.edu/publications/2012/Deelman-CLOSER-2012.pdf (Funding Acknowledgments: NSF OCI-0943725) 
    @inproceedings{deelman2012kicking,
  author = {Deelman, Ewa and Juve, Gideon and Berriman, G. Bruce},
  url = {http://pegasus.isi.edu/publications/2012/Deelman-CLOSER-2012.pdf},
  title = {Using Clouds for Science, Is it Just Kicking the Can Down The Road?},
  booktitle = {2nd International Conference on Cloud Computing and Services Science (CLOSER 2012)},
  year = {2012},
  note = {Funding Acknowledgments: NSF OCI-0943725}
}
  8. Duffy, C., Gil, Y., Deelman, E., Marru, S., Pierce, M., Demir, I., & Wiener, G. (2012). Designing a road map for geoscience workflows. Eos, Transactions American Geophysical Union, 93(24), 225–226. https://doi.org/10.1029/2012EO240002 
    @article{duffy2012designing,
  title = {Designing a road map for geoscience workflows},
  author = {Duffy, Christopher and Gil, Yolanda and Deelman, Ewa and Marru, Suresh and Pierce, Marlon and Demir, Ibrahim and Wiener, Gerry},
  journal = {Eos, Transactions American Geophysical Union},
  volume = {93},
  number = {24},
  pages = {225--226},
  year = {2012},
  publisher = {Wiley Online Library},
  doi = {10.1029/2012EO240002}
}
  9. Juve, G., Deelman, E., Berriman, G. B., Berman, B. P., & Maechling, P. J. (2012). An Evaluation of the Cost and Performance of Scientific Workflows on Amazon EC2. Journal of Grid Computing, 10(1), 5–21. http://pegasus.isi.edu/publications/2012/Juve-JGC-2012.pdf (Funding Acknowledgments: NSF CCF-0725332, NSF OCI-0722019, and NASA NCC5-626) 
    @article{juve2012jgc,
  author = {Juve, Gideon and Deelman, Ewa and Berriman, G. Bruce and Berman, Benjamin P. and Maechling, Philip J.},
  url = {http://pegasus.isi.edu/publications/2012/Juve-JGC-2012.pdf},
  title = {An Evaluation of the Cost and Performance of Scientific Workflows on Amazon EC2},
  journal = {Journal of Grid Computing},
  volume = {10},
  number = {1},
  pages = {5-21},
  year = {2012},
  note = {Funding Acknowledgments: NSF CCF-0725332, NSF OCI-0722019, and NASA NCC5-626}
}
  10. Malawski, M., Juve, G., Deelman, E., & Nabrzyski, J. (2012). Cost- and Deadline-Constrained Provisioning for Scientific Workflow Ensembles in IaaS Clouds. 24th IEEE/ACM International Conference on Supercomputing (SC12). http://pegasus.isi.edu/publications/2012/Malawski-Ensemble.pdf (Funding Acknowledgments: NSF OCI-0943725) 
    @inproceedings{malawski2012provisioning,
  author = {Malawski, Maciej and Juve, Gideon and Deelman, Ewa and Nabrzyski, Jarek},
  url = {http://pegasus.isi.edu/publications/2012/Malawski-Ensemble.pdf},
  title = {Cost- and Deadline-Constrained Provisioning for Scientific Workflow Ensembles in IaaS Clouds},
  booktitle = {24th IEEE/ACM International Conference on Supercomputing (SC12)},
  year = {2012},
  note = {Funding Acknowledgments: NSF OCI-0943725}
}
  11. Rynge, M., Juve, G., Vahi, K., Callaghan, S., Mehta, G., Maechling, P. J., & Deelman, E. (2012). Enabling Large-scale Scientific Workflows on Petascale Resources Using MPI Master/Worker. XSEDE12. http://pegasus.isi.edu/publications/2012/XSEDE12-Rynge-pegasus-mpi-cluster.pdf (Funding Acknowledgments: NSF OCI-0722019, NSF OCI-0943725, NSF EAR-0529922, USGS 07HQAG0008, NSF OCI-1053575) 
    @inproceedings{rynge2012pmc,
  author = {Rynge, Mats and Juve, Gideon and Vahi, Karan and Callaghan, Scott and Mehta, Gaurang and Maechling, Philip J. and Deelman, Ewa},
  url = {http://pegasus.isi.edu/publications/2012/XSEDE12-Rynge-pegasus-mpi-cluster.pdf},
  title = {Enabling Large-scale Scientific Workflows on Petascale Resources Using MPI Master/Worker},
  booktitle = {XSEDE12},
  year = {2012},
  note = {Funding Acknowledgments: NSF OCI-0722019, NSF OCI-0943725, NSF EAR-0529922, USGS 07HQAG0008, NSF OCI-1053575}
}
  12. Samak, T., Gunter, D., Goode, M., Deelman, E., Juve, G., & Silva, F. (2012). Failure Analysis of Distributed Scientific Workflows Executing in the Cloud. 8th International Conference on Network and Service Management (CNSM 2012). (Funding Acknowledgments: DOE DE-AC02-05CH11231 and NSF OCI-0943705) ) 
    @inproceedings{samak2012failure,
  author = {Samak, Taghrid and Gunter, Dan and Goode, Monte and Deelman, Ewa and Juve, Gideon and Silva, Fabio},
  title = {Failure Analysis of Distributed Scientific Workflows Executing in the Cloud},
  booktitle = {8th International Conference on Network and Service Management (CNSM 2012)},
  year = {2012},
  note = {Funding Acknowledgments: DOE DE-AC02-05CH11231 and NSF OCI-0943705)  }
}
  13. Vahi, K., Harvey, I., Samak, T., Gunter, D., Evans, K., Rogers, D., Taylor, I., Goode, M., Silva, F., Al-Shakarchi, E., andrew Jones, G. M., & Deelman, E. (2012). A General Approach to Real-time Workflow Monitoring. The 7th Workshop on Workflows in Support of Large-Scale Science (WORKS12). http://pegasus.isi.edu/publications/2012/Vahi-Stampede-WORKS-2012.pdf (Funding Acknowledgments: NSF OCI-0943705) ) 
    @inproceedings{vahi2012monitoring,
  author = {Vahi, Karan and Harvey, Ian and Samak, Taghrid and Gunter, Dan and Evans, Kieran and Rogers, David and Taylor, Ian and Goode, Monte and Silva, Fabio and Al-Shakarchi, Eddie and andrew Jones, Gaurang Mehta and Deelman, Ewa},
  url = {http://pegasus.isi.edu/publications/2012/Vahi-Stampede-WORKS-2012.pdf},
  title = {A General Approach to Real-time Workflow Monitoring},
  booktitle = {The 7th Workshop on Workflows in Support of Large-Scale Science (WORKS12)},
  year = {2012},
  note = {Funding Acknowledgments: NSF OCI-0943705)  }
}

2011

  1. Berriman, G. B., Good, J., Deelman, E., & Alexov, A. (2011). Ten years of software sustainability at the Infrared Processing and Analysis Center. Phil. Trans. R. Soc. A, 369, 3384–3397. http://doi.org/10.1098/rsta.2011.0136 
    @article{berriman2011tenyears,
  author = {Berriman, G. Bruce and Good, John and Deelman, Ewa and Alexov, Anastasia},
  title = {Ten years of software sustainability at the Infrared Processing and Analysis Center},
  journal = {Phil. Trans. R. Soc. A},
  volume = {369},
  pages = {3384-3397},
  year = {2011},
  url = {http://doi.org/10.1098/rsta.2011.0136}
}
  2. Byun, E.-K., Kee, Y.-S., Kim, J.-S., Deelman, E., & Maeng, S. (2011). BTS: Resource Capacity Estimate for Time-targeted Science Workflows. Journal of Parallel and Distributed Computing: Special Issue on Cloud Computing, 71(6), 848–862. http://www.sciencedirect.com/science/article/pii/S0743731511000207 
    @article{byun2011bts,
  author = {Byun, Eun-Kyu and Kee, Yang-Suk and Kim, Jin-Soo and Deelman, Ewa and Maeng, Seungryoul},
  url = {http://www.sciencedirect.com/science/article/pii/S0743731511000207},
  title = {BTS: Resource Capacity Estimate for Time-targeted Science Workflows},
  journal = {Journal of Parallel and Distributed Computing: Special Issue on Cloud Computing},
  volume = {71},
  number = {6},
  pages = {848-862},
  month = jun,
  year = {2011}
}
  3. Callaghan, S., Maechling, P., Small, P., Milner, K., Juve, G., Jordan, T. H., Deelman, E., Mehta, G., Vahi, K., Gunter, D., & Beattie, K. (2011). Metrics for Heterogeneous Scientific Workflows: A Case Study of an Earthquake Science Application. International Journal of High Performance Computing Applications, 25(3), 274–285. (Funding Acknowledgments: TeraGrid TG-MCA03S012, NSF OCI-0722019, NSF OCI-0749313, NSF EAR-0106924 and USGS 02HQAG0008) ) 
    @article{callaghan2011metrics,
  author = {Callaghan, Scott and Maechling, Philip and Small, Patrick and Milner, Kevin and Juve, Gideon and Jordan, Thomas H. and Deelman, Ewa and Mehta, Gaurang and Vahi, Karan and Gunter, Dan and Beattie, Keith},
  title = {Metrics for Heterogeneous Scientific Workflows: A Case Study of an Earthquake Science Application},
  journal = {International Journal of High Performance Computing Applications},
  volume = {25},
  number = {3},
  pages = {274-285},
  month = aug,
  year = {2011},
  note = {Funding Acknowledgments: TeraGrid TG-MCA03S012, NSF OCI-0722019, NSF OCI-0749313, NSF EAR-0106924 and USGS 02HQAG0008)  }
}
  4. Chen, W., & Deelman, E. (2011). Workflow Overhead Analysis and Optimizations. 6th Workshop on Workflows in Support of Large-Scale Science (WORKS 11). http://pegasus.isi.edu/publications/2011/WChen-Workflow_Overhead_Analysis_and_Optimizations.pdf (Funding Acknowledgments: NSF IIS-0905032) 
    @inproceedings{chen2011overhead,
  author = {Chen, Weiwei and Deelman, Ewa},
  url = {http://pegasus.isi.edu/publications/2011/WChen-Workflow_Overhead_Analysis_and_Optimizations.pdf},
  title = {Workflow Overhead Analysis and Optimizations},
  booktitle = {6th Workshop on Workflows in Support of Large-Scale Science (WORKS 11)},
  year = {2011},
  note = {Funding Acknowledgments: NSF IIS-0905032}
}
  5. Chen, W., & Deelman, E. (2011). Partitioning and Scheduling Workflows across Multiple Sites with Storage Constraints. 9th International Conference on Parallel Processing and Applied Mathmatics. http://pegasus.isi.edu/publications/2011/WChen-Partitioning_and_Scheduling.pdf (Funding Acknowledgments: NSF IIS-0905032) 
    @inproceedings{chen2011constraints,
  author = {Chen, Weiwei and Deelman, Ewa},
  url = {http://pegasus.isi.edu/publications/2011/WChen-Partitioning_and_Scheduling.pdf},
  title = {Partitioning and Scheduling Workflows across Multiple Sites with Storage Constraints},
  booktitle = {9th International Conference on Parallel Processing and Applied Mathmatics},
  year = {2011},
  note = {Funding Acknowledgments: NSF IIS-0905032}
}
  6. Gunter, D., Deelman, E., Samak, T., Brooks, C., Goode, M., Juve, G., Mehta, G., Moraes, P., Silva, F., Swany, M., & Vahi, K. (2011). Online Workflow Management and Performance Analysis with Stampede. 7th International Conference on Network and Service Management (CNSM-2011). 
    @inproceedings{gunter2011online,
  author = {Gunter, Dan and Deelman, Ewa and Samak, Taghrid and Brooks, Christopher and Goode, Monte and Juve, Gideon and Mehta, Gaurang and Moraes, Priscilla and Silva, Fabio and Swany, Martin and Vahi, Karan},
  title = {Online Workflow Management and Performance Analysis with Stampede},
  booktitle = {7th International Conference on Network and Service Management (CNSM-2011)},
  year = {2011}
}
  7. Juve, G., & Deelman, E. (2011). Automating Application Deployment in Infrastructure Clouds. 3rd IEEE International Conference on Cloud Computing Technology and Science (CloudCom 2011). (Funding Acknowlegements: DOE, NSF OCI-0943725, and NSF OCI-091812) 
    @inproceedings{juve2011automate,
  author = {Juve, Gideon and Deelman, Ewa},
  title = {Automating Application Deployment in Infrastructure Clouds},
  booktitle = {3rd IEEE International Conference on Cloud Computing Technology and Science (CloudCom 2011)},
  year = {2011},
  note = {Funding Acknowlegements: DOE, NSF OCI-0943725, and NSF OCI-091812}
}
  8. Juve, G., & Deelman, E. (2011). Wrangler: Virtual Cluster Provisioning for the Cloud. Proceedings of the 20th International Symposium on High Performance Distributed Computing (HPDC11). (Funding Acknowledgments: NSF OCI-0943725) 
    @inproceedings{juve2011wrangler,
  author = {Juve, Gideon and Deelman, Ewa},
  title = {Wrangler: Virtual Cluster Provisioning for the Cloud},
  booktitle = {Proceedings of the 20th International Symposium on High Performance Distributed Computing (HPDC11)},
  year = {2011},
  note = {Funding Acknowledgments: NSF OCI-0943725}
}
  9. Mehta, G., Deelman, E., Knowles, J. A., Chen, T., Wang, Y., Vöckler, J.-S., Buyske, S., & Matise, T. (2011). Enabling Data and Compute Intensive Workflows in Bioinformatics. 2nd International Workshop OnHigh Performance Bioinformatics and Biomedicine (HiBB 2011) in Conjunction with Euro-Par Conference 2011. 
    @inproceedings{mehta2011bio,
  author = {Mehta, Gaurang and Deelman, Ewa and Knowles, James A and Chen, Ting and Wang, Ying and Vöckler, Jens-S. and Buyske, Steven and Matise, Tara},
  title = {Enabling Data and Compute Intensive Workflows in Bioinformatics},
  booktitle = {2nd International Workshop onHigh Performance Bioinformatics and Biomedicine (HiBB 2011) in conjunction with Euro-Par Conference 2011},
  year = {2011}
}
  10. Nagavaram, A., Agrawal, G., Freitas, M., Mehta, G., Mayani, R., & Deelman, E. (2011). A Cloud‐based Dynamic Workflow for Mass Spectrometry Data Analysis. Proceedings of the 7th IEEE International Conference on e-Science (e-Science 2011). 
    @inproceedings{nagavaram2011massspec,
  author = {Nagavaram, Ashish and Agrawal, Gagan and Freitas, Michael and Mehta, Gaurang and Mayani, Rajiv and Deelman, Ewa},
  title = {A Cloud‐based Dynamic Workflow for Mass Spectrometry Data Analysis},
  booktitle = {Proceedings of the 7th IEEE International Conference on e-Science (e-Science 2011)},
  year = {2011}
}
  11. Rynge, M., Juve, G., Mehta, G., Deelman, E., Larson, K., Holzman, B., Sfiligoi, I., Würthwein, F., Berriman, G. B., & Callaghan, S. (2011). Experiences Using GlideinWMS and the Corral Frontend Across Cyberinfrastructures. Proceedings of the 7th IEEE International Conference on e-Science (e-Science 2011). (Funding Acknowledgments: Open Science Grid, NSF OCI-0943725, and TeraGrid TG-CCR1000018) ) 
    @inproceedings{rynge2011corralwms,
  author = {Rynge, Mats and Juve, Gideon and Mehta, Gaurang and Deelman, Ewa and Larson, Krista and Holzman, Burt and Sfiligoi, Igor and Würthwein, Frank and Berriman, G. Bruce and Callaghan, Scott},
  title = {Experiences Using GlideinWMS and the Corral Frontend Across Cyberinfrastructures},
  booktitle = {Proceedings of the 7th IEEE International Conference on e-Science (e-Science 2011)},
  year = {2011},
  note = {Funding Acknowledgments: Open Science Grid, NSF OCI-0943725, and TeraGrid TG-CCR1000018)  }
}
  12. Samak, T., Gunter, D., Deelman, E., Juve, G., Mehta, G., Silva, F., & Vahi, K. (2011). Online Fault and Anomaly Detection for Large-Scale Scientific Workflows. 13th IEEE International Conference on High Performance Computing and Communications (HPCC-2011). (Funding Acknowledgments: DOE DE-AC02-05CH11231, and NSF OCI-0943705) 
    @inproceedings{samak2011anomaly,
  author = {Samak, Taghrid and Gunter, Dan and Deelman, Ewa and Juve, Gideon and Mehta, Gaurang and Silva, Fabio and Vahi, Karan},
  title = {Online Fault and Anomaly Detection for Large-Scale Scientific Workflows},
  booktitle = {13th IEEE International Conference on High Performance Computing and Communications (HPCC-2011)},
  year = {2011},
  note = {Funding Acknowledgments: DOE DE-AC02-05CH11231, and NSF OCI-0943705}
}
  13. Samak, T., Gunter, D., Goode, M., Deelman, E., Mehta, G., Silva, F., & Vahi, K. (2011). Failure Prediction and Localization in Large Scientific Workflows. 6th Workshop on Workflows in Support of Large-Scale Science (WORKS 11). 
    @inproceedings{samak2011failure,
  author = {Samak, Taghrid and Gunter, Dan and Goode, Monte and Deelman, Ewa and Mehta, Gaurang and Silva, Fabio and Vahi, Karan},
  title = {Failure Prediction and Localization in Large Scientific Workflows},
  booktitle = {6th Workshop on Workflows in Support of Large-Scale Science (WORKS 11)},
  year = {2011}
}
  14. Vöckler, J.-S., Juve, G., Deelman, E., Rynge, M., & Berriman, G. B. (2011). Experiences Using Cloud Computing for A Scientific Workflow Application. Proceedings of 2nd Workshop on Scientific Cloud Computing (ScienceCloud 2011). http://portal.acm.org/citation.cfm?id=1996109.1996114 (Funding Acknowledgments: NSF OCI-0910812) 
    @inproceedings{voeckler2011cloud,
  author = {Vöckler, Jens-S. and Juve, Gideon and Deelman, Ewa and Rynge, Mats and Berriman, G. Bruce},
  url = {http://portal.acm.org/citation.cfm?id=1996109.1996114},
  title = {Experiences Using Cloud Computing for A Scientific Workflow Application},
  booktitle = {Proceedings of 2nd Workshop on Scientific Cloud Computing (ScienceCloud 2011)},
  year = {2011},
  note = {Funding Acknowledgments: NSF OCI-0910812}
}
  15. Wang, Y., Mehta, G., Mayani, R., Lu, J., Souaiaia, T., andrew Clark, Y. C., Yoon, H. J., Wan, L., Evgrafov, O. V., Knowles, J. A., Deelman, E., & Chen, T. (2011). RseqFlow: Workflows for RNA-Seq Data Analysis. Bioinformatics, 27(18), 2598–2600. http://doi.org/10.1093/bioinformatics/btr441 
    @article{want2011rseq,
  author = {Wang, Ying and Mehta, Gaurang and Mayani, Rajiv and Lu, Jingxi and Souaiaia, Tade and andrew Clark, Yangho Chen and Yoon, Hee Jae and Wan, Lin and Evgrafov, Oleg V. and Knowles, James A. and Deelman, Ewa and Chen, Ting},
  title = {RseqFlow: Workflows for RNA-Seq Data Analysis},
  journal = {Bioinformatics},
  volume = {27},
  number = {18},
  pages = {2598-2600},
  year = {2011},
  url = {http://doi.org/10.1093/bioinformatics/btr441}
}

2010

  1. Berriman, G. B., Deelman, E., Groth, P., & Juve, G. (2010). The Application of Cloud Computing to the Creation of Image Mosaics and Management of Their Provenance. SPIE Conference 7740: Software and Cyberinfrastructure for Astronomy. http://pegasus.isi.edu/publications/2010/BerrimanB-ApplicationCloud.pdf 
    @inproceedings{berriman2010provenance,
  author = {Berriman, G. Bruce and Deelman, Ewa and Groth, Paul and Juve, Gideon},
  url = {http://pegasus.isi.edu/publications/2010/BerrimanB-ApplicationCloud.pdf},
  title = {The Application of Cloud Computing to the Creation of Image Mosaics and Management of Their Provenance},
  booktitle = {SPIE Conference 7740: Software and Cyberinfrastructure for Astronomy},
  year = {2010}
}
  2. Berriman, G. B., Juve, G., Deelman, E., Regelson, M., & Plavchan, P. (2010). The Application of Cloud Computing to Astronomy: A Study of Cost and Performance. In Workshop on e-Science Challenges in Astronomy and Astrophysics in Conjunction with the 6th IEEE International Conference on e-Science (e-Science 2010). (Funding Acknowledgments: NSF OCI-0438712, and NSF CCF-0725332) 
    @inproceedings{berriman2010application,
  author = {Berriman, G. Bruce and Juve, Gideon and Deelman, Ewa and Regelson, Moira and Plavchan, Peter},
  title = {The Application of Cloud Computing to Astronomy: A Study of Cost and Performance},
  booktitle = {In Workshop on e-Science challenges in Astronomy and Astrophysics in conjunction with the 6th IEEE International Conference on e-Science (e-Science 2010)},
  year = {2010},
  note = {Funding Acknowledgments: NSF OCI-0438712, and NSF CCF-0725332}
}
  3. Bolze, R., & Deelman, E. (2010). Exploiting the Cloud of Computing Environments: An Application’s Perspective. In S. A. Ahson & M. Ilyas (Eds.), Cloud Computing and Software Services: Theory and Techniques. CRC Press. 
    @inbook{bolze2010exploiting,
  author = {Bolze, Raphael and Deelman, Ewa},
  title = {Exploiting the Cloud of Computing Environments: An Application's Perspective},
  booktitle = {Cloud Computing and Software Services: Theory and Techniques},
  editor = {Ahson, Syed A. and Ilyas, Mohammad},
  publisher = {CRC Press},
  year = {2010}
}
  4. Callaghan, S., Deelman, E., Gunter, D., Juve, G., Maechling, P., Brooks, C., Vahi, K., Milner, K., Graves, R., Field, E., Okaya, D., & Jordan, T. (2010). Scaling up Workflow-based Applications. Journal of Computer and System Sciences, 76(6), 428–446. http://pegasus.isi.edu/publications/2010/CallaghanS-ScalingUp.pdf (Funding Acknowledgments: TeraGrid TG-MCA03S012, NSF OCI-0722019, and NSF OCI-0749313) 
    @article{callaghan2010scalingup,
  author = {Callaghan, Scott and Deelman, Ewa and Gunter, Dan and Juve, Gideon and Maechling, Philip and Brooks, Christopher and Vahi, Karan and Milner, Kevin and Graves, Robert and Field, Edward and Okaya, David and Jordan, Thomas},
  url = {http://pegasus.isi.edu/publications/2010/CallaghanS-ScalingUp.pdf},
  title = {Scaling up Workflow-based Applications},
  journal = {Journal of Computer and System Sciences},
  volume = {76},
  number = {6},
  pages = {428-446},
  month = sep,
  year = {2010},
  note = {Funding Acknowledgments: TeraGrid TG-MCA03S012, NSF OCI-0722019, and NSF OCI-0749313}
}
  5. Gil, Y., Ratnakar, V., & et al, E. D. (2010). Wings: Intelligent Workflow-Based Design of Computational Experiments. IEEE Intelligent Systems. http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=5396300 
    @article{gil2010wings,
  author = {Gil, Yolanda and Ratnakar, Varun and et al, Ewa Deelman},
  url = {http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=5396300},
  title = {Wings: Intelligent Workflow-Based Design of Computational Experiments},
  journal = {IEEE Intelligent Systems},
  month = jan,
  year = {2010}
}
  6. Graves, R., Jordan, T., Callaghan, S., Deelman, E., Field, E., Juve, G., Kesselman, C., Maechling, P., Mehta, G., Milner, K., Okaya, D., Small, P., & Vahi, K. (2010). CyberShake: A Physics-Based Seismic Hazard Model for Southern California. Pure and Applied Geophysics. http://pegasus.isi.edu/publications/2010/GravesR-CyberShake.pdf (Funding Acknowledgments: NSF OCI-0438712, NSF CCF-0725332) 
    @article{graves2010cybershake,
  author = {Graves, Robert and Jordan, Thomas and Callaghan, Scott and Deelman, Ewa and Field, Edward and Juve, Gideon and Kesselman, Carl and Maechling, Philip and Mehta, Gaurang and Milner, Kevin and Okaya, David and Small, Patrick and Vahi, Karan},
  url = {http://pegasus.isi.edu/publications/2010/GravesR-CyberShake.pdf},
  title = {CyberShake: A Physics-Based Seismic Hazard Model for Southern California},
  journal = {Pure and Applied Geophysics},
  month = may,
  year = {2010},
  note = {Funding Acknowledgments: NSF OCI-0438712, NSF CCF-0725332}
}
  7. Juve, G., & Deelman, E. (2010). Scientific Workflows and Clouds. ACM Crossroads, 16(3), 14–18. 
    @article{juve2010xrds,
  author = {Juve, Gideon and Deelman, Ewa},
  title = {Scientific Workflows and Clouds},
  journal = {ACM Crossroads},
  volume = {16},
  number = {3},
  pages = {14-18},
  year = {2010}
}
  8. Juve, G., & Deelman, E. (2010). Scientific Workflows in the Cloud. In M. Cafaro & G. Aloisio (Eds.), Grids, Clouds and Virtualization (pp. 71–91). Springer. 
    @inbook{juve2010cloudchapter,
  author = {Juve, Gideon and Deelman, Ewa},
  booktitle = {Grids, Clouds and Virtualization},
  editor = {Cafaro, M. and Aloisio, G.},
  title = {Scientific Workflows in the Cloud},
  publisher = {Springer},
  pages = {71--91},
  year = {2010}
}
  9. Juve, G., Deelman, E., Vahi, K., & Mehta, G. (2010). Experiences with Resource Provisioning for Scientific Workflows Using Corral. Scientific Programming, 18(2), 77–92. (Funding Acknowledgments: NSF OCI-0943725 and NSF OCI-0749313) 
    @article{juve2010corral,
  author = {Juve, Gideon and Deelman, Ewa and Vahi, Karan and Mehta, Gaurang},
  title = {Experiences with Resource Provisioning for Scientific Workflows Using Corral},
  journal = {Scientific Programming},
  volume = {18},
  number = {2},
  pages = {77-92},
  month = apr,
  year = {2010},
  note = {Funding Acknowledgments: NSF OCI-0943725 and NSF OCI-0749313}
}
  10. Juve, G., Deelman, E., Vahi, K., Mehta, G., Berriman, B., Berman, B. P., & Maechling, P. J. (2010). Data Sharing Options for Scientific Workflows on Amazon EC2. 22nd IEEE/ACM Conference on Supercomputing (SC10). http://pegasus.isi.edu/publications/2010/JuveG-DataSharing.pdf (Funding Acknowledgments: NSF CCF-0725332, NSF OCI-0722019, and NASA NCC5-626) 
    @inproceedings{juve2010sc,
  author = {Juve, Gideon and Deelman, Ewa and Vahi, Karan and Mehta, Gaurang and Berriman, Bruce and Berman, Benjamin P. and Maechling, Philip J.},
  url = {http://pegasus.isi.edu/publications/2010/JuveG-DataSharing.pdf},
  title = {Data Sharing Options for Scientific Workflows on Amazon EC2},
  booktitle = {22nd IEEE/ACM Conference on Supercomputing (SC10)},
  year = {2010},
  note = {Funding Acknowledgments: NSF CCF-0725332, NSF OCI-0722019, and NASA NCC5-626}
}
  11. Kumar, V. S., Kurc, T., Ratnakar, V., Kim, J., Mehta, G., Vahi, K., Nelson, Y. L., Sadayappan, P., Deelman, E., Gil, Y., Hall, M., & Saltz, J. (2010). Parameterized Specification, Configuration and Execution of Data-intensive Scientific Workflows. Cluster Computing Journal, 13(3), 315–333. http://pegasus.isi.edu/publications/2010/Cluster-Computing-2010.pdf 
    @article{kumar2010ccj,
  author = {Kumar, Vijay S. and Kurc, Tahsin and Ratnakar, Varun and Kim, Jihie and Mehta, Gaurang and Vahi, Karan and Nelson, Yoonju Lee and Sadayappan, P. and Deelman, Ewa and Gil, Yolanda and Hall, Mary and Saltz, Joel},
  url = {http://pegasus.isi.edu/publications/2010/Cluster-Computing-2010.pdf},
  title = {Parameterized Specification, Configuration and Execution of Data-intensive Scientific Workflows},
  journal = {Cluster Computing Journal},
  volume = {13},
  number = {3},
  pages = {315-333},
  year = {2010}
}
  12. Sakellariou, R., Zhao, H., & Deelman, E. (2010). Mapping Workflows on Grid Resources: Experiments with the Montage Workflow. In Grids, P2P and Services Computing (pp. 119–132). Springer. 
    @inbook{sakellariou2010mapping,
  author = {Sakellariou, Rizos and Zhao, Henan and Deelman, Ewa},
  title = {Mapping Workflows on Grid Resources: Experiments with the Montage Workflow},
  booktitle = {Grids, P2P and Services Computing},
  publisher = {Springer},
  year = {2010},
  pages = {119-132}
}
  13. Sonntag, M., Karastoyanova, D., & Deelman, E. (2010). Bridging The Gap Between Business And Scientific Workflows. e-Science 2010. http://pegasus.isi.edu/publications/2010/Bridging_The_Gap_Between_Business_And_Scientific_Workflows.pdf 
    @inproceedings{sonntag2010bridging,
  author = {Sonntag, Mirko and Karastoyanova, Dimka and Deelman, Ewa},
  url = {http://pegasus.isi.edu/publications/2010/Bridging_The_Gap_Between_Business_And_Scientific_Workflows.pdf},
  title = {Bridging The Gap Between Business And Scientific Workflows},
  booktitle = {e-Science 2010},
  year = {2010}
}
  14. Sonntag, M., Karastoyanova, D., & Deelman, E. (2010). BPEL4Pegasus: Combining Business and Scientific Workflows. International Conference on Service-Oriented Computing (ICSOC). http://pegasus.isi.edu/publications/2010/100907-BPEL4Pegasus-camera-ready.pdf 
    @inproceedings{sonntag2010bpel,
  author = {Sonntag, Mirko and Karastoyanova, Dimka and Deelman, Ewa},
  url = {http://pegasus.isi.edu/publications/2010/100907-BPEL4Pegasus-camera-ready.pdf},
  title = {BPEL4Pegasus: Combining Business and Scientific Workflows},
  booktitle = {International Conference on Service-Oriented Computing (ICSOC)},
  year = {2010}
}

2009

  1. Deelman, E. (2009). Grids and Clouds: Making Workflow Applications Work in Heterogeneous Distributed Environments. International Journal of High Performance Computing Applications. http://pegasus.isi.edu/publications/2009/Deelman-GridAndClouds.pdf 
    @article{deelman2009gridcloud,
  author = {Deelman, Ewa},
  url = {http://pegasus.isi.edu/publications/2009/Deelman-GridAndClouds.pdf},
  title = {Grids and Clouds: Making Workflow Applications Work in Heterogeneous Distributed Environments},
  journal = {International Journal of High Performance Computing Applications},
  year = {2009}
}
  2. Groth, P., Deelman, E., Juve, G., Mehta, G., & Berriman, B. (2009). Pipeline-Centric Provenance Model. 4th Workshop on Workflows in Support of Large-Scale Science (WORKS 09). http://pegasus.isi.edu/publications/2009/GrothP-PipelineCentric.pdf 
    @inproceedings{groth2009pipeline,
  author = {Groth, Paul and Deelman, Ewa and Juve, Gideon and Mehta, Gaurang and Berriman, Bruce},
  url = {http://pegasus.isi.edu/publications/2009/GrothP-PipelineCentric.pdf},
  title = {Pipeline-Centric Provenance Model},
  booktitle = {4th Workshop on Workflows in Support of Large-Scale Science (WORKS 09)},
  year = {2009}
}
  3. Juve, G., Deelman, E., Vahi, K., Mehta, G., Berriman, B., Berman, B. P., & Maechling, P. J. (2009). Scientific Workflow Applications on Amazon EC2. Workshop on Cloud-Based Services and Applications. http://pegasus.isi.edu/publications/2009/JuveG-EC2.pdf 
    @inproceedings{juve2009ec2,
  author = {Juve, Gideon and Deelman, Ewa and Vahi, Karan and Mehta, Gaurang and Berriman, Bruce and Berman, Benjamin P. and Maechling, Philip J.},
  url = {http://pegasus.isi.edu/publications/2009/JuveG-EC2.pdf},
  title = {Scientific Workflow Applications on Amazon EC2},
  booktitle = {Workshop on Cloud-based Services and Applications},
  year = {2009}
}
  4. Kumar, V. S., Sadayappan, P., Mehta, G., Vahi, K., Deelman, E., Ratnakar, V., Kim, J., Gil, Y., Hall, M. W., Kurç, T. M., & Saltz, J. H. (2009). An Integrated Framework for Performance-based Optimization of Scientific Workflows. Conference on High Performance and Distributed Computing (HPDC). http://pegasus.isi.edu/publications/2009/hpdc153-kumar.pdf 
    @inproceedings{kumar2009optimization,
  author = {Kumar, Vijay S. and Sadayappan, P. and Mehta, Gaurang and Vahi, Karan and Deelman, Ewa and Ratnakar, Varun and Kim, Jihie and Gil, Yolanda and Hall, Mary W. and Kurç, Tahsin M. and Saltz, Joel H.},
  url = {http://pegasus.isi.edu/publications/2009/hpdc153-kumar.pdf},
  title = {An Integrated Framework for Performance-based Optimization of Scientific Workflows},
  booktitle = {Conference on High Performance and Distributed Computing (HPDC)},
  year = {2009}
}
  5. Lee, K., Paton, N. W., Sakellariou, R., Deelman, E., Fernandes, A. A. A., & Mehta, G. (2009). Adaptive Workflow Processing and Execution in Pegasus. Concurrency and Computation: Practice and Experience, 21(16), 1965–1981. http://pegasus.isi.edu/publications/2009/CCPE-2009.pdf 
    @article{lee2009adaptive,
  author = {Lee, Kevin and Paton, Norman W. and Sakellariou, Rizos and Deelman, Ewa and Fernandes, Alvaro A. A. and Mehta, Gaurang},
  url = {http://pegasus.isi.edu/publications/2009/CCPE-2009.pdf},
  title = {Adaptive Workflow Processing and Execution in Pegasus},
  journal = {Concurrency and Computation: Practice and Experience},
  volume = {21},
  number = {16},
  pages = {1965-1981},
  year = {2009}
}
  6. Sakellariou, R., Zhao, H., & Deelman, E. (2009). Mapping Workflows on Grid Resources: Experiments with the Montage Workflow. CoreGrid. http://pegasus.isi.edu/publications/2009/coregrid09.pdf 
    @inproceedings{sakellariou2009coregrid,
  author = {Sakellariou, Rizos and Zhao, Henan and Deelman, Ewa},
  url = {http://pegasus.isi.edu/publications/2009/coregrid09.pdf},
  title = {Mapping Workflows on Grid Resources: Experiments with the Montage Workflow},
  booktitle = {CoreGrid},
  year = {2009}
}

2008

  1. Bharathi, S., Chervenak, A., Deelman, E., Mehta, G., Su, M.-H., & Vahi, K. (2008). Characterization of Scientific Workflows. 3rd Workshop on Workflows in Support of Large-Scale Science (WORKS08). http://pegasus.isi.edu/publications/2008/bharathi-works08.pdf 
    @inproceedings{bharathi2008characterization,
  author = {Bharathi, Shishir and Chervenak, Ann and Deelman, Ewa and Mehta, Gaurang and Su, Mei-Hui and Vahi, Karan},
  url = {http://pegasus.isi.edu/publications/2008/bharathi-works08.pdf},
  title = {Characterization of Scientific Workflows},
  booktitle = {3rd Workshop on Workflows in Support of Large-Scale Science (WORKS08)},
  year = {2008}
}
  2. Callaghan, S., Maechling, P., Deelman, E., Vahi, K., Mehta, G., Juve, G., Milner, K., Graves, R., Field, E., Okaya, D., Gunter, D., Beattie, K., & Jordan, T. (2008). Reducing Time-to-Solution Using Distributed High-Throughput Mega-Workflows - Experiences from SCEC CyberShake. Fourth IEEE International Conference on e-Science (e-Science 2008). http://pegasus.isi.edu/publications/2008/CallaghanS-MegaWorkflowsCyberShake.pdf 
    @inproceedings{callaghan2009reducing,
  author = {Callaghan, Scott and Maechling, Philip and Deelman, Ewa and Vahi, Karan and Mehta, Gaurang and Juve, Gideon and Milner, Kevin and Graves, Robert and Field, Edward and Okaya, David and Gunter, Dan and Beattie, Keith and Jordan, Thomas},
  url = {http://pegasus.isi.edu/publications/2008/CallaghanS-MegaWorkflowsCyberShake.pdf},
  title = {Reducing Time-to-Solution Using Distributed High-Throughput Mega-Workflows - Experiences from SCEC CyberShake},
  booktitle = {Fourth IEEE International Conference on e-Science (e-Science 2008)},
  year = {2008}
}
  3. Deelman, E., & Chervenak, A. (2008). Data Management Challenges of Data-Intensive Scientific Workflows. 3rd International Workshop on Workflow Systems in e-Science (WSES 08), in Conjunction with CCGrid 2008. http://pegasus.isi.edu/publications/2008/wses2008.pdf 
    @inproceedings{deelman2008challenges,
  author = {Deelman, Ewa and Chervenak, Ann},
  url = {http://pegasus.isi.edu/publications/2008/wses2008.pdf},
  title = {Data Management Challenges of Data-Intensive Scientific Workflows},
  booktitle = {3rd International Workshop on Workflow Systems in e-Science (WSES 08), in conjunction with CCGrid 2008},
  year = {2008}
}
  4. Deelman, E., Gannon, D., Shields, M., & Taylor, I. (2008). Workflows and e-Science: An Overview of Workflow System Features and Capabilities. Future Generation Computer Systems. http://dx.doi.org/10.1016/j.future.2008.06.012 
    @article{deelman2008fgcs,
  author = {Deelman, Ewa and Gannon, Dennis and Shields, Matthew and Taylor, Ian},
  url = {http://dx.doi.org/10.1016/j.future.2008.06.012},
  title = {Workflows and e-Science: An Overview of Workflow System Features and Capabilities},
  journal = {Future Generation Computer Systems},
  month = jul,
  year = {2008}
}
  5. Deelman, E., Singh, G., Livny, M., Berriman, B., & Good, J. (2008). The Cost of Doing Science on the Cloud: The Montage Example. Supercomputing 2008. http://pegasus.isi.edu/publications/2008/deelman_sc08_corrected.pdf 
    @inproceedings{deelman2008cost,
  author = {Deelman, Ewa and Singh, Gurmeet and Livny, Miron and Berriman, Bruce and Good, John},
  url = {http://pegasus.isi.edu/publications/2008/deelman_sc08_corrected.pdf},
  title = {The Cost of Doing Science on the Cloud: The Montage Example},
  booktitle = {Supercomputing 2008},
  year = {2008}
}
  6. Hoffa, C., Mehta, G., Freeman, T., Deelman, E., Keahey, K., Berriman, B., & Good, J. (2008). On the Use of Cloud Computing for Scientific Workflows. 3rd International Workshop on Scientific Workflows and Business Workflow Standards in e-Science (SWBES) in Conjunction with Fourth IEEE International Conference on e-Science (e-Science 2008). http://pegasus.isi.edu/publications/2008/Hoffa-CloudComputing.pdf 
    @inproceedings{hoffa2008cloud,
  author = {Hoffa, Christina and Mehta, Gaurang and Freeman, Timothy and Deelman, Ewa and Keahey, Kate and Berriman, Bruce and Good, John},
  url = {http://pegasus.isi.edu/publications/2008/Hoffa-CloudComputing.pdf},
  title = {On the Use of Cloud Computing for Scientific Workflows},
  booktitle = {3rd International Workshop on Scientific Workflows and Business Workflow Standards in e-Science (SWBES) in conjunction with Fourth IEEE International Conference on e-Science (e-Science 2008)},
  year = {2008}
}
  7. Juve, G., & Deelman, E. (2008). Resource Provisioning Options for Large-Scale Scientific Workflows. Third International Workshop on Scientific Workflows and Business Workflow Standards in e-Science (SWBES) in Conjunction with Fourth IEEE International Conference on e-Science (e-Science 2008). http://pegasus.isi.edu/publications/2008/JuveG-ResourceProvisioningOptions.pdf 
    @inproceedings{juve2008provisioning,
  author = {Juve, Gideon and Deelman, Ewa},
  url = {http://pegasus.isi.edu/publications/2008/JuveG-ResourceProvisioningOptions.pdf},
  title = {Resource Provisioning Options for Large-Scale Scientific Workflows},
  booktitle = {Third International Workshop on Scientific Workflows and Business Workflow Standards in e-Science (SWBES) in conjunction with Fourth IEEE International Conference on e-Science (e-Science 2008)},
  year = {2008}
}
  8. Lee, K., Paton, N. W., Sakellariou, R., Deelman, E., Fernandes, A. A. A., & Mehta, G. (2008). Adaptive Workflow Processing and Execution in Pegasus. 3rd International Workshop on Workflow Management and Applications in Grid Environments (WaGe08). http://pegasus.isi.edu/publications/2008/lee-pegasus-wage.pdf 
    @inproceedings{lee2008adaptive,
  author = {Lee, Kevin and Paton, Norman W. and Sakellariou, Rizos and Deelman, Ewa and Fernandes, Alvaro A. A. and Mehta, Gaurang},
  url = {http://pegasus.isi.edu/publications/2008/lee-pegasus-wage.pdf},
  title = {Adaptive Workflow Processing and Execution in Pegasus},
  booktitle = {3rd International Workshop on Workflow Management and Applications in Grid Environments (WaGe08)},
  year = {2008}
}
  9. Miles, S., Groth, P., Deelman, E., Vahi, K., Mehta, G., & Moreau, L. (2008). Provenance: The Bridge Between Experiments and Data. Computing in Science and Engineering, 10(3), 38–46. http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=4488063 
    @article{miles2008provenance,
  author = {Miles, Simon and Groth, Paul and Deelman, Ewa and Vahi, Karan and Mehta, Gaurang and Moreau, Luc},
  url = {http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=4488063},
  title = {Provenance: The Bridge Between Experiments and Data},
  journal = {Computing in Science and Engineering},
  volume = {10},
  number = {3},
  pages = {38-46},
  month = may,
  year = {2008}
}
  10. Singh, G., Su, M.-H., Vahi, K., Deelman, E., Berriman, B., Good, J., Katz, D. S., & Mehta, G. (2008). Workflow Task Clustering for Best Effort Systems with Pegasus. Mardi Gras Conference. http://pegasus.isi.edu/publications/2008/MardiGras_v3.pdf 
    @inproceedings{singh2008clustering,
  author = {Singh, Gurmeet and Su, Mei-Hui and Vahi, Karan and Deelman, Ewa and Berriman, Bruce and Good, John and Katz, Daniel S. and Mehta, Gaurang},
  url = {http://pegasus.isi.edu/publications/2008/MardiGras_v3.pdf},
  title = {Workflow Task Clustering for Best Effort Systems with Pegasus},
  booktitle = {Mardi Gras Conference},
  year = {2008}
}

2007

  1. Berriman, G. B., Deelman, E., Good, J., Jacob, J. C., Katz, D. S., Laity, A. C., Prince, T. A., Singh, G., & Su, M.-H. (2007). Generating Complex Astronomy Workflows. In Workflows for e-Science. 
    @inbook{berriman2007complex,
  author = {Berriman, G. Bruce and Deelman, Ewa and Good, John and Jacob, Joseph C. and Katz, Daniel S. and Laity, Anastasia C. and Prince, Thomas A. and Singh, Gurmeet and Su, Mei-Hui},
  title = {Generating Complex Astronomy Workflows},
  booktitle = {Workflows for e-Science},
  year = {2007}
}
  2. Chervenak, A., Deelman, E., Livny, M., Su, M.-H., Schuler, R., Bharathi, S., Mehta, G., & Vahi, K. (2007). Data Placement for Scientific Applications in Distributed Environments. Proceedings of Grid Conference 2007. http://pegasus.isi.edu/publications/grid2007.pdf 
    @inproceedings{chervenak2007placement,
  author = {Chervenak, Ann and Deelman, Ewa and Livny, Miron and Su, Mei-Hui and Schuler, Rob and Bharathi, Shishir and Mehta, Gaurang and Vahi, Karan},
  url = {http://pegasus.isi.edu/publications/grid2007.pdf},
  title = {Data Placement for Scientific Applications in Distributed Environments},
  booktitle = {Proceedings of Grid Conference 2007},
  year = {2007}
}
  3. Deelman, E., Mehta, G., Singh, G., Su, M.-H., & Vahi, K. (2007). Pegasus: Mapping Large-Scale Workflows to Distributed Resources. In Workflows for e-Science. 
    @inbook{deelman2007pegasusmapping,
  author = {Deelman, Ewa and Mehta, Gaurang and Singh, Gurmeet and Su, Mei-Hui and Vahi, Karan},
  title = {Pegasus: Mapping Large-Scale Workflows to Distributed Resources},
  booktitle = {Workflows for e-Science},
  year = {2007}
}
  4. Gil, Y., Deelman, E., Ellisman, M., Fahringer, T., Fox, G., Gannon, D., Goble, C., Livny, M., Moreau, L., & Myers, J. (2007). Examining the Challenges of Scientific Workflows. IEEE Computer, 40(12), 24–32. http://ieeexplore.ieee.org/search/srchabstract.jsp?arnumber=4404805 
    @article{gil2007challenges,
  author = {Gil, Yolanda and Deelman, Ewa and Ellisman, M. and Fahringer, Thomas and Fox, Geoffrey and Gannon, Dennis and Goble, Carol and Livny, Miron and Moreau, Luc and Myers, J.},
  url = {http://ieeexplore.ieee.org/search/srchabstract.jsp?arnumber=4404805},
  title = {Examining the Challenges of Scientific Workflows},
  journal = {IEEE Computer},
  volume = {40},
  number = {12},
  pages = {24-32},
  month = dec,
  year = {2007}
}
  5. Gil, Y., Ratnakar, V., Deelman, E., Mehta, G., & Kim, J. (2007). Wings for Pegasus: Creating Large-Scale Scientific Applications Using Semantic Representations of Computational Workflows. Proceedings of the 19th Annual Conference on Innovative Applications of Artificial Intelligence (IAAI). http://pegasus.isi.edu/publications/gil-etal-iaai07.pdf 
    @inproceedings{gil2007wings,
  author = {Gil, Yolanda and Ratnakar, Varun and Deelman, Ewa and Mehta, Gaurang and Kim, Jihie},
  url = {http://pegasus.isi.edu/publications/gil-etal-iaai07.pdf},
  title = {Wings for Pegasus: Creating Large-Scale Scientific Applications Using Semantic Representations of Computational Workflows},
  booktitle = {Proceedings of the 19th Annual Conference on Innovative Applications of Artificial Intelligence (IAAI)},
  year = {2007}
}
  6. Kim, J., Deelman, E., Gil, Y., Mehta, G., & Ratnakar, V. (2007). Provenance Trails in the Wings/Pegasus Workflow System. Concurrency and Computation: Practice and Experience, Special Issue on the First Provenance Challenge. http://pegasus.isi.edu/publications/CCPE07-Provenance.pdf 
    @article{kim2007provenance,
  author = {Kim, Jihie and Deelman, Ewa and Gil, Yolanda and Mehta, Gaurang and Ratnakar, Varun},
  url = {http://pegasus.isi.edu/publications/CCPE07-Provenance.pdf},
  title = {Provenance Trails in the Wings/Pegasus Workflow System},
  journal = {Concurrency and Computation: Practice and Experience, Special Issue on the First Provenance Challenge},
  year = {2007}
}
  7. Maechling, P., Deelman, E., Zhao, L., Graves, R., Mehta, G., Gupta, N., Mehringer, J., Kesselman, C., Callaghan, S., Okaya, D., Francoeur, H., Gupta, V., Cui, Y., Vahi, K., Jordan, T., & Field, E. (2007). SCEC CyberShake Workflows: Automating Probabilistic Seismic Hazard Analysis Calculations. In Workflows for e-Science. 
    @inbook{maechling2007automating,
  author = {Maechling, Philip and Deelman, Ewa and Zhao, Li and Graves, Robert and Mehta, Gaurang and Gupta, Nitin and Mehringer, John and Kesselman, Carl and Callaghan, Scott and Okaya, David and Francoeur, Hunter and Gupta, Vipin and Cui, Yifeng and Vahi, Karan and Jordan, Thomas and Field, Edward},
  title = {SCEC CyberShake Workflows: Automating Probabilistic Seismic Hazard Analysis Calculations},
  booktitle = {Workflows for e-Science},
  year = {2007}
}
  8. Mandal, N., Deelman, E., Mehta, G., Su, M.-H., & Vahi, K. (2007). Integrating Existing Scientific Workflow Systems: The Kepler/Pegasus Example. Proceedings of the Second Workshop on Workflows in Support of Large-Scale Science (WORKS07). http://pegasus.isi.edu/publications/kepler-works07.pdf 
    @inproceedings{mandal2007works,
  author = {Mandal, Nandita and Deelman, Ewa and Mehta, Gaurang and Su, Mei-Hui and Vahi, Karan},
  url = {http://pegasus.isi.edu/publications/kepler-works07.pdf},
  title = {Integrating Existing Scientific Workflow Systems: The Kepler/Pegasus Example},
  booktitle = {Proceedings of the Second Workshop on Workflows in Support of Large-Scale Science (WORKS07)},
  year = {2007}
}
  9. Miles, S., Deelman, E., Groth, P., Vahi, K., Mehta, G., & Moreau, L. (2007). Connecting Scientific Data to Scientific Experiments with Provenance. Third IEEE International Conference on e-Science and Grid Computing (e-Science 2007). http://portal.acm.org/citation.cfm?id=1332478.1333573 
    @inproceedings{miles2007connecting,
  author = {Miles, Simon and Deelman, Ewa and Groth, Paul and Vahi, Karan and Mehta, Gaurang and Moreau, Luc},
  url = {http://portal.acm.org/citation.cfm?id=1332478.1333573},
  title = {Connecting Scientific Data to Scientific Experiments with Provenance},
  booktitle = {Third IEEE International Conference on e-Science and Grid Computing (e-Science 2007)},
  year = {2007}
}
  10. Ramakrishnan, A., Singh, G., Zhao, H., Deelman, E., Sakellariou, R., Vahi, K., Blackburn, K., Meyers, D., & Samidi, M. (2007). Scheduling Data-Intensive Workflows onto Storage-Constrained Distributed Resources. Seventh IEEE International Symposium on Cluster Computing and the Grid (CCGrid). http://pegasus.isi.edu/publications/Ramakrishnan-DataIntensiveWorkflow.pdf 
    @inproceedings{ramakrishnan2007data,
  author = {Ramakrishnan, Arun and Singh, Gurmeet and Zhao, Henan and Deelman, Ewa and Sakellariou, Rizos and Vahi, Karan and Blackburn, Kent and Meyers, David and Samidi, Michael},
  url = {http://pegasus.isi.edu/publications/Ramakrishnan-DataIntensiveWorkflow.pdf},
  title = {Scheduling Data-Intensive Workflows onto Storage-Constrained Distributed Resources},
  booktitle = {Seventh IEEE International Symposium on Cluster Computing and the Grid (CCGrid)},
  year = {2007}
}
  11. Singh, G., Vahi, K., Ramakrishnan, A., Mehta, G., Deelman, E., Zhao, H., Sakellariou, R., Blackburn, K., Brown, D., Fairhurst, S., Meyers, D., & Berriman, G. B. (2007). Optimizing Workflow Data Footprint. Special Issue of the Scientific Programming Journal Dedicated to Dynamic Computational Workflows: Discovery, Optimisation and Scheduling. http://pegasus.isi.edu/publications/Footprint-final.pdf 
    @article{singh2007optimizing,
  author = {Singh, Gurmeet and Vahi, Karan and Ramakrishnan, Arun and Mehta, Gaurang and Deelman, Ewa and Zhao, Henan and Sakellariou, Rizos and Blackburn, Kent and Brown, Duncan and Fairhurst, Stephen and Meyers, David and Berriman, G. Bruce},
  url = {http://pegasus.isi.edu/publications/Footprint-final.pdf},
  title = {Optimizing Workflow Data Footprint},
  journal = {Special issue of the Scientific Programming Journal dedicated to Dynamic Computational Workflows: Discovery, Optimisation and Scheduling},
  year = {2007}
}

2006

  1. Deelman, E., Callaghan, S., Field, E., Francoeur, H., Graves, R., Gupta, N., Gupta, V., Jordan, T. H., Kesselman, C., Maechling, P., Mehringer, J., Mehta, G., Okaya, D., Vahi, K., & Zhao, L. (2006). Managing Large-Scale Workflow Execution from Resource Provisioning to Provenance tracking: The CyberShake Example. e-Science 2006. http://pegasus.isi.edu/publications/deelman_Ecybershake.pdf (Best paper award) 
    @inproceedings{deelman2006cybershake,
  author = {Deelman, Ewa and Callaghan, Scott and Field, Edward and Francoeur, Hunter and Graves, Robert and Gupta, Nitin and Gupta, Vipin and Jordan, Thomas H. and Kesselman, Carl and Maechling, Philip and Mehringer, John and Mehta, Gaurang and Okaya, David and Vahi, Karan and Zhao, Li},
  url = {http://pegasus.isi.edu/publications/deelman_Ecybershake.pdf},
  title = {Managing Large-Scale Workflow Execution from Resource Provisioning to Provenance tracking: The CyberShake Example},
  booktitle = {e-Science 2006},
  year = {2006},
  note = {Best paper award}
}
  2. Deelman, E., & Gil, Y. (2006). Managing Large-Scale Scientific Workflows in Distributed Environments: Experiences and Challenges. Workflows in e-Science. http://pegasus.isi.edu/publications/deelman_EworkflowExperiences_v2.pdf 
    @inproceedings{deelman2006experiences,
  author = {Deelman, Ewa and Gil, Yolanda},
  url = {http://pegasus.isi.edu/publications/deelman_EworkflowExperiences_v2.pdf},
  title = {Managing Large-Scale Scientific Workflows in Distributed Environments: Experiences and Challenges},
  booktitle = {Workflows in e-Science},
  year = {2006}
}
  3. Lathers, A., Su, M.-H., Kulungowski, A., Lin, A. W., Mehta, G., Peltier, S. T., Deelman, E., & Ellisman, M. H. (2006). Enabling Parallel Scientific Applications with Workflow Tools. Proceedings of Challenges of Large Applications in Distributed Environments (CLADE). http://pegasus.isi.edu/publications/alathers_clade.pdf 
    @inproceedings{lathers2006clade,
  author = {Lathers, Adam and Su, Mei-Hui and Kulungowski, Alex and Lin, Abel W. and Mehta, Gaurang and Peltier, Steven T. and Deelman, Ewa and Ellisman, Mark H.},
  url = {http://pegasus.isi.edu/publications/alathers_clade.pdf},
  title = {Enabling Parallel Scientific Applications with Workflow Tools},
  booktitle = {Proceedings of Challenges of Large Applications in Distributed Environments (CLADE)},
  year = {2006}
}
  4. Nefedova, V., Jacob, R., Foster, I., Liu, Z., Liu, Y., Deelman, E., Mehta, G., Su, M.-H., & Vahi, K. (2006). Automating Climate Science: Large Ensemble Simulations on the TeraGrid with the GriPhyN Virtual Data System. e-Science 2006. http://pegasus.isi.edu/publications/Foam-submit.pdf 
    @inproceedings{nefedova2006climage,
  author = {Nefedova, Veronika and Jacob, Robert and Foster, Ian and Liu, Zhengyu and Liu, Yun and Deelman, Ewa and Mehta, Gaurang and Su, Mei-Hui and Vahi, Karan},
  url = {http://pegasus.isi.edu/publications/Foam-submit.pdf},
  title = {Automating Climate Science: Large Ensemble Simulations on the TeraGrid with the GriPhyN Virtual Data System},
  booktitle = {e-Science 2006},
  year = {2006}
}
  5. Singh, G., Kesselman, C., & Deelman, E. (2006). Application-level Resource Provisioning on the Grid. e-Science 2006. http://pegasus.isi.edu/publications/Singh-AppResProvisioning.pdf 
    @inproceedings{singh2006provisioning,
  author = {Singh, Gurmeet and Kesselman, Carl and Deelman, Ewa},
  url = {http://pegasus.isi.edu/publications/Singh-AppResProvisioning.pdf},
  title = {Application-level Resource Provisioning on the Grid},
  booktitle = {e-Science 2006},
  year = {2006}
}
  6. Taylor, I., Deelman, E., Gannon, D., & Shield, M. (2006). Workflows for e-Science. Springer. http://www.springer.com/computer/communication+networks/book/978-1-84628-519-6 
    @book{taylor2006workflows,
  author = {Taylor, Ian and Deelman, Ewa and Gannon, Dennis and Shield, Matthew},
  url = {http://www.springer.com/computer/communication+networks/book/978-1-84628-519-6},
  title = {Workflows for e-Science},
  publisher = {Springer},
  year = {2006}
}
  7. Vöckler, J.-S., Mehta, G., Zhao, Y., Deelman, E., & Wilde, M. (2006). Kickstarting Remote Applications. Second International Workshop on Grid Computing Environments (GCE06). http://pegasus.isi.edu/publications/kickstart.pdf 
    @inproceedings{voeckler2006kickstart,
  author = {Vöckler, Jens-S. and Mehta, Gaurang and Zhao, Yong and Deelman, Ewa and Wilde, Mike},
  url = {http://pegasus.isi.edu/publications/kickstart.pdf},
  title = {Kickstarting Remote Applications},
  booktitle = {Second International Workshop on Grid Computing Environments (GCE06)},
  year = {2006}
}

2005

  1. Blythe, J., Jain, S., Deelman, E., Gil, Y., Vahi, K., Mandal, A., & Kennedy, K. (2005). Task Scheduling Strategies for Workflow-based Applications in Grids. CCGrid 2005. http://pegasus.isi.edu/publications/ccgrid05-correction.pdf 
    @inproceedings{blythe2005scheduling,
  author = {Blythe, Jim and Jain, Sonal and Deelman, Ewa and Gil, Yolanda and Vahi, Karan and Mandal, Anirban and Kennedy, Ken},
  url = {http://pegasus.isi.edu/publications/ccgrid05-correction.pdf},
  title = {Task Scheduling Strategies for Workflow-based Applications in Grids},
  booktitle = {CCGrid 2005},
  year = {2005}
}
  2. Deelman, E., Singh, G., Su, M.-H., Blythe, J., Gil, Y., Kesselman, C., Mehta, G., Vahi, K., Berriman, G. B., Good, J., Laity, A., Jacob, J. C., & Katz, D. S. (2005). Pegasus: a Framework for Mapping Complex Scientific Workflows onto Distributed Systems. Scientific Programming Journal, 13(3), 219–237. http://pegasus.isi.edu/publications/Sci.pdf 
    @article{deelman2005pegasus,
  author = {Deelman, Ewa and Singh, Gurmeet and Su, Mei-Hui and Blythe, James and Gil, Yolanda and Kesselman, Carl and Mehta, Gaurang and Vahi, Karan and Berriman, G. Bruce and Good, John and Laity, Anastasia and Jacob, Joseph C. and Katz, Daniel S.},
  url = {http://pegasus.isi.edu/publications/Sci.pdf},
  title = {Pegasus: a Framework for Mapping Complex Scientific Workflows onto Distributed Systems},
  journal = {Scientific Programming Journal},
  volume = {13},
  number = {3},
  pages = {219-237},
  year = {2005}
}
  3. Katz, D. S., Jacob, J. C., Berriman, G. B., Good, J., Laity, A. C., Deelman, E., Kesselman, C., Singh, G., Su, M.-H., & Prince, T. A. (2005). Comparison of Two Methods for Building Astronomical Image Mosaics on a Grid. International Conference on Parallel Processing (ICPP). http://pegasus.isi.edu/publications/Comp.pdf 
    @inproceedings{katz2005comparison,
  author = {Katz, Daniel S. and Jacob, Joseph C. and Berriman, G. Bruce and Good, John and Laity, Anastasia C. and Deelman, Ewa and Kesselman, Carl and Singh, Gurmeet and Su, Mei-Hui and Prince, Thomas A.},
  url = {http://pegasus.isi.edu/publications/Comp.pdf},
  title = {Comparison of Two Methods for Building Astronomical Image Mosaics on a Grid},
  booktitle = {International Conference on Parallel Processing (ICPP)},
  year = {2005}
}
  4. Maechling, P., Chalupsky, H., Dougherty, M., Deelman, E., Gil, Y., Gullapalli, S., Gupta, V., Kesselman, C., Kim, J., Mehta, G., Mendenhall, B., Russ, T. A., Singh, G., Spraragen, M., Staples, G., & Vahi, K. (2005). Simplifying construction of complex workflows for non-expert users of the Southern California Earthquake Center Community Modeling Environment. SIGMOD Record, 34(3), 24–30. http://pegasus.isi.edu/publications/scec.pdf 
    @article{maechling2005sigmod,
  author = {Maechling, Philip and Chalupsky, Hans and Dougherty, Maureen and Deelman, Ewa and Gil, Yolanda and Gullapalli, Sridhar and Gupta, Vipin and Kesselman, Carl and Kim, Jihie and Mehta, Gaurang and Mendenhall, Brian and Russ, Thomas A. and Singh, Gurmeet and Spraragen, Marc and Staples, Garrick and Vahi, Karan},
  url = {http://pegasus.isi.edu/publications/scec.pdf},
  title = {Simplifying construction of complex workflows for non-expert users of the Southern California Earthquake Center Community Modeling Environment},
  journal = {SIGMOD Record},
  volume = {34},
  number = {3},
  pages = {24-30},
  year = {2005}
}
  5. Singh, G., Deelman, E., Mehta, G., Vahi, K., Su, M.-H., Berriman, G. B., Good, J., Jacob, J. C., Katz, D. S., Lazzarini, A., Blackburn, K., & Koranda, S. (2005). The Pegasus Portal: Web Based Grid Computing. The 20th Annual ACM Symposium on Applied Computing. http://pegasus.isi.edu/publications/Pegasus_Portal_final2.pdf 
    @inproceedings{singh2005portal,
  author = {Singh, Gurmeet and Deelman, Ewa and Mehta, Gaurang and Vahi, Karan and Su, Mei-Hui and Berriman, G. Bruce and Good, John and Jacob, Joseph C. and Katz, Daniel S. and Lazzarini, Albert and Blackburn, Kent and Koranda, Scott},
  url = {http://pegasus.isi.edu/publications/Pegasus_Portal_final2.pdf},
  title = {The Pegasus Portal: Web Based Grid Computing},
  booktitle = {The 20th Annual ACM Symposium on Applied Computing},
  year = {2005}
}
  6. Singh, G., Kesselman, C., & Deelman, E. (2005). Optimizing Grid-Based Workflow Execution. Journal of Grid Computing, 3(3-4), 201–219. http://pegasus.isi.edu/publications/Opt.pdf 
    @article{singh2005optimizing,
  author = {Singh, Gurmeet and Kesselman, Carl and Deelman, Ewa},
  url = {http://pegasus.isi.edu/publications/Opt.pdf},
  title = {Optimizing Grid-Based Workflow Execution},
  journal = {Journal of Grid Computing},
  volume = {3},
  number = {3-4},
  pages = {201-219},
  month = dec,
  year = {2005}
}

2004

  1. Deelman, E., Blythe, J., Gil, Y., Kesselman, C., Mehta, G., Patil, S., Su, M.-H., Vahi, K., & Livny, M. (2004). Pegasus: Mapping Scientific Workflows onto the Grid. Across Grids Conference. http://pegasus.isi.edu/publications/ewa/Pegasus_final.pdf 
    @inproceedings{deelman2004pegasus,
  author = {Deelman, Ewa and Blythe, James and Gil, Yolanda and Kesselman, Carl and Mehta, Gaurang and Patil, Sonal and Su, Mei-Hui and Vahi, Karan and Livny, Miron},
  url = {http://pegasus.isi.edu/publications/ewa/Pegasus_final.pdf},
  title = {Pegasus: Mapping Scientific Workflows onto the Grid},
  booktitle = {Across Grids Conference},
  year = {2004}
}
  2. Gil, Y., Deelman, E., Blythe, J., Kesselman, C., & Tangmurarunkit, H. (2004). Artificial Intelligence and Grids: Workflow Planning and Beyond. IEEE Intelligent Systems. http://pegasus.isi.edu/publications/ewa/ieee_is04.pdf 
    @article{gil2004ai,
  author = {Gil, Yolanda and Deelman, Ewa and Blythe, Jim and Kesselman, Carl and Tangmurarunkit, Hongsuda},
  url = {http://pegasus.isi.edu/publications/ewa/ieee_is04.pdf},
  title = {Artificial Intelligence and Grids: Workflow Planning and Beyond},
  journal = {IEEE Intelligent Systems},
  month = jan,
  year = {2004}
}

2003

  1. Berriman, G. B., Good, J. C., Laity, A. C., Bergou, A., Jacob, J. C., Katz, D. S., Deelman, E., Kesselman, C., Singh, G., Su, M.-H., & Williams, R. (2003). Montage: A Grid Enabled Image Mosaic Service for the National Virtual Observatory. ADASS XIII. http://pegasus.isi.edu/publications/ewa/adass_03.pdf 
    @inproceedings{berriman2003montage,
  author = {Berriman, G. Bruce and Good, John C. and Laity, Anastasia C. and Bergou, A. and Jacob, Joseph C. and Katz, Daniel S. and Deelman, Ewa and Kesselman, Carl and Singh, Gurmeet and Su, Mei-Hui and Williams, Roy},
  url = {http://pegasus.isi.edu/publications/ewa/adass_03.pdf},
  title = {Montage: A Grid Enabled Image Mosaic Service for the National Virtual Observatory},
  booktitle = {ADASS XIII},
  year = {2003}
}
  2. Blythe, J., Cavanaugh, R., Deelman, E., Foster, I., Jang, S.-H., Kesselman, C., Marzullo, K., Moore, R., Taylor, V., & Zhang, X. (2003). Types of Editors and Specifications (Technical Report 2004-23; Number Technical Report 2004-23). GriPhyN. http://pegasus.isi.edu/publications/editors.pdf 
    @techreport{blythe2003editors,
  author = {Blythe, James and Cavanaugh, Richard and Deelman, Ewa and Foster, Ian and Jang, Seung-Hye and Kesselman, Carl and Marzullo, Keith and Moore, Reagan and Taylor, Valerie and Zhang, Xianan},
  url = {http://pegasus.isi.edu/publications/editors.pdf},
  title = {Types of Editors and Specifications},
  institution = {GriPhyN},
  number = {Technical Report 2004-23},
  year = {2003}
}
  3. Blythe, J., Deelman, E., & Gil, Y. (2003). Planning for workflow construction and maintenance on the Grid. 2003 ICAPS Workshop on Planning for Web Services. http://pegasus.isi.edu/publications/ewa/icaps_workshop.pdf 
    @inproceedings{blythe2003workshop,
  author = {Blythe, Jim and Deelman, Ewa and Gil, Yolanda},
  url = {http://pegasus.isi.edu/publications/ewa/icaps_workshop.pdf},
  title = {Planning for workflow construction and maintenance on the Grid},
  booktitle = {2003 ICAPS Workshop on Planning for Web Services},
  year = {2003}
}
  4. Blythe, J., Deelman, E., Gil, Y., & Kesselman, C. (2003). Transparent Grid Computing: a Knowledge-Based Approach. IAAI. http://pegasus.isi.edu/publications/ewa/iaai_2003.pdf 
    @inproceedings{blythe2003transparent,
  author = {Blythe, Jim and Deelman, Ewa and Gil, Yolanda and Kesselman, Carl},
  url = {http://pegasus.isi.edu/publications/ewa/iaai_2003.pdf},
  title = {Transparent Grid Computing: a Knowledge-Based Approach},
  booktitle = {IAAI},
  year = {2003}
}
  5. Blythe, J., Deelman, E., Gil, Y., Kesselman, C., Agarwal, A., Mehta, G., & Vahi, K. (2003). The Role of Planning in Grid Computing. ICAPS. http://pegasus.isi.edu/publications/ewa/icaps03.pdf 
    @inproceedings{blythe2003planning,
  author = {Blythe, Jim and Deelman, Ewa and Gil, Yolanda and Kesselman, Carl and Agarwal, Amit and Mehta, Gaurang and Vahi, Karan},
  url = {http://pegasus.isi.edu/publications/ewa/icaps03.pdf},
  title = {The Role of Planning in Grid Computing},
  booktitle = {ICAPS},
  year = {2003}
}
  6. Deelman, E., Blythe, J., Gil, Y., & Kesselman, C. (2003). Workflow Management in GriPhyN. In J. S. J. Nabrzyski & J. Weglarz (Eds.), Grid Resource Management. Kluwer. http://pegasus.isi.edu/publications/ewa/grm_chapter.pdf 
    @inbook{deelman2003griphyn,
  author = {Deelman, Ewa and Blythe, James and Gil, Yolanda and Kesselman, Carl},
  url = {http://pegasus.isi.edu/publications/ewa/grm_chapter.pdf},
  title = {Workflow Management in GriPhyN},
  booktitle = {Grid Resource Management},
  editor = {J. Nabrzyski, J. Schopf and Weglarz, J.},
  publisher = {Kluwer},
  year = {2003}
}
  7. Deelman, E., Blythe, J., Gil, Y., Kesselman, C., Koranda, S., Lazzarini, A., Mehta, G., Papa, M. A., & Vahi, K. (2003). Pegasus and the Pulsar Search: From Metadata to Execution on the Grid. Applications Grid Workshop, PPAM 2003. http://pegasus.isi.edu/publications/ewa/agw_ppam2003.pdf 
    @inproceedings{deelman2003pulsar,
  author = {Deelman, Ewa and Blythe, James and Gil, Yolanda and Kesselman, Carl and Koranda, Scott and Lazzarini, Albert and Mehta, Gaurang and Papa, Maria Alessandra and Vahi, Karan},
  url = {http://pegasus.isi.edu/publications/ewa/agw_ppam2003.pdf},
  title = {Pegasus and the Pulsar Search: From Metadata to Execution on the Grid},
  booktitle = {Applications Grid Workshop, PPAM 2003},
  year = {2003}
}
  8. Deelman, E., Blythe, J., Gil, Y., Kesselman, C., Mehta, G., Vahi, K., Blackburn, K., Lazzarini, A., Arbree, A., Cavanaugh, R., & Koranda, S. (2003). Mapping Abstract Complex Workflows onto Grid Environments. Journal of Grid Computing, 1(1), 25–39. http://pegasus.isi.edu/publications/ewa/jogc.pdf 
    @article{deelman2003mapping,
  author = {Deelman, Ewa and Blythe, James and Gil, Yolanda and Kesselman, Carl and Mehta, Gaurang and Vahi, Karan and Blackburn, Kent and Lazzarini, Albert and Arbree, Adam and Cavanaugh, Richard and Koranda, Scott},
  url = {http://pegasus.isi.edu/publications/ewa/jogc.pdf},
  title = {Mapping Abstract Complex Workflows onto Grid Environments},
  journal = {Journal of Grid Computing},
  volume = {1},
  number = {1},
  pages = {25-39},
  year = {2003}
}
  9. Deelman, E., Blythe, J., Gil, Y., Kesselman, C., Mehta, G., Vahi, K., Koranda, S., Lazzarini, A., & Papa, M. A. (2003). From Metadata to Execution on the Grid Pegasus and the Pulsar Search (Technical Report 2003-15; Number Technical Report 2003-15). GriPhyN. http://pegasus.isi.edu/publications/ewa/griphyn_2003_15.pdf 
    @techreport{deelman2003metadata,
  author = {Deelman, Ewa and Blythe, James and Gil, Yolanda and Kesselman, Carl and Mehta, Gaurang and Vahi, Karan and Koranda, Scott and Lazzarini, Albert and Papa, Maria Alessandra},
  url = {http://pegasus.isi.edu/publications/ewa/griphyn_2003_15.pdf},
  title = {From Metadata to Execution on the Grid Pegasus and the Pulsar Search},
  institution = {GriPhyN},
  number = {Technical Report 2003-15},
  year = {2003}
}
  10. Deelman, E., Foster, I., Kesselman, C., Moore, R., & Ranka, S. (2003). Overall Architecture and Control Flow (Technical Report 2004-24; Number Technical Report 2004-24). GriPhyN. http://pegasus.isi.edu/publications/architecture.pdf 
    @techreport{deelman2003architecture,
  author = {Deelman, Ewa and Foster, Ian and Kesselman, Carl and Moore, Reagan and Ranka, Sanjay},
  url = {http://pegasus.isi.edu/publications/architecture.pdf},
  title = {Overall Architecture and Control Flow},
  institution = {GriPhyN},
  number = {Technical Report 2004-24},
  year = {2003}
}
  11. Deelman, E., Plante, R., Kesselman, C., Singh, G., Su, M.-H., Greene, G., Hanisch, R., Gaffney, N., Volpicelli, A., Annis, J., Sekhri, V., Budavari, T., Nieto-Santisteban, M., O’Mullane, W., Bohlender, D., McGlynn, T., Rots, A., & Pevunova, O. (2003). Grid-Based Galaxy Morphology Analysis for the National Virtual Observatory. Supercomputing 2003. http://pegasus.isi.edu/publications/ewa/galmorph_sc03.pdf 
    @inproceedings{deelman2003nvo,
  author = {Deelman, Ewa and Plante, Raymond and Kesselman, Carl and Singh, Gurmeet and Su, Mei-Hui and Greene, Gretchen and Hanisch, Robert and Gaffney, Niall and Volpicelli, Antonio and Annis, James and Sekhri, Vijay and Budavari, Tamas and Nieto-Santisteban, Maria and O'Mullane, William and Bohlender, David and McGlynn, Tom and Rots, Arnold and Pevunova, Olga},
  url = {http://pegasus.isi.edu/publications/ewa/galmorph_sc03.pdf},
  title = {Grid-Based Galaxy Morphology Analysis for the National Virtual Observatory},
  booktitle = {Supercomputing 2003},
  year = {2003}
}
  12. Singh, G., & Deelman, E. (2003). Montage on the Grid (Technical Report; Number Technical Report). NVO. http://pegasus.isi.edu/publications/ewa/montage_pegasus.pdf 
    @techreport{singh2003nvo,
  author = {Singh, Gurmeet and Deelman, Ewa},
  url = {http://pegasus.isi.edu/publications/ewa/montage_pegasus.pdf},
  title = {Montage on the Grid},
  institution = {NVO},
  number = {Technical Report},
  month = apr,
  year = {2003}
}
  13. Williams, R., Berriman, G. B., Deelman, E., Good, J., Jacob, J. C., Kesselman, C., Lonsdale, C., Oliver, S., & Prince, T. A. (2003). Multi-Wavelength Image Space: Another Grid-Enabled Science. Journal of Concurrency and Computation: Practice and Experience. http://pegasus.isi.edu/publications/ewa/montage_paper.pdf 
    @article{williams2003image,
  author = {Williams, Roy and Berriman, G. Bruce and Deelman, Ewa and Good, John and Jacob, Joseph C. and Kesselman, Carl and Lonsdale, Carol and Oliver, Seb and Prince, Thomas A.},
  url = {http://pegasus.isi.edu/publications/ewa/montage_paper.pdf},
  title = {Multi-Wavelength Image Space: Another Grid-Enabled Science},
  journal = {Journal of Concurrency and Computation: Practice and Experience},
  month = mar,
  year = {2003}
}

2002

  1. Deelman, E., Blythe, J., Gil, Y., & Kesselman, C. (2002). Pegasus: Planning for Execution in Grids (Technical Report 2002-20; Number Technical Report 2002-20). GriPhyN. http://pegasus.isi.edu/publications/ewa/pegasus_overview.pdf 
    @techreport{deelman2002pegasus,
  author = {Deelman, Ewa and Blythe, James and Gil, Yolanda and Kesselman, Carl},
  url = {http://pegasus.isi.edu/publications/ewa/pegasus_overview.pdf},
  title = {Pegasus: Planning for Execution in Grids},
  institution = {GriPhyN},
  number = {Technical Report 2002-20},
  year = {2002}
}
  2. Deelman, E., Kesselman, C., Mehta, G., Meshkat, L., Pearlman, L., Blackburn, K., Ehrens, P., Lazzarini, A., Williams, R., & Koranda, S. (2002). GriPhyN and LIGO, Building a Virtual Data Grid for Gravitational Wave Scientists. High Performance Distributed Computing (HPDC). http://pegasus.isi.edu/publications/ewa/hpdc11.pdf 
    @inproceedings{deelman2002ligo,
  author = {Deelman, Ewa and Kesselman, Carl and Mehta, Gaurang and Meshkat, Leila and Pearlman, Laura and Blackburn, Kent and Ehrens, Phil and Lazzarini, Albert and Williams, Roy and Koranda, Scott},
  url = {http://pegasus.isi.edu/publications/ewa/hpdc11.pdf},
  title = {GriPhyN and LIGO, Building a Virtual Data Grid for Gravitational Wave Scientists},
  booktitle = {High Performance Distributed Computing (HPDC)},
  year = {2002}
}