@inproceedings{carvalho-etal-escience18,
  author = {Lucas Carvalho and Daniel Garijo and Claudia Bauzer Medeiros and Yolanda Gil},
  title = {Semantic Software Metadata for Workflow Exploration and Evolution},
  booktitle = {Proceedings of the Fourteenth IEEE International Conference on eScience},
  address = {Amsterdam, The Netherlands},
  year = {2018}
}

@inproceedings{gil-etal-automl18,
  title = {P4ML: A Phased Performance-Based Pipeline Planner for Automated Machine Learning},
  author = {Yolanda Gil and Ke-Thia Yao and Varun Ratnakar and Daniel Garijo and Greg Ver Steeg and Pedro Szekely and Rob Brekelmans and Mayank Kejriwal and Fanghao Luo and I-Hui Huang},
  booktitle = {Proceedings of Machine Learning Research, ICML 2018 AutoML Workshop},
  year = {2018},
  url = {http://www.isi.edu/~gil/papers/gil-etal-automl18.pdf}
}

@inproceedings{gil-etal-iemss18,
  author = {Yolanda Gil and Kelly Cobourn and Ewa Deelman and Chris Duffy and Rafael Ferreira da Silva and 
Armen Kemanian and Craig Knoblock and Vipin Kumar and Scott Peckham and Lucas Carvalho and 
Yao-Yi Chiang and Daniel Garijo and Deborah Khider and Ankush Khandelwal and Minh Pahm and  
Jay Pujara and Varun Ratnakar and Maria Stoica and Binh Vu},
  title = {MINT: Model Integration Through Knowledge-Powered Data and Process Composition},
  booktitle = {Proceedings of the Ninth International Congress on Environmental Modeling and Software},
  address = {Ft Collins, CO},
  year = {2018},
  url = {http://www.isi.edu/~gil/papers/gil-etal-iemss18.pdf}
}

@inproceedings{ferreira-etal-iemss18,
  author = {Rafael Ferreira da Silva and Daniel Garijo and Scott D. Peckham and Yolanda Gil and Ewa Deelman and Varun Ratnakar},
  title = {Towards Model Integration via Abductive Workflow Composition and Multi-Method Scalable Model Execution},
  booktitle = {Proceedings of the Ninth International Congress on Environmental Modeling and Software},
  address = {Ft Collins, CO},
  year = {2018},
  url = {http://www.isi.edu/~gil/papers/ferreira-etal-iemss18.pdf}
}

@inproceedings{ carvalho-etal-sciknow2017b,
  title = {NiW: Converting Notebooks into Workflows to Capture Dataflow and Provenance},
  author = {Lucas A. M. C. Carvalho and Regina Wang and Yolanda Gil and Daniel Garijo},
  booktitle = {Proceedings of the Workshop on Capturing Scientific Knowledge (SciKnow), 
  held in conjunction with the ACM International Conference on Knowledge Capture (K-CAP)},
  address = {Austin, Texas},
  url = {http://www.isi.edu/~gil/papers/carvalho-etal-sciknow2017b.pdf },
  year = {2017}
}

@inproceedings{ carvalho-etal-sciknow2017a,
  title = {Requirements for Supporting the Iterative Exploration of Scientific Workflow Variants},
  author = {Lucas A. M. C. Carvalho and Bakinam T. Essawy and Daniel Garijo and Claudia Bauzer Medeiros and Yolanda Gil  },
  booktitle = {Proceedings of the Workshop on Capturing Scientific Knowledge (SciKnow), 
  held in conjunction with the ACM International Conference on Knowledge Capture (K-CAP)},
  address = {Austin, Texas},
  url = {http://www.isi.edu/~gil/papers/carvalho-etal-sciknow2017a.pdf },
  year = {2017}
}

@inproceedings{ gil-etal-sciknow2017,
  title = {Improving Publication and Reproducibility of Computational Experiments through Workflow Abstractions},
  author = {Yolanda Gil and Daniel Garijo and Margaret Knoblock and Alyssa Deng and 
  Ravali Adusumilli and Varun Ratnakar and Parag Mallick},
  booktitle = {Proceedings of the Workshop on Capturing Scientific Knowledge (SciKnow), 
  held in conjunction with the ACM International Conference on Knowledge Capture (K-CAP)},
  address = {Austin, Texas},
  url = {http://www.isi.edu/~gil/papers/gil-etal-sciknow2017.pdf },
  year = {2017}
}

@article{ sethi-gil-fgcs17,
  title = {Scientific Workflows in Data Analysis: Bridging Expertise Across
Multiple Domains},
  author = {Ricky Sethi and Yolanda Gil },
  journal = {Future Generation Computer Systems},
  volume = {75},
  ee = {http://doi.org/10.1016/j.future.2017.01.001},
  doi = {10.1016/j.future.2017.01.001},
year = {2017}
}

@article{ garijo-etal-fgcs17,
  title = {Abstract, Link, Publish, Exploit: An End to End Framework for Workflow Sharing},
  author = {Daniel Garijo and Yolanda Gil and Oscar Corcho},
  journal = {Future Generation Computer Systems},
  volume = {75},
  url = {http://www.isi.edu/~gil/papers/garijo-etal-fgcs17.pdf},
  ee = {http://doi.org/10.1016/j.future.2017.01.008},
  doi = {10.1016/j.future.2017.01.008},
year = {2017}
}

@inproceedings{ gil-garijo-iui17,
  title = {Towards Automating Data Narratives},
  author = {Yolanda Gil and Daniel Garijo},
  booktitle = {Proceedings of the Twenty-Second ACM International Conference on Intelligent User Interfaces (IUI-17)},
  address = {Limassol, Cyprus},
  year = {2017},
  url = {http://www.isi.edu/~gil/papers/gil-garijo-iui17.pdf },
  doi = {10.1145/3025171.3025193},
  ee = {http://dx.doi.org/10.1145/3025171.3025193}
}

@inproceedings{ gil-etal-aaai17,
  title = {Towards Continuous Scientific Data Analysis and Hypothesis Evolution},
  author = {Yolanda Gil and Daniel Garijo and Varun Ratnakar and Rajiv Mayani and Ravali Adusumilli and Hunter Boyce and Arunima Srivastava and Parag Mallick},
  booktitle = {Proceedings of the Thirty-First AAAI Conference on Artificial Intelligence (AAAI-17)},
  address = {San Francisco, CA},
  year = {2017},
  url = {http://www.isi.edu/~gil/papers/gil-etal-aaai17.pdf }
}

@article{ stodden-etal-science16,
  title = {Enhancing Reproducibility for Computational Methods},
  author = {Victoria Stodden and Marcia McNutt and David H. Bailey and Ewa Deelman and Yolanda Gil and Brooks Hanson and Michael A. Heroux and John P.A. Ioannidis and Michela Taufer},
  journal = {Science},
  ee = {http://dx.doi.org/10.1126/science.aah6168},
  doi = {10.1126/science.aah6168},
  volume = {354},
  issue = {6317},
  year = {2016}
}

@inproceedings{sethi-gil-escience16,
  title = {Reproducibility in Computer Vision: Towards Open Publication of Image Analysis Experiments as Semantic Workflows},
  author = {Ricky J. Sethi and Yolanda Gil},
  booktitle = {Proceedings of the Twelfth IEEE Conference on eScience},
  address = {Baltimore, MD},
  year = {2016},
  doi = {10.1109/eScience.2016.7870918},
  ee = {http://dx.doi.org/10.1109/eScience.2016.7870918},
  url = {http://www.isi.edu/~gil/papers/sethi-gil-escience16.pdf }
}

@inproceedings{ gil-etal-acs16,
  title = {Automated Hypothesis Testing with Large Scientific Data Repositories},
  author = {Yolanda Gil and Daniel Garijo and Varun Ratnakar and Rajiv Mayani and Ravali Adusumilli and Hunter Boyce and Parag Mallick},
  booktitle = {Proceedings of the Fourth Annual Conference on Advances in Cognitive Systems (ACS)},
  address = {Evanston, IL},
  year = {2016},
  url = {http://www.isi.edu/~gil/papers/gil-etal-acs16.pdf }
}

@inproceedings{ gil-eaai16,
  title = {Teaching Big Data Analytics Skills with Intelligent Workflow Systems},
  author = {Yolanda Gil},
  booktitle = {Proceedings of the Sixth Symposium on Educational Advances in Artificial Intelligence (EAAI), colocated with the National Conference of the Association for the Advancement of Artificial Intelligence (AAAI)},
  address = {Phoenix, AZ},
  year = {2016},
  url = {http://www.isi.edu/~gil/papers/gil-eaai16.pdf }
}

@inproceedings{ gil-ratnakar-icsc16,
  title = {Dynamically Generated Metadata and Replanning by Interleaving Workflow Generation and Execution},
  author = {Yolanda Gil and Varun Ratnakar},
  booktitle = {Proceedings of the Tenth IEEE International Conference on Semantic Computing (ICSC)},
  address = {Irvine, CA},
  year = {2016},
  doi = {10.1109/ICSC.2016.89},
  ee = {http://dx.doi.org/10.1109/ICSC.2016.89},
  url = {http://www.isi.edu/~gil/papers/gil-ratnakar-icsc16.pdf }
}

@article{ zheng-etal-gm15,
  title = {Use of Semantic Workflows to Enhance Transparency and Reproducibility in Clinical Omics},
  author = {Christina L Zheng and Varun Ratnakar and Yolanda Gil and Shannon K McWeeney},
  journal = {Genome Medicine},
  volume = {7},
  number = {73},
  year = {2015},
  doi = {10.1186/s13073-015-0202-y},
  url = {http://www.isi.edu/~gil/papers/zheng-etal-gm15.pdf },
  ee = {http://dx.doi.org/10.1186/s13073-015-0202-y}
}

@inproceedings {gil-eduhpc14, 
  title = {Teaching Parallelism Without Programming: A Data Science Curriculum for Non-CS Students},
  author = {Yolanda Gil},
  year      = {2014},
 address = {New Orleans, LA},
  booktitle = {Proceedings of the Workshop on Education for High-Performance Computing (EduHPC), held in conjunction with the IEEE ACM International Conference on High Performance Computing (SC)},
 url = {http://www.isi.edu/~gil/papers/gil-eduhpc14.pdf }
}

@inproceedings{garijo-etal-works14, 
  title = {Towards Workflow Ecosystems Through Semantic and Standard Representations},
  author = {Daniel Garijo and Yolanda Gil and Oscar Corcho},
  year      = {2014},
 address = {New Orleans, LA},
  booktitle = {Proceedings of the Ninth Workshop on Workflows in Support of Large-Scale Science (WORKS), held in conjunction with the IEEE ACM International Conference on High-Performance Computing (SC)},
 url = {http://www.isi.edu/~gil/papers/garijo-etal-works14.pdf}
}

@inproceedings{garijo-etal-escience14a, 
  title = {Workflow Reuse in Practice: A Study of Neuroimaging Pipeline Users },
  author = {Daniel Garijo and Oscar Corcho and Yolanda Gil and Meredith N. Braskie and Derrek Hibar and Xue Hua and Neda Jahanshad and Paul Thompson and Arthur W. Toga},
  year      = {2014},
 address = {Guarujua, Brazil},
  booktitle = {Proceedings of the IEEE Conference on e-Science},
  ee = {http://dx.doi.org/10.1109/eScience.2014.33},
  doi = {10.1109/eScience.2014.33},
url = {http://www.isi.edu/~gil/papers/garijo-etal-escience14a.pdf}
}

@inproceedings{garijo-etal-escience14b, 
  title = {FragFlow: Automated Fragment Detection in Scientific Workflows },
  author = {Daniel Garijo and Oscar Corcho and Yolanda Gil and Boris A. Gutman and Ivo D. Dinov and Paul Thompson and Arthur W. Toga},
  year      = {2014},
 address = {Guarujua, Brazil},
  booktitle = {Proceedings of the IEEE Conference on e-Science},
    ee = {http://dx.doi.org/10.1109/eScience.2014.32},
  doi = {10.1109/eScience.2014.32},
 url = {http://www.isi.edu/~gil/papers/garijo-etal-escience14b.pdf}
}

@inproceedings{gil-iemss14,
  author = {Yolanda Gil},
  title = {Intelligent Workflow Systems and Provenance-Aware Software},
  booktitle = {Proceedings of the Seventh International Congress on Environmental Modeling and Software},
  address = {San Diego, CA},
  year = {2014},
  url = {http://www.isi.edu/~gil/papers/gil-iemss14.pdf },
  ee = {http://www.iemss.org/sites/iemss2014/http://www.isi.edu/~gil/papers/iemss2014_submission_384.pdf}
}

@article{bergmann-gil-isj12,
 title = {Similarity Assessment and Efficient Retrieval of Semantic Workflows},
 author = {Ralph Bergmann and Yolanda Gil},
 journal = {Information Systems Journal},
   volume = 40,
  year      = {2014},
 url = {http://www.isi.edu/~gil/papers/bergmann-gil-isj12.pdf},
   ee = {http://dx.doi.org/10.1016/j.is.2012.07.005}
 }

@article{garijo-etal-plosone13, 
  title = {Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome},
  author = {Daniel Garijo and Sarah Kinnings and Li Xie and Lei Xie and Yinliang Zhang and Philip E. Bourne and Yolanda Gil},
 journal = {PLOS ONE},
  year      = {2013},
  ee = {http://dx.doi.org/10.1371/journal.pone.0080278}
  }

@inproceedings{gil-etal-works13, 
  title = {Time-Bound Analytic Tasks on Large Datasets through Dynamic Configuration of Workflows},
  author = {Yolanda Gil and Varun Ratnakar and Rishi Verma and Andrew Hart and Paul Ramirez and Chris Mattmann and Arni Sumarlidason and Samuel L. Park},
  year      = {2013},
 address = {Denver, CO},
  booktitle = {Proceedings of the Eighth Workshop on Workflows in Support of Large-Scale Science (WORKS), held in conjunction with SC 2013},
 url = {http://www.isi.edu/~gil/papers/gil-etal-works13.pdf}
}

@inproceedings{kale-etal-aaaifssdi13, 
  title = {Capturing Data Analysis Expertise with Visualization in Workflows},
  author = {David Kale and Samuel Di and Yan Liu and Yolanda Gil},
  year      = {2013},
 address = {Arlington, Virginia},
  booktitle = {AAAI Fall Symposium on Discovery Informatics: AI Takes a Science-Centered View on Big Data},
 url = {http://www.isi.edu/~gil/papers/kale-etal-aaaifss13.pdf}
}

@article{garijo-etal-fgcs13, 
  title = {Common Motifs in Scientific Workflows: An Empirical Analysis},
  author = {Daniel Garijo and Pinar Alper and Khalid Belhajjame and Oscar Corcho and Yolanda Gil and Carole Goble},
  year      = {2013},
 journal = {Future Generation Computer Systems},
  ee = {http://dx.doi.org/10.1016/j.future.2013.09.018}
}

@inproceedings{sethi-etal-mm13, 
  title = {Large-Scale Multimedia Content Analysis Using Scientific Workflows},
  author = {Ricky J. Sethi and Yolanda Gil and Hyunjoon Jo and Andrew Philpot},
  year      = {2013},
 address = {Barcelona, Spain},
  booktitle = {Twenty-First ACM International Conference on Multimedia},
 url = {http://www.isi.edu/~gil/papers/sethi-etal-mm13.pdf}
}

@article{sethi-etal-prl13, 
  title = {Structured Analysis of the ISI Atomic Pair Actions Dataset Using Workflows},
  author = {Ricky J. Sethi and Hyunjoon Jo and Yolanda Gil},
   volume=34,
 number=15,
  year      = {2013},
 journal = {Pattern Recognition Letters},
  ee = {http://dx.doi.org/10.1016/j.patrec.2012.12.015}
}

@inproceedings{gil-icsc13, 
  title = {Mapping Semantic Workflows to Alternative Workflow Execution Engines},
  author = {Yolanda Gil},
  year      = {2013},
 address = {Irvine, CA},
  booktitle = {Seventh IEEE International Conference on Semantic Computing (ICSC)},
 url = {http://www.isi.edu/~gil/papers/gil-icsc13.pdf}
}

@inproceedings{garijo-etal-kcap13, 
  title = {Detecting Common Scientific Workflow Fragments Using Templates and Execution Provenance},
  author = {Daniel Garijo and Oscar Corcho and Yolanda Gil},
  year      = {2013},
 address = {Banff, Canada},
  booktitle = {Seventh ACM International Conference on Knowledge Capture (K-CAP)},
 url = {http://www.isi.edu/~gil/papers/garijo-etal-kcap13.pdf}
}

@inproceedings{gil-etal-hiai13, 
  title = {Using Semantic Workflows to Disseminate Best Practices and Accelerate Discoveries in Multi-Omic Data Analysis},
  author = {Yolanda Gil and Shannon McWeeney and Christopher E. Mason},
  year      = {2013},
 address = {Bellevue, WA},
  booktitle = {AAAI Workshop on Expanding the Boundaries of Health Informatics using AI (HIAI), held in conjunction with the Conference of the Association for the Advancement of Artificial Intelligence (AAAI)},
 url = {http://www.isi.edu/~gil/papers/gil-etal-hiai13.pdf}
}

@misc{gil-etal-cbbw13, 
  title = {Intelligent Assistance to Disseminate Best Practices and Accelerate Discoveries in Cancer Omics},
  author = {Yolanda Gil and Christopher E. Mason and Christina Zheng and Shannon McWeeney},
  year      = {2013},
  note = {2013 NCI EDRN Cancer Biomarkers Bioinformatics Workshop, Pasadena, CA},
  url = {http://www.isi.edu/~gil/papers/gil-etal-cbbw13.pdf} 
}

@inproceedings{gil-isi13,
title = {Towards Task-Centered Network Models through Semantic Workflows},
author = {Yolanda Gil},
  year      = {2013},
 address = {Seattle, WA},
  booktitle = {Proceedings of the IEEE Conference on Intelligence and Security Informatics (ISI)},
 url = {http://www.isi.edu/~gil/papers/gil-isi13.pdf}
}

@misc{mccann-etal-ocean12, 
  title = {Scientific Workflows: The Key to Convergence?},
  author = {Mike P. McCann and Andreas F. Hofmann and Thomas C. Harmon and Yolanda Gil},
  year      = {2012},
  note = {Ocean Sciences Meeting, Salt Lake City, Utah}
}

@misc{gil-etal-agu12, 
  title = {Designing a Roadmap for Workflow Cyberinfrastructure in the Geosciences: From Big Data to the Long Tail},
  author = {Yolanda Gil and Ewa Deelman and Ibrahim Demir and Chris Duffy and Marlon Pierce and Suresh Marru and Gerry Wiener},
  year      = {2012},
  note = {American Geophysical Union Fall Meeting, San Francisco, CA}
}

@misc{gil-etal-ismb12, 
  title = {Using Semantic Workflows for Genome-Scale Analysis},
  author = {Yolanda Gil and Varun Ratnakar and Ewa Deelman and Christopher Mason},
  year      = {2012},
  note = {International Conference on Intelligent Systems for Molecular Biology (ISMB), Long Beach, CA}
}

@inproceedings{sethi-etal-works12, 
  title = {Reusing Workflow Fragments Across Multiple Data Domains},
  author = {Ricky J. Sethi and Hyunjoon Jo and Yolanda Gil},
  year      = {2012},
 address = {Salt Lake City, Utah},
  booktitle = {Proceedings of the Seventh Workshop on Workflows in Support of Large-Scale Science (WORKS'12), held in conjunction with SC 2012},
 url = {http://www.isi.edu/~gil/papers/sethi-etal-works12.pdf }
}

@inproceedings{garijo-etal-escience12, 
  title = {Common Motifs in Scientific Workflows: An Empirical Analysis},
  author = {Daniel Garijo and Pinar Alper and Khalid Belhajjame and Oscar Corcho and Yolanda Gil and Carole Goble},
  year      = {2012},
 address = {Chicago, Illinois},
  booktitle = {Proceedings of the IEEE Conference on e-Science},
 url = {http://www.isi.edu/~gil/papers/garijo-etal-escience12.pdf}
}

@article{ gil-etal-jetai11,
 title = {A Semantic Framework for Automatic Generation of Computational Workflows Using Distributed Data and Component Catalogs},
 author = {Yolanda Gil and Pedro Antonio Gonzalez-Calero and Jihie Kim and Joshua Moody and Varun Ratnakar},
 journal = {Journal of Experimental and Theoretical Artificial Intelligence},
  volume = 23,
  number = 4,
  year      = {2011},
 url = {http://www.isi.edu/~gil/papers/gil-etal-jetai11.pdf }
 }

@inproceedings{garijo-gil-works11, 
  title = {A New Approach for Publishing Workflows: Abstractions, Standards, and Linked Data},
  author = {Daniel Garijo and Yolanda Gil},
  year      = {2011},
 address = {Seattle, Washington},
  booktitle = {Proceedings of the Sixth Workshop on Workflows in Support of Large-Scale Science (WORKS'11), held in conjunction with SC 2011},
 url = {http://www.isi.edu/~gil/papers/garijo-gil-works11.pdf }
}

@inproceedings{hauder-etal-works11, 
  title = {Making Data Analysis Expertise Broadly Accessible through Workflows},
  author = {Matheus Hauder and Yolanda Gil and Ricky Sethi and Yan Liu and Hyunjoon Jo},
  year      = {2011},
 address = {Seattle, Washington},
  booktitle = {Proceedings of the Sixth Workshop on Workflows in Support of Large-Scale Science (WORKS'11), held in conjunction with SC 2011},
 url = {http://www.isi.edu/~gil/papers/hauder-etal-works11.pdf }
}

@inproceedings{hauder-etal-escience11, 
  title = {A Framework for Efficient Text Analytics through Automatic Configuration and Customization of Scientific Workflows},
  author = {Matheus Hauder and Yolanda Gil and Yan Liu},
  year      = {2011},
 address = {Stockholm, Sweden},
  booktitle = {Proceedings of the Seventh IEEE International Conference on e-Science},
 url = {http://www.isi.edu/~gil/papers/hauder-etal-eScience2011.pdf }
}

@inproceedings{gil-etal-iswc11, 
  title = {Mind Your Metadata: Exploiting Semantics for Configuration, Adaptation, and Provenance in Scientific Workflows},
  author = {Yolanda Gil and Pedro Szekely and Sandra Villamizar and Thomas Harmon and Varun Ratnakar and Shubham Gupta and Maria Muslea and Fabio Silva and Craig Knoblock},
  year      = {2011},
 address = {Bonn, Germany},
  booktitle = {Proceedings of the Tenth International Semantic Web Conference (ISWC)},
 url = {http://www.isi.edu/~gil/papers/gil-etal-iswc11.pdf }
}

@inproceedings{ bergmann-gil-iccbr11,
 title = {Retrieval of Semantic Workflows with Knowledge Intensive Similarity Metrics},
 author = {Ralph Bergmann and Yolanda Gil},
 booktitle = {Proceedings of the Nineteenth International Conference on Case Based Reasoning (ICCBR)}, 
 address = {Greenwich, London},
  year      = {2011},
 url = {http://www.isi.edu/~gil/papers/bergmann-gil-iccbr11.pdf }
 }

@inproceedings{ gil-etal-iui11,
 title = {TellMe:  Learning Procedures from Tutorial Instruction},
 author = {Yolanda Gil and Varun Ratnakar and Christian Fritz},
 booktitle = {Proceedings of the ACM International Conference on Intelligent User Interfaces}, 
 address = {Palo Alto, CA},
  year      = {2011},
 url = {http://www.isi.edu/~gil/papers/gil-etal-iui11.pdf }
 }

@article{ gil-etal-ieee-is-11,
 title = {Wings: Intelligent Workflow-Based Design of Computational Experiments},
 author = {Yolanda Gil and Varun Ratnakar and Jihie Kim and Pedro Antonio Gonzalez-Calero and Paul Groth and Joshua Moody and Ewa Deelman},
 journal = {IEEE Intelligent Systems},
  volume = 26,
  number = 1,
  year      = {2011},
 url = {http://www.isi.edu/~gil/papers/gil-etal-ieee-is-11.pdf }
 }

@inproceedings{ gil-etal-aaaifss10,
 title = {Assisting Scientists with Complex Data Analysis Tasks through Semantic Workflows},
 author = {Yolanda Gil and Varun Ratnakar and Christian Fritz},
 booktitle = {Proceedings of the AAAI Fall Symposium on Proactive Assistant Agents }, 
 address = {Arlington, VA},
  year      = {2010},
 url = {http://www.isi.edu/~gil/papers/gil-etal-aaaifss10.pdf }
 }

@article{ kumar-etal-ccj10,
 title = {Parameterized Specification, Configuration, and Execution of Data-Intensive Scientific Workflows},
 author = {Vijay Kumar and Tahsin Kurc and Varun Ratnakar and Jihie Kim and Gaurang Mehta and Karan Vahi and Yoonju Lee Nelson and P. Sadayappan and Ewa Deelman and Yolanda Gil and Mary Hall and Joel Saltz},
 journal = {Cluster Computing Journal},
 volume = {13},
 number = {3},
  year      = {2010},
 pages     = {315-333},
 ee = {http://dx.doi.org/10.1007/s10586-010-0133-8},
 url = {http://www.isi.edu/~gil/papers/kumar-etal-ccj10.pdf }
 }

@article{kim-gil-spraragen-jetai09,
  author    = {Jihie Kim and
               Yolanda Gil and
               Marc Spraragen},
  title     = {Principles for Interactive Acquisition and Validation of
               Workflows},
  journal   = {Journal of Experimental and Theoretical Artificial Intelligence},
  volume    = {22},
  number    = {2},
  year      = {2010},
  pages     = {103-134},
  ee        = {http://dx.doi.org/10.1080/09528130902823698},
  url = {http://www.isi.edu/~gil/papers/kim-gil-spraragen-jetai09.pdf }
}

@inproceedings{ gil-fritz-aaaisss10,
 title = {Reasoning about the Appropriate Use of Private Data through Computational Workflows},
 author = {Yolanda Gil and Christian Fritz},
 booktitle = {Proceedings of the AAAI Spring Symposium on Privacy Management}, 
 address = {Stanford, CA},
  year = {2010},
 url = {http://www.isi.edu/~gil/papers/gil-fritz-aaaisss10.pdf }
 }

@article{kurc-et-al-hpc09,
  author    = {Tahsin M. Kur\c{c} and Shannon Hastings and Vijay S. Kumar and
               Stephen Langella and Ashish Sharma and Tony Pan and
               Scott Oster and David Ervin and Justin Permar and
               Sivaramakrishnan Narayanan and Yolanda Gil and Ewa Deelman and
               Mary W. Hall and Joel H. Saltz},
  title     = {High Performance Computing and Grid Computing for Integrative Biomedical Research},
  journal   = {Journal of High Performance Computing Applications},
  volume    = {23},
  number    = {3},
  year      = {2009},
  pages     = {252-264},
  ee        = {http://dx.doi.org/10.1177/1094342009106192},
  url = {http://www.isi.edu/~gil/papers/kurc-et-al-hpc09.pdf }
}

@inproceedings{ gil-etal-escience09,
 title = {Expressive Reusable Workflow Templates},
 author = {Yolanda Gil and Paul Groth and Varun Ratnakar and Christian Fritz},
 booktitle = {Proceedings of the Fifth IEEE International Conference on e-Science (e-Science)}, 
 address = {Oxford, UK},
  year = {2009},
 url = {http://www.isi.edu/~gil/papers/gil-etal-escience09.pdf }
 }

@inproceedings{gil-etal-kcap09,
  author = {Yolanda Gil and Jihie Kim and Gonzalo Fl{\'o}rez Puga and Varun Ratnakar and Pedro A. Gonz{\'a}lez-Calero},
  title = {Workflow Matching using Semantic Metadata},
  booktitle = {Proceedings of the Fifth International Conference on Knowledge Capture (K-CAP)}, 
  address = {Redondo Beach, CA},
  year = {2009},
  pages = {121-128},
  ee = {http://doi.acm.org/10.1145/1597735.1597757},
  url = {http://www.isi.edu/~gil/papers/gil-etal-kcap09.pdf }
}

@inproceedings{groth-gil-swf09,
  author = {Paul T. Groth and Yolanda Gil},
  title = {Analyzing the Gap between Workflows and their Natural Language Descriptions},
  booktitle = {Proceedings of the IEEE International Workshop on Scientific Workflows (SWF)},
  address = {Los Angeles, CA},
  year = {2009},
  pages = {299-305},
  ee = {http://doi.ieeecomputersociety.org/10.1109/SERVICES-I.2009.55},
  url = {http://www.isi.edu/~gil/papers/groth-gil-swf09.pdf }
}

@inproceedings{kumar-et-al-hpdc09,
  author    = {Vijay S. Kumar and P. Sadayappan and Gaurang Mehta and Karan Vahi and Ewa Deelman and Varun Ratnakar and
               Jihie Kim and Yolanda Gil and Mary W. Hall and Tahsin M. Kur\c{c} and Joel H. Saltz},
  title     = {An Integrated Framework for Performance-Based Optimization
               of Scientific Workflows},
  booktitle = {Proceedings of the Eighteenth ACM International Symposium on High
               Performance Distributed Computing (HPDC)},
  address = {Garching, Germany},
  year      = {2009},
  pages     = {177-186},
  ee        = {http://doi.acm.org/10.1145/1551609.1551638},
  url = {http://www.isi.edu/~gil/papers/kumar-et-al-hpdc09.pdf }, 
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@article{gil-sp08,
  author    = {Yolanda Gil},
  title     = {From Data to Knowledge to Discoveries: Artificial Intelligence
               and Scientific Workflows},
  journal   = {Scientific Programming},
  volume    = {17},
  number    = {3},
  year      = {2009},
  pages     = {231-246},
  ee        = {http://dx.doi.org/10.3233/SPR-2009-0261},
  url = {http://www.isi.edu/~gil/papers/gil-sp08.pdf }
}

@inproceedings{groth-gil-iui09,
  author = {Paul T. Groth and Yolanda Gil},
  title = {A Scientific Workflow Construction Command Line},
  booktitle = {Proceedings of the ACM International Conference on Intelligent User Interfaces (IUI)}, 
  address = {Sanibel Island, FL},
  year = {2009},
  pages = {445-450},
  ee = {http://doi.acm.org/10.1145/1502650.1502716},
  url = {http://www.isi.edu/~gil/papers/groth-gil-iui09.pdf }
}

@article{woollard-etal-ieee08,
  author = {David Woollard and Nenad Medvidovic and Yolanda Gil and Chris Mattmann},
  title = {Scientific Software as Workflows: From Discovery to Distribution},
  journal = {IEEE Software},
  volume = {25},
  number = {4},
  year = {2008},
  pages = {37-43},
  ee = {http://dx.doi.org/10.1109/MS.2008.92},
  url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4548406 }
}

@article {CCPE07-Provenance, 
  title = {Provenance Trails in the Wings/Pegasus Workflow System},
  author = {Jihie Kim and Ewa Deelman and Yolanda Gil and Gaurang Mehta and Varun Ratnakar},
  year = {2008},
  journal = {Concurrency and Computation: Practice and Experience, Special Issue on the First Provenance Challenge},
  volume = {20},
  number = {5},
  url = {http://www.isi.edu/~gil/papers/CCPE07-Provenance.pdf }
}

@inproceedings{kumar-etal-ipdps08,
  author = {Vijay S. Kumar and Mary W. Hall and Jihie Kim and Yolanda Gil and Tahsin M. Kur\c{c} and Ewa Deelman and Varun Ratnakar and Joel H. Saltz},
  title = {Designing and Parameterizing a Workflow for Optimization: A Case Study in Biomedical Imaging},
  booktitle = {Proceedings of the Twentysecond IEEE International Symposium on Parallel and Distributed Processing (IPDPS)},
  address = {Miami, FL},
  year = {2008},
  ee = {http://dx.doi.org/10.1109/IPDPS.2008.4536411}
}

@article{computer-NSFworkflows07,
  author = {Yolanda Gil and Ewa Deelman and Mark H. Ellisman and Thomas Fahringer and Geoffrey Fox and Dennis Gannon and Carole A. Goble and Miron Livny and Luc Moreau and Jim Myers},
  title = {Examining the Challenges of Scientific Workflows},
  journal = {IEEE Computer},
  volume = {40},
  number = {12},
  year = {2007},
  pages = {24-32},
  ee = {http://doi.ieeecomputersociety.org/10.1109/MC.2007.421},
  url = {http://www.isi.edu/~gil/papers/computer-NSFworkflows07.pdf }
}

@inproceedings{ gil-etal-peas07,
 title = {Privacy Enforcement in Data Analysis Workflows},
 author = {Yolanda Gil and William K. Cheung and Varun Ratnakar and Kai-kin Chan},
 booktitle = {Proceedings of the AAAI Workshop on Privacy Enforcement and Accountability with Semantics (PEAS), held in conjunction with the Sixth International Semantic Web Conference (ISWC) and the Second Asian Semantic Web Conference (ASWC)},
 address = {Busan, Korea},
 year = {2007},
 url = {http://www.isi.edu/~gil/papers/gil-etal-peas07.pdf }
 }

@inproceedings{gil-etal-iaai07,
  author = {Yolanda Gil and Varun Ratnakar and Ewa Deelman and Gaurang Mehta and Jihie Kim},
  title = {Wings for Pegasus: Creating Large-Scale Scientific Applications Using Semantic Representations of Computational Workflows},
  booktitle = {Proceedings of the Twenty-Second National Conference on Artificial Intelligence (AAAI)}, 
  address = {Vancouver, British Columbia, Canada},
  year = {2007},
  pages = {1767-1774},
  url = {http://www.isi.edu/~gil/papers/gil-etal-iaai07.pdf }
}

@inproceedings{ cheung-gil-aaai-ses-07,
 title = {Towards Privacy Aware Data Analysis Workflows for e-Science},
 author = {William Cheung and Yolanda Gil},
 booktitle = {Proceedings of the AAAI Workshop on Semantic e-Science (SeS2007), held in conjunction with the Twenty-Second Conference of the  Association for the Advancement of Artificial Intelligence (AAAI)}, 
 address = {Vancouver, British Columbia, Canada},
 year = {2007},
 url = {http://www.isi.edu/~gil/papers/cheung-gil-aaai-ses-07.pdf }
 }

@inproceedings{ gil-etal-works07,
 title = {On the Black Art of Designing Computational Workflows},
 author = {Yolanda Gil and Pedro A. Gonzalez-Calero and Ewa Deelman},
 booktitle = {Proceedings of the Second Workshop on Workflows in Support of Large-Scale Science (WORKS), held in conjunction with the  IEEE International Symposium on High Performance Distributed Computing (HPDC)},
 address = {Monterrey, CA},
 year = {2007},
 url = {http://www.isi.edu/~gil/papers/gil-etal-works07.pdf }
 }

@inproceedings{ipdps07,
  author = {Bhupesh Bansal and {\"U}mit V. \c{C}ataly{\"u}rek and Jacqueline Chame and Chun Chen and Ewa Deelman and Yolanda Gil and Mary W. Hall and Vijay S. Kumar and Tahsin M. Kur\c{c} and Kristina Lerman and Aiichiro Nakano and Yoon-Ju Lee Nelson and Joel H. Saltz and Ashish Sharma and Priya Vashishta},
  title = {Intelligent Optimization of Parallel and Distributed Applications},
  booktitle = {Proceedings of the Twentyfirst International Parallel and Distributed Processing Symposium (IPDPS)},
  address = {Long Beach, CA},
  year = {2007},
  ee = {http://dx.doi.org/10.1109/IPDPS.2007.370490}
}

@inproceedings{deelman-gil-escience06,
  author = {Ewa Deelman and Yolanda Gil},
  title = {Managing Large-Scale Scientific Workflows in Distributed Environments: Experiences and Challenges},
  booktitle = {Proceedings of the Workshop on Scientific Workflows and Business Workflow Standards in e-Science of the Second International Conference on e-Science and Grid Technologies (e-Science)}, 
  address = {Amsterdam, The Netherlands},
  year = {2006},
  ee = {http://doi.ieeecomputersociety.org/10.1109/E-SCIENCE.2006.161},
  url = {http://www.isi.edu/~gil/papers/deelman-gil-escience06.pdf }
}

@inproceedings{wings-owl06,
  author = {Yolanda Gil and Jihie Kim and Varun Ratnakar and Ewa Deelman},
  title = {Wings for Pegasus: A Semantic Approach to Creating Very Large Scientific Workflows},
  booktitle = {Proceedings of the 2006 Workshop on OWL: Experiences and Directions (OWL-ED)}, 
  address = {Athens, GA},
  year = {2006},
  ee = {http://ceur-ws.org/Vol-216/submission_29.pdf},
  url = {http://www.isi.edu/~gil/papers/wings-owl06.pdf }
}

@inproceedings{kim-gil-ratnakar-iswc06,
  author = {Jihie Kim and Yolanda Gil and Varun Ratnakar},
  title = {Semantic Metadata Generation for Large Scientific Workflows},
  booktitle = {Proceedings of the Fifth International Semantic Web Conference (ISWC)},
  address = {Athens, GA},
  year = {2006},
  pages = {357-370},
  ee = {http://dx.doi.org/10.1007/11926078_26},
  url = {http://www.isi.edu/~gil/papers/kim-gil-ratnakar-iswc06.pdf }
}

@incollection {workflow-bookchapter-06, 
  title = {Workflow Composition},
  author = {Yolanda Gil},
  year = {2006},
  booktitle = {Workflows for e-Science}, 
  editors = {Dennis Gannon and Ewa Deelman and Matthew Shields and Ian Taylor (Eds)}, 
  publisher = "Springer Verlag",
  url = {http://www.isi.edu/~gil/papers/workflow-bookchapter-06.pdf }
}

@article{ maechlin-etal-sigmod05,
 title = {Simplifying Construction of Complex Workflows for Non-Expert Users of the Southern California Earthquake Center Community Modelling Environment},
 author = {P. Maechling and H. Chalupsky and M. Dougherty and E. Deelman and Y. Gil and S. Gullapalli and V. Gupta and C. Kesselman and J. Kim and G. Mehta and B. Mendenhall and T. Russ and G. Singh and M. Spraragen and G. Staples and K. Vahi},
 journal = {ACM SIGMOD Record, Special Issue on Scientific Workflows},
 volume = {34},
 number = {3}, 
 year = {2005},
 url = {http://portal.acm.org/citation.cfm?id=1084811 }
 }

@article{ deelman-etal-sp05,
 title = {Pegasus: A Framework for Mapping Complex Scientific Workflows onto Distributed Systems},
 author = {E. Deelman and G. Singh and M. Su and J. Blythe and Y. Gil and C. Kesselman and J. Kim and G. Mehta and K. Vahi and G. B. Berriman and J. Good and A. Laity and J. C. Jacob and D. S. Katz},
 journal = {Scientific Programming},
 volume = {13}, 
 number = {3},
 year = {2005}
 }

@inproceedings{blythe-etal-ccgrid05,
  author = {James Blythe and S. Jain and Ewa Deelman and Yolanda Gil and Karan Vahi and Anirban Mandal and Ken Kennedy},
  title = {Task scheduling strategies for workflow-based applications in grids},
  booktitle = {Proceedings of the Fifth International Symposium on Cluster Computing and the Grid (CCGrid)},
  address = {Cardiff, UK},
  year = {2005},
  pages = {759-767},
  ee = {http://doi.ieeecomputersociety.org/10.1109/CCGRID.2005.1558639},
}

@inproceedings{deelman-etal-axgrids04,
  author = {Ewa Deelman and James Blythe and Yolanda Gil and Carl Kesselman and Gaurang Mehta and Sonal Patil and Mei-Hui Su and Karan Vahi and Miron Livny},
  title = {Pegasus: Mapping Scientific Workflows onto the Grid},
  booktitle = {Proceedings of the Second European Across Grids Conference (AxGrids)},
  address = {Nicosia, Cyprus},
  year = {2004},
  pages = {11-20},
  ee = {http://springerlink.metapress.com/openurl.asp?genre=article{\&}issn=0302-9743{\&}volume=3165{\&}spage=11}
}

@article{blythe-etal-ieeeis04,
  author = {Jim Blythe and Ewa Deelman and Yolanda Gil},
  title = {Automatically Composed Workflows for Grid Environments},
  journal = {IEEE Intelligent Systems},
  volume = {19},
  number = {4},
  year = {2004},
  pages = {16-23},
  ee = {http://doi.ieeecomputersociety.org/10.1109/MIS.2004.24}
}

@article{ieee-is-04,
  author = {Yolanda Gil and Ewa Deelman and Jim Blythe and Carl Kesselman and Hongsuda Tangmunarunkit},
  title = {Artificial Intelligence and Grids: Workflow Planning and Beyond},
  journal = {IEEE Intelligent Systems},
  volume = {19},
  number = {1},
  year = {2004},
  pages = {26-33},
  ee = {http://csdl.computer.org/comp/mags/ex/2004/01/x1026abs.htm},
  url = {http://www.isi.edu/~gil/papers/ieee-is-04.pdf }
}

@inproceedings{iui04,
  author = {Jihie Kim and Marc Spraragen and Yolanda Gil},
  title = {An intelligent assistant for interactive workflow composition},
  booktitle = {Proceedings of the ACM International Conference on Intelligent User Interfaces}, 
  address = {Funchal, Madeira, Portugal},
  year = {2004},
  pages = {125-131},
  ee = {http://doi.acm.org/10.1145/964442.964466},
  url = {http://www.isi.edu/~gil/papers/iui04.pdf }
}

@inproceedings{deelman-etal-ppam03,
  author = {Ewa Deelman and James Blythe and Yolanda Gil and Carl Kesselman and Scott Koranda and Albert Lazzarini and Gaurang Mehta and Maria Alessandra Papa and Karan Vahi},
  title = {Pegasus and the Pulsar Search: From Metadata to Execution on the Grid},
  booktitle = {Applications Grid Workshop at the Fifth International Conference on Parallel Processing and Applied Mathematics (PPAM)},
  address = "Czestochowa, Poland",
  year = {2003},
  pages = {821-830},
  ee = {http://springerlink.metapress.com/openurl.asp?genre=article{\&}issn=0302-9743{\&}volume=3019{\&}spage=821}
}

@incollection {deelman-etal-03, 
  title = {Workflow Management in GriPhyN},
  author = {Ewa Deelman and James Blythe and Yolanda Gil and Carl Kesselman},
  year = {2003},
  booktitle = "Grid Resource Management", 
  editors = "J. Nabrzyski, J. Schopf, and J. Weglarz editors",
  publisher = "Kluwer"
}

@article{ deelman-etal-jogc03,
 title = {Mapping Abstract Workflows onto Grid Environments},
 author = {Ewa Deelman and Jim Blythe and Yolanda Gil and Carl Kesselman and Gaurang Mehta and Karan Vahi and Kent Blackburn and Albert Lazzarini and Adam Arbree and Richard Cavanaugh and Scott Koranda},
 journal = {Journal of Grid Computing}, 
 volume = {1},
 number = {1},
 year = {2003},
 url = {http://www.isi.edu/~gil/papers/deelman-etal-jogc03.pdf }
 }

@inproceedings{iaai03,
  author = {Jim Blythe and Ewa Deelman and Yolanda Gil and Carl Kesselman},
  title = {Transparent Grid Computing: A Knowledge-Based Approach},
  booktitle = {Proceedings of the Fifteenth Conference on Innovative Applications of Artificial Intelligence (IAAI)}, 
  address = {Acapulco, Mexico},
  year = {2003},
  pages = {57-64},
  url = {http://www.isi.edu/~gil/papers/iaai03.pdf }
}