An approach for pipelining nested collections in scientific workflows. - Timothy M. McPhillips; Shawn Bowers (SIGMOD Rec., 2005)

Collection-Oriented Scientific Workflows for Integrating and Analyzing Biological Data. - Timothy M. McPhillips; Shawn Bowers; Bertram Ludäscher (DILS, 2006)

Scientific Workflows: More e-Science Mileage from Cyberinfrastructure. - Bertram Ludäscher; Shawn Bowers; Timothy M. McPhillips; Norbert Podhorszki (e-Science, 2006)

A Model for User-Oriented Data Provenance in Pipelined Scientific Workflows. - Shawn Bowers; Timothy M. McPhillips; Bertram Ludäscher; Shirley Cohen; Susan B. Davidson (IPAW, 2006)

Project Histories: Managing Data Provenance Across Collection-Oriented Scientific Workflow Runs. - Shawn Bowers; Timothy M. McPhillips; Martin Wu; Bertram Ludäscher (DILS, 2007)

Provenance in Scientific Workflow Systems. - Susan B. Davidson; Sarah Cohen Boulakia; Anat Eyal; Bertram Ludäscher; Timothy M. McPhillips; Shawn Bowers; Manish Kumar Anand; Juliana Freire (IEEE Data Eng. Bull., 2007)

Kepler/pPOD: Scientific Workflow and Provenance Support for Assembling the Tree of Life. - Shawn Bowers; Timothy M. McPhillips; Sean Riddle; Manish Kumar Anand; Bertram Ludäscher (IPAW, 2008)

Flexible Scientific Workflow Modeling Using Frames, Templates, and Dynamic Embedding. - Anne H. H. Ngu; Shawn Bowers; Nicholas Haasch; Timothy M. McPhillips; Terence Critchlow (SSDBM, 2008)

Provenance in collection-oriented scientific workflows. - Shawn Bowers; Timothy M. McPhillips; Bertram Ludäscher (Concurr. Comput. Pract. Exp., 2008)

From computation models to models of provenance: the RWS approach. - Bertram Ludäscher; Norbert Podhorszki; Ilkay Altintas; Shawn Bowers; Timothy M. McPhillips (Concurr. Comput. Pract. Exp., 2008)

Special Issue: The First Provenance Challenge. - Luc Moreau 001; Bertram Ludäscher; Ilkay Altintas; Roger S. Barga; Shawn Bowers; Steven P. Callahan; George Chin Jr.; Ben Clifford; Shirley Cohen; Sarah Cohen Boulakia; Susan B. Davidson; Ewa Deelman; et al. (Concurr. Comput. Pract. Exp., 2008)

Scientific Process Automation and Workflow Management. - Bertram Ludäscher; Ilkay Altintas; Shawn Bowers; Julian Cummings; Terence Critchlow; Ewa Deelman; David De Roure; Juliana Freire; Carole A. Goble; Matthew B. Jones; Scott Klasky; Timothy M. McPhillips; et al. (Scientific Data Management, 2009)

Scientific Workflows: Business as Usual? - Bertram Ludäscher; Mathias Weske; Timothy M. McPhillips; Shawn Bowers (BPM, 2009)

Efficient provenance storage over nested data collections. - Manish Kumar Anand; Shawn Bowers; Timothy M. McPhillips; Bertram Ludäscher (EDBT, 2009)

X-CSR: Dataflow Optimization for Distributed XML Process Pipelines. - Daniel Zinn; Shawn Bowers; Timothy M. McPhillips; Bertram Ludäscher (ICDE, 2009)

Scientific workflow design with data assembly lines. - Daniel Zinn; Shawn Bowers; Timothy M. McPhillips; Bertram Ludäscher (SC-WORKS, 2009)

Exploring Scientific Workflow Provenance Using Hybrid Queries over Nested Data and Lineage Graphs. - Manish Kumar Anand; Shawn Bowers; Timothy M. McPhillips; Bertram Ludäscher (SSDBM, 2009)

Scientific workflow design for mere mortals. - Timothy M. McPhillips; Shawn Bowers; Daniel Zinn; Bertram Ludäscher (Future Gener. Comput. Syst., 2009)

Scientific Workflows. - Bertram Ludäscher; Shawn Bowers; Timothy M. McPhillips (Encyclopedia of Database Systems, 2009)

WATERS: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences. - Amber L. Hartman; Sean Riddle; Timothy M. McPhillips; Bertram Ludäscher; Jonathan A. Eisen (BMC Bioinform., 2010)

Towards Reliable, Performant Workflows for Streaming-Applications on Cloud Platforms. - Daniel Zinn; Quinn J. Hart; Timothy M. McPhillips; Bertram Ludäscher; Yogesh Simmhan; Michail Giakkoupis; Viktor K. Prasanna (CCGRID, 2011)

Scientific workflow design 2.0: Demonstrating streaming data collections in Kepler. - Lei Dou; Daniel Zinn; Timothy M. McPhillips; Sven Köhler 003; Sean Riddle; Shawn Bowers; Bertram Ludäscher (ICDE, 2011)

Improving Workflow Fault Tolerance through Provenance-Based Recovery. - Sven Köhler 003; Sean Riddle; Daniel Zinn; Timothy M. McPhillips; Bertram Ludäscher (SSDBM, 2011)

Declarative Rules for Inferring Fine-Grained Data Provenance from Scientific Workflow Execution Traces. - Shawn Bowers; Timothy M. McPhillips; Bertram Ludäscher (IPAW, 2012)

Workflows for microarray data processing in the Kepler environment. - Thomas Stropp; Timothy M. McPhillips; Bertram Ludäscher; Mark Bieda (BMC Bioinform., 2012)

Golden Trail: Retrieving the Data History that Matters from a Comprehensive Provenance Repository. - Paolo Missier; Bertram Ludäscher; Saumen C. Dey; Michael Wang; Timothy M. McPhillips; Shawn Bowers; Michael Agun; Ilkay Altintas (Int. J. Digit. Curation, 2012)

Retrospective Provenance Without a Runtime Provenance Recorder. - Timothy M. McPhillips; Shawn Bowers; Khalid Belhajjame; Bertram Ludäscher (TaPP, 2015)

YesWorkflow: A User-Oriented, Language-Independent Tool for Recovering Workflow Information from Scripts. - Timothy M. McPhillips; Tianhong Song; Tyler Kolisnik; Steve Aulenbach; Khalid Belhajjame; R. Kyle Bocinsky; Yang Cao; Fernando Chirigati; Saumen C. Dey; Juliana Freire; Deborah N. Huntzinger; Christopher Jones; et al. (CoRR, 2015)

DataONE: A Data Federation with Provenance Support. - Yang Cao; Christopher Jones; Víctor Cuevas-Vicenttín; Matthew B. Jones; Bertram Ludäscher; Timothy M. McPhillips; Paolo Missier; Christopher R. Schwalm; Peter Slaughter; David Vieglais; Lauren Walker; Yaxing Wei (IPAW, 2016)

Yin & Yang: Demonstrating Complementary Provenance from noWorkflow & YesWorkflow. - João Felipe Pimentel; Saumen C. Dey; Timothy M. McPhillips; Khalid Belhajjame; David Koop; Leonardo Murta 001; Vanessa Braganholo; Bertram Ludäscher (IPAW, 2016)

Revealing the Detailed Lineage of Script Outputs Using Hybrid Provenance. - Qian Zhang 022; Yang Cao; Qiwen Wang; Duc Vu; Priyaa Thavasimani; Timothy M. McPhillips; Paolo Missier; Peter Slaughter; Christopher Jones; Matthew B. Jones; Bertram Ludäscher (Int. J. Digit. Curation, 2017)

Validation and Inference of Schema-Level Workflow Data-Dependency Annotations. - Shawn Bowers; Timothy M. McPhillips; Bertram Ludäscher (IPAW, 2018)

Scientific Workflows. - Bertram Ludäscher; Shawn Bowers; Timothy M. McPhillips (Encyclopedia of Database Systems (2nd ed.), 2018)

Application of BagIt-Serialized Research Object Bundles for Packaging and Re-Execution of Computational Analyses. - Kyle Chard; Thomas Thelen; Matthew J. Turk; Craig Willis; Niall Gaffney; Matthew B. Jones; Kacper Kowalik; Bertram Ludäscher; Timothy M. McPhillips; Jarek Nabrzyski; Victoria Stodden; Ian J. Taylor (eScience, 2019)

Reproducibility by Other Means: Transparent Research Objects. - Timothy M. McPhillips; Craig Willis; Michael R. Gryk; Santiago Núñez-Corrales; Bertram Ludäscher (eScience, 2019)

Toward Enabling Reproducibility for Data-Intensive Research Using the Whole Tale Platform. - Kyle Chard; Niall Gaffney; Mihael Hategan; Kacper Kowalik; Bertram Ludäscher; Timothy M. McPhillips; Jarek Nabrzyski; Victoria Stodden; Ian J. Taylor; Thomas Thelen; Matthew J. Turk; Craig Willis (PARCO, 2019)

Modeling Provenance and Understanding Reproducibility for OpenRefine Data Cleaning Workflows. - Timothy M. McPhillips; Lan Li 002; Nikolaus Nova Parulian; Bertram Ludäscher (TaPP, 2019)

CPR-A Comprehensible Provenance Record for Verification Workflows in Whole Tale. - Timothy M. McPhillips; Thomas Thelen; Craig Willis; Kacper Kowalik; Matthew B. Jones; Bertram Ludäscher (IPAW, 2021)

A Model and System for Querying Provenance from Data Cleaning Workflows. - Nikolaus Nova Parulian; Timothy M. McPhillips; Bertram Ludäscher (IPAW, 2021)

Detailed Provenance Metadata from Statistical Analysis Software: TaPP Applications Track. - George Alter; Jack Gager; Pascal Heus; Carson Hunter; Sanda Ionescu; Jeremy Iverson; H. V. Jagadish; Bertram Ludäscher; Jared Lyle; Timothy M. McPhillips; Alexander Mueller; Sigve Nordgaard; et al. (TaPP, 2021)

Synthesizing Knowledge of Past Environments (SKOPE) Web Application. - R. Kyle Bocinsky; Andrew Gillreath-Brown; Keith Kintigh; Ann Kinzig; Tim Kohler; Allen Lee; Bertram Ludäscher; Timothy M. McPhillips; Christine Nguyen; Calvin Pritchard (Zenodo, 2022)

Synthesizing Knowledge of Past Environments (SKOPE) Web Application. - R. Kyle Bocinsky; Andrew Gillreath-Brown; Keith Kintigh; Ann Kinzig; Tim Kohler; Allen Lee; Bertram Ludäscher; Timothy M. McPhillips; Christine Nguyen; Calvin Pritchard (Zenodo, 2022)

Synthesizing Knowledge of Past Environments (SKOPE) Web Application. - R. Kyle Bocinsky; Andrew Gillreath-Brown; Keith Kintigh; Ann Kinzig; Tim Kohler; Allen Lee; Bertram Ludäscher; Timothy M. McPhillips; Christine Nguyen; Calvin Pritchard (Zenodo, 2023)

Synthesizing Knowledge of Past Environments (SKOPE) Web Application. - R. Kyle Bocinsky; Andrew Gillreath-Brown; Keith Kintigh; Ann Kinzig; Tim Kohler; Allen Lee; Bertram Ludäscher; Timothy M. McPhillips (Zenodo, 2023)

TROV - A Model and Vocabulary for Describing Transparent Research Objects. - Meng Li; Timothy M. McPhillips; Craig Willis; Nikolaus Nova Parulian; Bertram Ludäscher; Kacper Kowalik; Lars Vilhuber; Thu-Mai Lewis; Mandy Gooch (Int. J. Digit. Curation, 2025)

CRABS: A syntactic-semantic pincer strategy for bounding LLM interpretation of Python notebooks. - Meng Li; Timothy M. McPhillips; Dingmin Wang; Shin-Rong Tsai; Bertram Ludäscher (CoRR, 2025)