Publications

2025

Computational Grids

Ian Foster, Carl Kesselman
arXiv preprint arXiv:2501.01316, 2025

IHMValidation: Assessment of Integrative Structure Models Deposited to the Protein Data Bank

Arthur O Zalevsky, Brinda Vallat, Benjamin M Webb, Hongsuda Tangmunarunkit, Monica R Sekharan, Aref Shafaeibejestan, Sai Ganesan, Jared Sagendorf, Cy M Jeffries, Jill Trewhella, Andrea Graziadei, Juan Antonio Vizcaíno, Alexander Leitner, Juri Rappsilber, Ezra Peisach, Justin W Flatt, Jasmine Y Young, Kartik Majila, Shruthi Viswanath, Carl Kesselman, Jeffrey C Hoch, Genji Kurisu, Kyle L Morris, Sameer Velankar, Helen M Berman, Stephen K Burley, Andrej Sali
Journal of Molecular Biology, 169598, 2025

It’s the Data Stupid

Carl Kesselman, Robert Schuler
2025 IEEE International Conference on eScience (eScience), 377-378, 2025

Comparison of Foundation and Supervised Learning-Based Models for Detection of Referable Glaucoma from Fundus Photographs

Kyle Bolo, Tran Huy Nguyen, Sreenidhi Iyengar, Zhiwei Li, Van Nguyen, Brandon Wong, Jiun Do, Jose-Luis Ambite, Carl Kesselman, Lauren Daskivich, Benjamin Xu
medRxiv.08. 21.25334170, 2025

Comparison of Deep Learning and Clinician Performance for Detecting Referable Glaucoma from Fundus Photographs in a Safety Net Population

Van Nguyen, Sreenidhi Iyengar, Haroon Rasheed, Galo Apolo, Zhiwei Li, Aniket Kumar, Hong Nguyen, Austin Bohner, Kyle Bolo, Rahul Dhodapkar, Jiun Do, Andrew T Duong, Jeffrey Gluckstein, Kendra Hong, Lucas L Humayun, Alanna James, Junhui Lee, Kent Nguyen, Brandon J Wong, Jose-Luis Ambite, Carl Kesselman, Lauren P Daskivich, Michael Pazzani, Benjamin Y Xu
Ophthalmology Science 5 (4), 100751, 2025

From Data to Decision: Data-Centric Infrastructure for Reproducible ML in Collaborative eScience

Zhiwei Li, Carl Kesselman, Tran Huy Nguyen, Benjamin Yixing Xu, Kyle Bolo, Kimberley Yu
arXiv preprint arXiv:2506.16051, 2025

PDB-IHM: A system for deposition, curation, validation, and dissemination of integrative structures

Brinda Vallat, Benjamin M Webb, Arthur Zalevsky, Hongsuda Tangmunarunkit, Monica R Sekharan, Serban Voinea, Aref Shafaeibejestan, Jared Sagendorf, Jeffrey C Hoch, Genji Kurisu, Kyle L Morris, Sameer Velankar, Carl Kesselman, Stephen K Burley, Helen M Berman, Andrej Sali
Journal of Molecular Biology, 168963, 2025

2024

Development and Validation of a Deep Learning Algorithm to Automate Detection of Referable Glaucoma in a Safety Net Teleretinal Program

Haroon Rasheed, Sreenidhi Iyengar, Van Nguyen, Zhiwei Li, Aniket Kumar, Aidan Lee, Andrew Duong, Brandon Wong, Jeffrey Gluckstein, Kendra Hong, Kent Nguyen, Rahul Dhodapkar, Carl Kesselman, Lauren Daskivich, Michael Pazzani, Benjamin Y Xu
Investigative Ophthalmology & Visual Science 65 (7), 372-372, 2024

Deriva-ML: A Continuous FAIRness Approach to Reproducible Machine Learning Models

Zhiwei Li, Carl Kesselman, Mike D’Arcy, Michael Pazzani, Benjamin Yizing Xu
2024 IEEE 20th International Conference on e-Science (e-Science), 1-10, 2024

IHMCIF: an extension of the PDBx/mmCIF data standard for integrative structure determination methods

Brinda Vallat, Benjamin M Webb, John D Westbrook, Thomas D Goddard, Christian A Hanke, Andrea Graziadei, Ezra Peisach, Arthur Zalevsky, Jared Sagendorf, Hongsuda Tangmunarunkit, Serban Voinea, Monica Sekharan, Jian Yu, Alexander AMJJ Bonvin, Frank DiMaio, Gerhard Hummer, Jens Meiler, Emad Tajkhorshid, Thomas E Ferrin, Catherine L Lawson, Alexander Leitner, Juri Rappsilber, Claus AM Seidel, Cy M Jeffries, Stephen K Burley, Jeffrey C Hoch, Genji Kurisu, Kyle Morris, Ardan Patwardhan, Sameer Velankar, Torsten Schwede, Jill Trewhella, Carl Kesselman, Helen M Berman, Andrej Sali
Journal of molecular biology, 168546, 2024

Creating Thriving Data-Centric Communities from Basic Research to Commercial Applications

Robert Schuler, Carl Kesselman
2024 IEEE 20th International Conference on e-Science (e-Science), 1-3, 2024

2023

MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses (vol 9, 230, 2022)

Jay Devine, Marta Vidal-Garcia, Wei Liu, Amanda Neves, Lucas D Lo Vercio, Rebecca M Green, Heather A Richbourg, Marta Marchini, Colton M Unger, Audrey C Nickle, Bethany Radford, Nathan M Young, Paula N Gonzalez, Robert E Schuler, Alejandro Bugacov, Campbell Rolian, Christopher J Percival, Trevor Williams, Lee Niswander, Anne L Calof, Arthur D Lander, Axel Visel, Frank R Jirik, James M Cheverud, Ophir D Klein, Ramon Y Birnbaum, Amy E Merrill, Rebecca R Ackermann, Daniel Graf, Myriam Hemberger, Wendy Dean, Nils D Forkert, Stephen A Murray, Henrik Westerberg, Ralph S Marcucio, Benedikt Hallgrimsson
SCIENTIFIC DATA 10 (1), 2023

PDB-Dev: A prototype system for archiving integrative structures

Brinda Vallat, Benjamin Webb, Arthur Zalevsky, Serban Voinea, Hongsuda Tangmunarunkit, Monica Sekharan, John D Westbrook, Carl Kesselman, Stephen K Burley, Helen M Berman, Andrej Sali
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 79, C72-C72, 2023

Reproducible big data science: A case study in continuous FAIRness (vol 14, e0213013, 2019)

Ravi Madduri, Kyle Chard, Mike D'Arcy, Segun C Jung, Alexis Rodriguez, Dinanath Sulakhe, Eric Deutsch, Cory Funk, Ben Heavner, Matthew Richards, Paul Shannon, Gustavo Glusman, Nathan Price, Carl Kesselman, Ian Foster
PLOS ONE 18 (11), 2023

Correction: Reproducible big data science: A case study in continuous FAIRness

Ravi Madduri, Kyle Chard, Mike D’Arcy, Segun C Jung, Alexis Rodriguez, Dinanath Sulakhe, Eric Deutsch, Cory Funk, Ben Heavner, Matthew Richards, Paul Shannon, Gustavo Glusman, Nathan Price, Carl Kesselman, Ian Foster
Plos one 18 (11), e0294883, 2023

Let's Put the Science in eScience

Carl Kesselman, Robert Schuler, Ian Foster
2023 IEEE 19th International Conference on e-Science (e-Science), 1-3, 2023

Database Evolution, by Scientists, for Scientists: A Case Study

Robert E Schuler, Jitin Singla, Brinda Vallat, Kate L White, Helen M Berman, Carl Kesselman
2023 IEEE 19th International Conference on e-Science (e-Science), 1-10, 2023

Author Correction: MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses

Jay Devine, Marta Vidal-García, Wei Liu, Amanda Neves, Lucas D Lo Vercio, Rebecca M Green, Heather A Richbourg, Marta Marchini, Colton M Unger, Audrey C Nickle, Bethany Radford, Nathan M Young, Paula N Gonzalez, Robert E Schuler, Alejandro Bugacov, Campbell Rolian, Christopher J Percival, Trevor Williams, Lee Niswander, Anne L Calof, Arthur D Lander, Axel Visel, Frank R Jirik, James M Cheverud, Ophir D Klein, Ramon Y Birnbaum, Amy E Merrill, Rebecca R Ackermann, Daniel Graf, Myriam Hemberger, Wendy Dean, Nils D Forkert, Stephen A Murray, Henrik Westerberg, Ralph S Marcucio, Benedikt Hallgrímsson
Scientific data 10 (1), 420, 2023

2022

Sharing begins at home

William Dempsey, Ian Foster, Scott Fraser, Carl Kesselman
arXiv preprint arXiv:2201.06564, 2022

CUF-Links: Continuous and Ubiquitous FAIRness Linkages for Reproducible Research

Ian Foster, Carl Kesselman
Computer 55 (8), 20-30, 2022