Publications
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
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
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
It’s the Data Stupid
Carl Kesselman, Robert Schuler
2025 IEEE International Conference on eScience (eScience), 377-378, 2025
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
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
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
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
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
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
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
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
2022
Managing Database-Application Co-Evolution in a Scientific Data Ecosystem
Robert E Schuler, Carl Kesselman
2022 IEEE 18th International Conference on e-Science (e-Science), 214-224, 2022
FaceBase: a community-driven hub for data-intensive research
RE Schuler, A Bugacov, JG Hacia, TV Ho, J Iwata, L Pearlman, BD Samuels, C Williams, Z Zhao, C Kesselman, Y Chai
Journal of Dental Research 101 (11), 1289-1298, 2022
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 9 (1), 230, 2022
Making Common Fund data more findable: catalyzing a data ecosystem
Amanda L Charbonneau, Arthur Brady, Karl Czajkowski, Jain Aluvathingal, Saranya Canchi, Robert Carter, Kyle Chard, Daniel JB Clarke, Jonathan Crabtree, Heather H Creasy, Mike D'Arcy, Victor Felix, Michelle Giglio, Alicia Gingrich, Rayna M Harris, Theresa K Hodges, Olukemi Ifeonu, Minji Jeon, Eryk Kropiwnicki, Marisa CW Lim, R Lee Liming, Jessica Lumian, Anup A Mahurkar, Meisha Mandal, James B Munro, Suvarna Nadendla, Rudyard Richter, Cia Romano, Philippe Rocca-Serra, Michael Schor, Robert E Schuler, Hongsuda Tangmunarunkit, Alex Waldrop, Cris Williams, Karen Word, Susanna-Assunta Sansone, Avi Ma'ayan, Rick Wagner, Ian Foster, Carl Kesselman, C Titus Brown, Owen White
GigaScience 11, giac105, 2022