{"id":234,"date":"2025-06-23T17:09:50","date_gmt":"2025-06-23T17:09:50","guid":{"rendered":"https:\/\/www.isi.edu\/isr\/?page_id=234"},"modified":"2026-04-01T22:21:49","modified_gmt":"2026-04-01T22:21:49","slug":"publications","status":"publish","type":"page","link":"https:\/\/www.isi.edu\/isr\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"\n\n\t\n
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2025<\/h2>\n \n
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\n \n Computational Grids <\/a>\n <\/h3>\n\n
\n Ian Foster, Carl Kesselman <\/div>\n \n
\n arXiv preprint arXiv:2501.01316<\/i>, 2025\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n \n
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\n \n IHMValidation: Assessment of Integrative Structure Models Deposited to the Protein Data Bank <\/a>\n <\/h3>\n\n
\n 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 Vizca\u00edno, 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 <\/div>\n \n
\n Journal of Molecular Biology, 169598<\/i>, 2025\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n \n
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\n \n It\u2019s the Data Stupid <\/a>\n <\/h3>\n\n
\n Carl Kesselman, Robert Schuler <\/div>\n \n
\n 2025 IEEE International Conference on eScience (eScience), 377-378<\/i>, 2025\n\n <\/div>\n\n <\/div>\n\n \n
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\n \n Comparison of Foundation and Supervised Learning-Based Models for Detection of Referable Glaucoma from Fundus Photographs <\/a>\n <\/h3>\n\n
\n Kyle Bolo, Tran Huy Nguyen, Sreenidhi Iyengar, Zhiwei Li, Van Nguyen, Brandon Wong, Jiun Do, Jose-Luis Ambite, Carl Kesselman, Lauren Daskivich, Benjamin Xu <\/div>\n \n
\n medRxiv.08. 21.25334170<\/i>, 2025\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n \n
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\n \n Comparison of Deep Learning and Clinician Performance for Detecting Referable Glaucoma from Fundus Photographs in a Safety Net Population <\/a>\n <\/h3>\n\n
\n 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 <\/div>\n \n
\n Ophthalmology Science 5 (4), 100751<\/i>, 2025\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n \n
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\n \n From Data to Decision: Data-Centric Infrastructure for Reproducible ML in Collaborative eScience <\/a>\n <\/h3>\n\n
\n Zhiwei Li, Carl Kesselman, Tran Huy Nguyen, Benjamin Yixing Xu, Kyle Bolo, Kimberley Yu <\/div>\n \n
\n arXiv preprint arXiv:2506.16051<\/i>, 2025\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n \n
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\n \n PDB-IHM: A system for deposition, curation, validation, and dissemination of integrative structures <\/a>\n <\/h3>\n\n
\n 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 <\/div>\n \n
\n Journal of Molecular Biology, 168963<\/i>, 2025\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n

2024<\/h2>\n \n
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\n \n Development and Validation of a Deep Learning Algorithm to Automate Detection of Referable Glaucoma in a Safety Net Teleretinal Program <\/a>\n <\/h3>\n\n
\n 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 <\/div>\n \n
\n Investigative Ophthalmology & Visual Science 65 (7), 372-372<\/i>, 2024\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n \n
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\n \n Deriva-ML: A Continuous FAIRness Approach to Reproducible Machine Learning Models <\/a>\n <\/h3>\n\n
\n Zhiwei Li, Carl Kesselman, Mike D\u2019Arcy, Michael Pazzani, Benjamin Yizing Xu <\/div>\n \n
\n 2024 IEEE 20th International Conference on e-Science (e-Science), 1-10<\/i>, 2024\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n \n
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\n \n IHMCIF: an extension of the PDBx\/mmCIF data standard for integrative structure determination methods <\/a>\n <\/h3>\n\n
\n 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 <\/div>\n \n
\n Journal of molecular biology, 168546<\/i>, 2024\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n \n
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\n \n Creating Thriving Data-Centric Communities from Basic Research to Commercial Applications <\/a>\n <\/h3>\n\n
\n Robert Schuler, Carl Kesselman <\/div>\n \n
\n 2024 IEEE 20th International Conference on e-Science (e-Science), 1-3<\/i>, 2024\n\n <\/div>\n\n <\/div>\n\n

2023<\/h2>\n \n
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\n \n MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses (vol 9, 230, 2022) <\/a>\n <\/h3>\n\n
\n 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 <\/div>\n \n
\n SCIENTIFIC DATA 10 (1)<\/i>, 2023\n\n <\/div>\n\n <\/div>\n\n \n
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\n \n PDB-Dev: A prototype system for archiving integrative structures <\/a>\n <\/h3>\n\n
\n 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 <\/div>\n \n
\n ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 79, C72-C72<\/i>, 2023\n\n <\/div>\n\n <\/div>\n\n \n
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\n \n Reproducible big data science: A case study in continuous FAIRness (vol 14, e0213013, 2019) <\/a>\n <\/h3>\n\n
\n 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 <\/div>\n \n
\n PLOS ONE 18 (11)<\/i>, 2023\n\n <\/div>\n\n <\/div>\n\n \n
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\n \n Correction: Reproducible big data science: A case study in continuous FAIRness <\/a>\n <\/h3>\n\n
\n Ravi Madduri, Kyle Chard, Mike D\u2019Arcy, 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 <\/div>\n \n
\n Plos one 18 (11), e0294883<\/i>, 2023\n\n <\/div>\n\n <\/div>\n\n \n
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\n \n Let's Put the Science in eScience <\/a>\n <\/h3>\n\n
\n Carl Kesselman, Robert Schuler, Ian Foster <\/div>\n \n
\n 2023 IEEE 19th International Conference on e-Science (e-Science), 1-3<\/i>, 2023\n\n <\/div>\n\n <\/div>\n\n \n
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\n \n Database Evolution, by Scientists, for Scientists: A Case Study <\/a>\n <\/h3>\n\n
\n Robert E Schuler, Jitin Singla, Brinda Vallat, Kate L White, Helen M Berman, Carl Kesselman <\/div>\n \n
\n 2023 IEEE 19th International Conference on e-Science (e-Science), 1-10<\/i>, 2023\n\n <\/div>\n\n <\/div>\n\n \n
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\n \n Author Correction: MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses <\/a>\n <\/h3>\n\n
\n Jay Devine, Marta Vidal-Garc\u00eda, 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 Hallgr\u00edmsson <\/div>\n \n
\n Scientific data 10 (1), 420<\/i>, 2023\n\n <\/div>\n\n <\/div>\n\n

2022<\/h2>\n \n
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\n \n Sharing begins at home <\/a>\n <\/h3>\n\n
\n William Dempsey, Ian Foster, Scott Fraser, Carl Kesselman <\/div>\n \n
\n arXiv preprint arXiv:2201.06564<\/i>, 2022\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n \n
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\n \n CUF-Links: Continuous and Ubiquitous FAIRness Linkages for Reproducible Research <\/a>\n <\/h3>\n\n
\n Ian Foster, Carl Kesselman <\/div>\n \n
\n Computer 55 (8), 20-30<\/i>, 2022\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n \n <\/div>\n\n