Publications
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
CUF-Links: Continuous and Ubiquitous FAIRness Linkages for Reproducible Research
Ian Foster, Carl Kesselman
Computer 55 (8), 20-30, 2022
Kidney repair and regeneration: perspectives of the NIDDK (Re) Building a Kidney consortium
Bilal A Naved, Joseph V Bonventre, Jeffrey A Hubbell, Neil A Hukriede, Benjamin D Humphreys, Carl Kesselman, M Todd Valerius, Andrew P McMahon, Stuart J Shankland, Jason A Wertheim, Michael JV White, Mark P de Caestecker, Iain A Drummond
Kidney international 101 (5), 845-853, 2022
Regional synapse gain and loss accompany memory formation in larval zebrafish
William P Dempsey, Zhuowei Du, Anna Nadtochiy, Colton D Smith, Karl Czajkowski, Andrey Andreev, Drew N Robson, Jennifer M Li, Serina Applebaum, Thai V Truong, Carl Kesselman, Scott E Fraser, Don B Arnold
Proceedings of the National Academy of Sciences 119 (3), e2107661119, 2022
Sharing begins at home: How continuous and ubiquitous FAIRness can enhance research productivity and data reuse
William Dempsey, Ian Foster, Scott Fraser, Carl Kesselman
Harvard data science review 4 (3), 2022
2021
Model-Adaptive Interface Generation for Data-Driven Discovery
Hongsuda Tangmunarunkit, Aref Shafaeibejestan, Joshua Chudy, Karl Czajkowski, Robert Schuler, Carl Kesselman
arXiv preprint arXiv:2110.01781, 2021
CHiSEL: a user-oriented framework for simplifing database evolution
Robert Schuler, Carl Kesselman
Distributed and Parallel Databases 39 (2), 483-543, 2021
New system for archiving integrative structures
Brinda Vallat, Benjamin Webb, Maryam Fayazi, Serban Voinea, Hongsuda Tangmunarunkit, Sai J Ganesan, Catherine L Lawson, John D Westbrook, Carl Kesselman, Andrej Sali, Helen M Berman
Acta Crystallographica Section D: Structural Biology 77 (12), 1486-1496, 2021
Translating the grid: How a translational approach shaped the development of grid computing
Ian Foster, Carl Kesselman
Journal of Computational Science 52, 101214, 2021
Archiving Integrative Structural Models
Brinda Vallat, Benjamin Webb, John Westbrook, Hongsuda Tangmunarunkit, Serban Voinea, Carl Kesselman, Andrej Sali, Helen M Berman
Biophysical Journal 120 (3), 266a, 2021
Bayesian metamodeling of complex biological systems across varying representations
Barak Raveh, Liping Sun, Kate L White, Tanmoy Sanyal, Jeremy Tempkin, Dongqing Zheng, Kala Bharath, Jitin Singla, ChenXi Wang, Jihui Zhao, Angdi Li, Nicholas A Graham, Carl Kesselman, Raymond C Stevens, Andrej Sali
Proceedings of the National Academy of Sciences 118 (35), e2104559118, 2021
2020
FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research
Bridget D Samuels, Robert Aho, James F Brinkley, Alejandro Bugacov, Eleanor Feingold, Shannon Fisher, Ana S Gonzalez-Reiche, Joseph G Hacia, Benedikt Hallgrimsson, Karissa Hansen, Matthew P Harris, Thach-Vu Ho, Greg Holmes, Joan E Hooper, Ethylin Wang Jabs, Kenneth L Jones, Carl Kesselman, Ophir D Klein, Elizabeth J Leslie, Hong Li, Eric C Liao, Hannah Long, Na Lu, Richard L Maas, Mary L Marazita, Jaaved Mohammed, Sara Prescott, Robert Schuler, Licia Selleri, Richard A Spritz, Tomek Swigut, Harm van Bakel, Axel Visel, Ian Welsh, Cristina Williams, Trevor J Williams, Joanna Wysocka, Yuan Yuan, Yang Chai
Development 147 (18), dev191213, 2020
An Open Ecosystem for Pervasive Use of Persistent Identifiers
Rachana Ananthakrishnan, Kyle Chard, Mike D'Arcy, Ian Foster, Carl Kesselman, Brendan McCollam, Jim Pruyne, Philippe Rocca-Serra, Robert Schuler, Rick Wagner
Practice and Experience in Advanced Research Computing, 99-105, 2020
Towards co-evolution of data-centric ecosystems
Robert Schuler, Karl Czajkowski, Mike D'Arcy, Hongsuda Tangmunarunkit, Carl Kesselman
Proceedings of the 32nd International Conference on Scientific and …, 2020
Model-Adaptive User Interfaces For Collaborative Scientific Data Management
Hongsuda Tangmunarunkit, Aref Shafaeibejestan, Joshua Chudy, Karl Czajkowski, Robert Schuler, Carl Kesselman
2020
Atlas of transcription factor binding sites from ENCODE DNase hypersensitivity data across 27 tissue types
Cory C Funk, Alex M Casella, Segun Jung, Matthew A Richards, Alex Rodriguez, Paul Shannon, Rory Donovan-Maiye, Ben Heavner, Kyle Chard, Yukai Xiao, Gustavo Glusman, Nilufer Ertekin-Taner, Todd E Golde, Arthur Toga, Leroy Hood, John D Van Horn, Carl Kesselman, Ian Foster, Ravi Madduri, Nathan D Price, Seth A Ament
Cell reports 32 (7), 2020
CC* Compute: A Customizable, Reproducible, and Secure Cloud Infrastructure as a Service for Scientific Research in Southern California
Carl F Kesselman
NSF Award Number 2019220. Directorate for Computer and Information Science …, 2020
2019
Toward FAIR Knowledge Turns in Bioinformatics
Robert Schuler, Alejandro Bugacov, Matthew Blow, Carl Kesselman
2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM …, 2019
A high-level user-oriented framework for database evolution
Robert E Schuler, Carl Kessleman
Proceedings of the 31st International Conference on Scientific and …, 2019
Computational operations research exchange (core): A cyber-infrastructure for analytics
Yunxiao Deng, Carl Kesselman, Suvrajeet Sen, Jiajun Xu
2019 Winter Simulation Conference (WSC), 3447-3456, 2019