Publications

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

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

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

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

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

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

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

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

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