Publications

2019

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 14 (4), e0213013, 2019

Big Data Bags: A Scalable Packaging Format for Science.

Mike D'Arcy, Kyle Chard, Ian T Foster, Carl Kesselman, Ravi K Madduri, Nickolaus D Saint, Rick Wagner
RO, 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

2018

Neuroanatomical morphometric characterization of sex differences in youth using statistical learning

Farshid Sepehrband, Kirsten M Lynch, Ryan P Cabeen, Clio Gonzalez-Zacarias, Lu Zhao, Mike D'Arcy, Carl Kesselman, Megan M Herting, Ivo D Dinov, Arthur W Toga, Kristi A Clark
Neuroimage 172, 217-227, 2018

BDQC: a general-purpose analytics tool for domain-blind validation of Big Data

Eric W Deutsch, Roger Kramer, Joseph Ames, Andrew Bauman, David S Campbell, Kyle Chard, Kristi Clark, Mike D’Arcy, Ivo D Dinov, Rory Donovan, Ian Foster, Benjamin D Heavner, Leroy E Hood, Carl Kesselman, Ravi Madduri, Huaiyu Mi, Anushya Muruganujan, Judy Pa, Nathan D Price, Max Robinson, Farshid Sepehrband, Arthur W Toga, John Van Horn, Lu Zhao, Gustavo Glusman
bioRxiv, 258822, 2018

Towards an efficient and effective framework for the evolution of scientific databases

Robert E Schuler, Carl Kesselman
Proceedings of the 30th International Conference on Scientific and …, 2018

Ermrest: a web service for collaborative data management

Karl Czajkowski, Carl Kesselman, Robert E Schuler, Hongsuda Tangmunarunkit
Proceedings of the 30th International Conference on Scientific and …, 2018

Conserved and divergent features of human and mouse kidney organogenesis

Nils O Lindström, Jill A McMahon, Jinjin Guo, Tracy Tran, Qiuyu Guo, Elisabeth Rutledge, Riana K Parvez, Gohar Saribekyan, Robert E Schuler, Christopher Liao, Albert D Kim, Ahmed Abdelhalim, Seth W Ruffins, Matthew E Thornton, Laurence Basking, Brendan Grubbs, Carl Kesselman, Andrew P McMahon
Journal of the American Society of Nephrology 29 (3), 785-805, 2018

2017

(Re) Building a kidney

Leif Oxburgh, Thomas J Carroll, Ondine Cleaver, Daniel R Gossett, Deborah K Hoshizaki, Jeffrey A Hubbell, Benjamin D Humphreys, Sanjay Jain, Jan Jensen, David L Kaplan, Carl Kesselman, Christian J Ketchum, Melissa H Little, Andrew P McMahon, Stuart J Shankland, Jason R Spence, M Todd Valerius, Jason A Wertheim, Oliver Wessely, Ying Zheng, Iain A Drummond
Journal of the American Society of Nephrology 28 (5), 1370-1378, 2017

Experiences with DERIVA: An asset management platform for accelerating eScience

Alejandro Bugacov, Karl Czajkowski, Carl Kesselman, Anoop Kumar, Robert E Schuler, Hongsuda Tangmunarunkit
2017 IEEE 13th International Conference on e-Science (e-Science), 79-88, 2017

ERMREST: A collaborative data catalog with fine grain access control

Karl Czajkowski, Carl Kesselman, Robert Schuler
2017 Ieee 13th international conference on E-science (E-science), 510-517, 2017

2016

MultiCellDS: a standard and a community for sharing multicellular data

Samuel H Friedman, Alexander RA Anderson, David M Bortz, Alexander G Fletcher, Hermann B Frieboes, Ahmadreza Ghaffarizadeh, David Robert Grimes, Andrea Hawkins-Daarud, Stefan Hoehme, Edwin F Juarez, Carl Kesselman, Roeland MH Merks, Shannon M Mumenthaler, Paul K Newton, Kerri-Ann Norton, Rishi Rawat, Russell C Rockne, Daniel Ruderman, Jacob Scott, Suzanne S Sindi, Jessica L Sparks, Kristin Swanson, David B Agus, Paul Macklin
bioRxiv, 090696, 2016

I'll take that to go: Big data bags and minimal identifiers for exchange of large, complex datasets

Kyle Chard, Mike D'Arcy, Ben Heavner, Ian Foster, Carl Kesselman, Ravi Madduri, Alexis Rodriguez, Stian Soiland-Reyes, Carole Goble, Kristi Clark, Eric W Deutsch, Ivo Dinov, Nathan Price, Arthur Toga
2016 Ieee international conference on big data (big data), 319-328, 2016

MultiCellDS: a community-developed standard for curating microenvironment-dependent multicellular data

Samuel H Friedman, Alexander RA Anderson, David M Bortz, Alexander G Fletcher, Hermann B Frieboes, Ahmadreza Ghaffarizadeh, David Robert Grimes, Andrea Hawkins-Daarud, Stefan Hoehme, Edwin F Juarez, Carl Kesselman, Roeland MH Merks, Shannon M Mumenthaler, Paul K Newton, Kerri-Ann Norton, Rishi Rawat, Russell C Rockne, Daniel Ruderman, Jacob Scott, Suzanne S Sindi, Jessica L Sparks, Kristin Swanson, David B Agus, Paul Macklin
bioRxiv, 090456, 2016

Predictive big data analytics: a study of Parkinson’s disease using large, complex, heterogeneous, incongruent, multi-source and incomplete observations

Ivo D Dinov, Ben Heavner, Ming Tang, Gustavo Glusman, Kyle Chard, Mike Darcy, Ravi Madduri, Judy Pa, Cathie Spino, Carl Kesselman, Ian Foster, Eric W Deutsch, Nathan D Price, John D Van Horn, Joseph Ames, Kristi Clark, Leroy Hood, Benjamin M Hampstead, William Dauer, Arthur W Toga
PloS one 11 (8), e0157077, 2016

Managing Big Neuroimaging Data

Carl Kesselman
International Journal of Psychophysiology 100 (108), 30, 2016

Accelerating data-driven discovery with scientific asset management

Robert E Schuler, Carl Kesselman, Karl Czajkowski
2016 IEEE 12th International Conference on e-Science (e-Science), 31-40, 2016

ERMrest: an entity-relationship data storage service for web-based, data-oriented collaboration

Karl Czajkowski, Carl Kesselman, Robert Schuler, Hongsuda Tangmunarunkit
arXiv preprint arXiv:1610.06044, 2016

The FaceBase Consortium: a comprehensive resource for craniofacial researchers

James F Brinkley, Shannon Fisher, Matthew P Harris, Greg Holmes, Joan E Hooper, Ethylin Wang Jabs, Kenneth L Jones, Carl Kesselman, Ophir D Klein, Richard L Maas, Mary L Marazita, Licia Selleri, Richard A Spritz, Harm van Bakel, Axel Visel, Trevor J Williams, Joanna Wysocka, FaceBase Consortium, Yang Chai
Development 143 (14), 2677-2688, 2016