Steven H. Kleinstein

36 papers Misc 2Journal 27Unranked 7
YearRankTypeTitle / Venue / Authors
2025 J jnl
<tt>nipalsMCIA</tt> : flexible multi-block dimensionality reduction in R via nonlinear iterative partial least squares.
Bioinform.
Max Mattessich, Joaquin Reyna, Edel Aron, Ferhat Ay, Misha E. Kilmer, Steven H. Kleinstein, Anna Konstorum
2025 J jnl
Putting computational models of immunity to the test - An invited challenge to predict B.pertussis vaccination responses.
PLoS Comput. Biol.
Pramod Shinde, Lisa Willemsen, Michael Anderson, Minori Aoki, Saonli Basu, Julie G. Burel, Peng Cheng, Souradipto Ghosh Dastidar, Aidan Dunleavy, Tal Einav, Jamie Forschmiedt, Slim Fourati, Javier Garcia, William Gibson, Jason A. Greenbaum, Leying Guan, Weikang Guan, Jeremy P. Gygi, Brendan Ha, Joe Hou, Jason Hsiao, Yunda Huang, Rick Jansen, Bhargob Kakoty, Zhiyu Kang, James J. Kobie, Mari Kojima, Anna Konstorum, Jiyeun Lee, Sloan A. Lewis, Aixin Li, Eric F. Lock, Jarjapu Mahita, Marcus Mendes, Hailong Meng, Aidan Neher, Somayeh Nili, Lars Rønn Olsen, Shelby Orfield, James A. Overton, Nidhi Pai, Cokie Parker, Brian Qian, Mikkel Rasmussen, Joaquin Reyna, Eve Richardson, Sandra Safo, Josey Sorenson, Aparna Srinivasan, Nicola Thrupp, Rashmi Tippalagama, Raphael Trevizani, Steffen Ventz, Jiuzhou Wang, Cheng-Chang Wu, Ferhat Ay, Barry Grant, Steven H. Kleinstein, Bjoern Peters
2025 J jnl
Supervised fine-tuning of pre-trained antibody language models improves antigen specificity prediction.
PLoS Comput. Biol.
Meng Wang, Jonathan Patsenker, Henry Li, Yuval Kluger, Steven H. Kleinstein
2024 J jnl
A supervised Bayesian factor model for the identification of multi-omics signatures.
Bioinform.
Jeremy P. Gygi, Anna Konstorum, Shrikant Pawar, Edel Aron, Steven H. Kleinstein, Leying Guan
2024 J jnl
nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework.
PLoS Comput. Biol.
Gisela Gabernet, Susanna Marquez, Robert Bjornson, Alexander Peltzer, Hailong Meng, Edel Aron, Noah Y. Lee, Cole G. Jensen, David Ladd, Mark Polster, Friederike Hanssen, Simon Heumos, Gur Yaari, Markus C. Kowarik, Sven Nahnsen, Steven H. Kleinstein
2023 J jnl
A pipeline for the retrieval and extraction of domain-specific information with application to COVID-19 immune signatures.
BMC Bioinform.
Adam J. H. Newton, David Chartash, Steven H. Kleinstein, Robert A. McDougal
2023 J jnl
Author Correction: Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data.
Nat. Comput. Sci.
Xi Chen, Yuan Wang, Antonio Cappuccio, Wan-Sze Cheng, Frederique Ruf Zamojski, Venugopalan D. Nair, Clare M. Miller, Aliza B. Rubenstein, German Nudelman, Alicja Tadych, Chandra L. Theesfeld, Alexandria Vornholt, Mary-Catherine George, Felicia Ruffin, Michael Dagher, Daniel G. Chawla, Alessandra Soares-Schanoski, Rachel R. Spurbeck, Lishomwa C. Ndhlovu, Robert P. Sebra, Steven H. Kleinstein, Andrew G. Letizia, Irene Ramos, Vance G. Fowler, Christopher W. Woods, Elena Zaslavsky, Olga G. Troyanskaya, Stuart C. Sealfon
2023 J jnl
Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data.
Nat. Comput. Sci.
Xi Chen, Yuan Wang, Antonio Cappuccio, Wan-Sze Cheng, Frederique Ruf Zamojski, Venugopalan D. Nair, Clare M. Miller, Aliza B. Rubenstein, German Nudelman, Alicja Tadych, Chandra L. Theesfeld, Alexandria Vornholt, Mary-Catherine George, Felicia Ruffin, Michael Dagher, Daniel G. Chawla, Alessandra Soares-Schanoski, Rachel R. Spurbeck, Lishomwa C. Ndhlovu, Robert P. Sebra, Steven H. Kleinstein, Andrew G. Letizia, Irene Ramos, Vance G. Fowler, Christopher W. Woods, Elena Zaslavsky, Olga G. Troyanskaya, Stuart C. Sealfon
2022 J jnl
Phylogenetic analysis of migration, differentiation, and class switching in B cells.
PLoS Comput. Biol.
Kenneth B. Hoehn, Oliver G. Pybus, Steven H. Kleinstein
2021 J jnl
LinkedImm: a linked data graph database for integrating immunological data.
BMC Bioinform.
Syed Ahmad Chan Bukhari, Shrikant Pawar, Jeff Mandell, Steven H. Kleinstein, Kei-Hoi Cheung
2020 J jnl
A structured model for immune exposures.
Database J. Biol. Databases Curation
Randi Vita, James A. Overton, Patrick Dunn, Kei-Hoi Cheung, Steven H. Kleinstein, Alessandro Sette, Bjoern Peters
2020 J jnl
Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data.
PLoS Comput. Biol.
Nima Nouri, Steven H. Kleinstein
2019 — conf
A linked data graph approach to integration of immunological data.
BIBM
Syed Ahmad Chan Bukhari, Jeff Mandell, Steven H. Kleinstein, Kei-Hoi Cheung
2019 J jnl
Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE).
PLoS Comput. Biol.
Hailong Meng, Gur Yaari, Christopher R. Bolen, Stefan Avey, Steven H. Kleinstein
2019 J jnl
Reporting and connecting cell type names and gating definitions through ontologies.
BMC Bioinform.
James A. Overton, Randi Vita, Patrick Dunn, Julie G. Burel, Syed Ahmad Chan Bukhari, Kei-Hoi Cheung, Steven H. Kleinstein, Alexander D. Diehl, Bjoern Peters
2018 J jnl
A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data.
Bioinform.
Nima Nouri, Steven H. Kleinstein
2018 J jnl
CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata.
BMC Bioinform.
Syed Ahmad Chan Bukhari, Marcos Martínez Romero, Martin J. O'Connor, Attila L. Egyedi, Debra Willrett, John B. Graybeal, Mark A. Musen, Kei-Hoi Cheung, Steven H. Kleinstein
2018 — conf
CEDAR: Semantic Web Technology to Support Open Science.
WWW (Companion Volume)
Mark A. Musen, Susanna-Assunta Sansone, Kei-Hoi Cheung, Steven H. Kleinstein, Morgan Crafts, Stephan C. Schürer, John B. Graybeal
2018 — conf
Formalizing the Representation of Immune Exposures for Human Immunology Studies.
ICBO
Randi Vita, Bjoern Peters, James A. Overton, Kei-Hoi Cheung, Steven H. Kleinstein
2017 J jnl
Multiple network-constrained regressions expand insights into influenza vaccination responses.
Bioinform.
Stefan Avey, Subhasis Mohanty, Jean Wilson, Heidi Zapata, Samit R. Joshi, Barbara Siconolfi, Sui Tsang, Albert C. Shaw, Steven H. Kleinstein
2016 — conf
Graded Vector Representations of Immunoglobulins Produced in Response to West Nile Virus.
QI
Trevor Cohen, Dominic Widdows, Jason A. Vander Heiden, Namita T. Gupta, Steven H. Kleinstein
2016 J jnl
VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements.
BMC Bioinform.
Inimary T. Toby, Mikhail K. Levin, Edward Salinas, Scott Christley, Sanchita Bhattacharya, Felix Breden, Adam Buntzman, Brian Corrie, John M. Fonner, Namita T. Gupta, Uri Hershberg, Nishanth Marthandan, Aaron M. Rosenfeld, William Rounds, Florian Rubelt, Walter Scarborough, Jamie K. Scott, Mohamed Uduman, Jason A. Vander Heiden, Richard H. Scheuermann, Nancy Monson, Steven H. Kleinstein, Lindsay G. Cowell
2015 J jnl
Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data.
Bioinform.
Namita T. Gupta, Jason A. Vander Heiden, Mohamed Uduman, Daniel Gadala-Maria, Gur Yaari, Steven H. Kleinstein
2015 Misc conf
Improvement of cytokine annotation using ontology synonym mapping.
AMIA
Demetrios Sarantis, Steven H. Kleinstein, Kei Cheung
2015 J jnl
The center for expanded data annotation and retrieval.
J. Am. Medical Informatics Assoc.
Mark A. Musen, Carol A. Bean, Kei-Hoi Cheung, Michel Dumontier, Kim A. Durante, Olivier Gevaert, Alejandra N. González-Beltrán, Purvesh Khatri, Steven H. Kleinstein, Martin J. O'Connor, Yannick Pouliot, Philippe Rocca-Serra, Susanna-Assunta Sansone, Jeffrey A. Wiser
2014 J jnl
pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires.
Bioinform.
Jason A. Vander Heiden, Gur Yaari, Mohamed Uduman, Joel N. H. Stern, Kevin C. O'Connor, David A. Hafler, Francois Vigneault, Steven H. Kleinstein
2013 J jnl
Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection.
BMC Bioinform.
Elena Zaslavsky, German Nudelman, Susanna Marquez, Uri Hershberg, Boris M. Hartmann, Juilee Thakar, Stuart C. Sealfon, Steven H. Kleinstein
2011 J jnl
Activated germinal centre B cells undergo directed migration.
Int. J. Data Min. Bioinform.
Mark J. O'Connor, Anja E. Hauser, Ann M. Haberman, Steven H. Kleinstein
2011 — conf
Association between response to brief trastuzumab exposure in cell lines and early stage HER2+ breast tumors.
BCB
Emmett Sprecher, Sudipa Sarkar, Steven H. Kleinstein, Murli Narayan, Eric P. Winer, David Tuck, Kimberly Lezon-Geyda, Ian Krop, Lyndsay Harris
2011 J jnl
Cell Subset Prediction for Blood Genomic Studies.
BMC Bioinform.
Christopher R. Bolen, Mohamed Uduman, Steven H. Kleinstein
2011 J jnl
Detecting selection in immunoglobulin sequences.
Nucleic Acids Res.
Mohamed Uduman, Gur Yaari, Uri Hershberg, Jacob A. Stern, Mark J. Shlomchik, Steven H. Kleinstein
2009 — conf
Activated Germinal-Center B Cells Undergo Directed Migration.
BIBM
Mark J. O'Connor, Anja E. Hauser, Ann M. Haberman, Steven H. Kleinstein
2008 J jnl
Getting Started in Computational Immunology.
PLoS Comput. Biol.
Steven H. Kleinstein
2006 — conf
Mutation parameters from DNA sequence data using graph theoretic measures on lineage trees.
ISMB (Supplement of Bioinformatics)
Reuma Magori-Cohen, Yoram Louzoun, Steven H. Kleinstein
2006 Misc conf
Nonuniform sampling for global optimization of kinetic rate constants in biological pathways.
WSC
Steven H. Kleinstein, Dean Bottino, Anna Georgieva, Ramesh Sarangapani, G. Scott Lett
2000 J jnl
Simulating the immune system.
Comput. Sci. Eng.
Steven H. Kleinstein, Philip E. Seiden