Steven H. Kleinstein

Publication Activity (10 Years)

Years Active: 2000-2023
Publications (10 Years): 17

Top Topics

Semantically Annotated

Gene Expression

Clonal Selection

Top Venues

PLoS Comput. Biol.

Nat. Comput. Sci.

Publications

Adam J. H. Newton, David Chartash, Steven H. Kleinstein, Robert A. McDougal
A pipeline for the retrieval and extraction of domain-specific information with application to COVID-19 immune signatures. BMC Bioinform. 24 (1) (2023)
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
Author Correction: Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data. Nat. Comput. Sci. 3 (9) (2023)
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
Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data. Nat. Comput. Sci. 3 (7) (2023)
Kenneth B. Hoehn, Oliver G. Pybus, Steven H. Kleinstein
Phylogenetic analysis of migration, differentiation, and class switching in B cells. PLoS Comput. Biol. 18 (4) (2022)
Syed Ahmad Chan Bukhari, Shrikant Pawar, Jeff Mandell, Steven H. Kleinstein, Kei-Hoi Cheung
LinkedImm: a linked data graph database for integrating immunological data. BMC Bioinform. (9) (2021)
Randi Vita, James A. Overton, Patrick Dunn, Kei-Hoi Cheung, Steven H. Kleinstein, Alessandro Sette, Bjoern Peters
A structured model for immune exposures. Database J. Biol. Databases Curation 2020 (2020)
Nima Nouri, Steven H. Kleinstein
Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data. PLoS Comput. Biol. 16 (6) (2020)
Hailong Meng, Gur Yaari, Christopher R. Bolen, Stefan Avey, Steven H. Kleinstein
Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE). PLoS Comput. Biol. 15 (4) (2019)
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
Reporting and connecting cell type names and gating definitions through ontologies. BMC Bioinform. (5) (2019)
Syed Ahmad Chan Bukhari, Jeff Mandell, Steven H. Kleinstein, Kei-Hoi Cheung
A linked data graph approach to integration of immunological data. BIBM (2019)
Nima Nouri, Steven H. Kleinstein
A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data. Bioinform. 34 (13) (2018)
Syed Ahmad Chan Bukhari, Marcos Martínez Romero, Martin J. O'Connor, Attila L. Egyedi, Debra Willrett, John Graybeal, Mark A. Musen, Kei-Hoi Cheung, Steven H. Kleinstein
CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata. BMC Bioinform. 19 (1) (2018)
Randi Vita, Bjoern Peters, James A. Overton, Kei-Hoi Cheung, Steven H. Kleinstein
Formalizing the Representation of Immune Exposures for Human Immunology Studies. ICBO (2018)
Mark A. Musen, Susanna-Assunta Sansone, Kei-Hoi Cheung, Steven H. Kleinstein, Morgan Crafts, Stephan C. Schürer, John Graybeal
CEDAR: Semantic Web Technology to Support Open Science. WWW (Companion Volume) (2018)
Stefan Avey, Subhasis Mohanty, Jean Wilson, Heidi Zapata, Samit R. Joshi, Barbara Siconolfi, Sui Tsang, Albert C. Shaw, Steven H. Kleinstein
Multiple network-constrained regressions expand insights into influenza vaccination responses. Bioinform. 33 (14) (2017)
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
VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements. BMC Bioinform. 17 (S-13) (2016)
Trevor Cohen, Dominic Widdows, Jason A. Vander Heiden, Namita T. Gupta, Steven H. Kleinstein
Graded Vector Representations of Immunoglobulins Produced in Response to West Nile Virus. QI (2016)
Namita T. Gupta, Jason A. Vander Heiden, Mohamed Uduman, Daniel Gadala-Maria, Gur Yaari, Steven H. Kleinstein
Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data. Bioinform. 31 (20) (2015)
Demetrios Sarantis, Steven H. Kleinstein, Kei Cheung
Improvement of cytokine annotation using ontology synonym mapping. AMIA (2015)
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
The center for expanded data annotation and retrieval. J. Am. Medical Informatics Assoc. 22 (6) (2015)
Jason A. Vander Heiden, Gur Yaari, Mohamed Uduman, Joel N. H. Stern, Kevin C. O'Connor, David A. Hafler, Francois Vigneault, Steven H. Kleinstein
pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. Bioinform. 30 (13) (2014)
Elena Zaslavsky, German Nudelman, Susanna Marquez, Uri Hershberg, Boris M. Hartmann, Juilee Thakar, Stuart C. Sealfon, Steven H. Kleinstein
Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection. BMC Bioinform. 14 (S-6) (2013)
Mohamed Uduman, Gur Yaari, Uri Hershberg, Jacob A. Stern, Mark J. Shlomchik, Steven H. Kleinstein
Detecting selection in immunoglobulin sequences. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)
Emmett Sprecher, Sudipa Sarkar, Steven H. Kleinstein, Murli Narayan, Eric P. Winer, David Tuck, Kimberly Lezon-Geyda, Ian Krop, Lyndsay Harris
Association between response to brief trastuzumab exposure in cell lines and early stage HER2+ breast tumors. BCB (2011)
Mark J. O'Connor, Anja E. Hauser, Ann M. Haberman, Steven H. Kleinstein
Activated germinal centre B cells undergo directed migration. Int. J. Data Min. Bioinform. 5 (3) (2011)
Christopher R. Bolen, Mohamed Uduman, Steven H. Kleinstein
Cell Subset Prediction for Blood Genomic Studies. BMC Bioinform. 12 (2011)
Mark J. O'Connor, Anja E. Hauser, Ann M. Haberman, Steven H. Kleinstein
Activated Germinal-Center B Cells Undergo Directed Migration. BIBM (2009)
Steven H. Kleinstein
Getting Started in Computational Immunology. PLoS Comput. Biol. 4 (8) (2008)
Reuma Magori-Cohen, Yoram Louzoun, Steven H. Kleinstein
Mutation parameters from DNA sequence data using graph theoretic measures on lineage trees. ISMB (Supplement of Bioinformatics) (2006)
Steven H. Kleinstein, Dean Bottino, Anna Georgieva, Ramesh Sarangapani, G. Scott Lett
Nonuniform sampling for global optimization of kinetic rate constants in biological pathways. WSC (2006)
Steven H. Kleinstein, Philip E. Seiden
Simulating the immune system. Comput. Sci. Eng. 2 (4) (2000)