Steven H. Kleinstein

According to our database, Steven H. Kleinstein authored at least 32 papers between 2000 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework.

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

PLoS Comput. Biol., 2024

2023

A pipeline for the retrieval and extraction of domain-specific information with application to COVID-19 immune signatures.

Adam J. H. Newton, David Chartash, Steven H. Kleinstein, Robert A. McDougal

BMC Bioinform., December, 2023

Author Correction: Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data.

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

Nat. Comput. Sci., 2023

Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data.

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

Nat. Comput. Sci., 2023

2022

Phylogenetic analysis of migration, differentiation, and class switching in B cells.

Kenneth B. Hoehn, Oliver G. Pybus, Steven H. Kleinstein

PLoS Comput. Biol., 2022

2021

LinkedImm: a linked data graph database for integrating immunological data.

Syed Ahmad Chan Bukhari, Shrikant Pawar, Jeff Mandell, Steven H. Kleinstein, Kei-Hoi Cheung

BMC Bioinform., 2021

2020

Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data.

Nima Nouri, Steven H. Kleinstein

PLoS Comput. Biol., 2020

A structured model for immune exposures.

Randi Vita, James A. Overton, Patrick Dunn, Kei-Hoi Cheung, Steven H. Kleinstein, Alessandro Sette, Bjoern Peters

Database J. Biol. Databases Curation, 2020

2019

Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE).

Hailong Meng, Gur Yaari, Christopher R. Bolen, Stefan Avey, Steven H. Kleinstein

PLoS Comput. Biol., 2019

Reporting and connecting cell type names and gating definitions through ontologies.

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

BMC Bioinform., 2019

A linked data graph approach to integration of immunological data.

Syed Ahmad Chan Bukhari, Jeff Mandell, Steven H. Kleinstein, Kei-Hoi Cheung

Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

2018

CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata.

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

BMC Bioinform., 2018

A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data.

Nima Nouri, Steven H. Kleinstein

Bioinform., 2018

CEDAR: Semantic Web Technology to Support Open Science.

Mark A. Musen, Susanna-Assunta Sansone, Kei-Hoi Cheung, Steven H. Kleinstein, Morgan Crafts, Stephan C. Schürer, John Graybeal

Proceedings of the Companion of the The Web Conference 2018 on The Web Conference 2018, 2018

Formalizing the Representation of Immune Exposures for Human Immunology Studies.

Randi Vita, Bjoern Peters, James A. Overton, Kei-Hoi Cheung, Steven H. Kleinstein

Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), 2018

2017

Multiple network-constrained regressions expand insights into influenza vaccination responses.

Stefan Avey, Subhasis Mohanty, Jean Wilson, Heidi Zapata, Samit R. Joshi, Barbara Siconolfi, Sui Tsang, Albert C. Shaw, Steven H. Kleinstein

Bioinform., 2017

2016

VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements.

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

BMC Bioinform., 2016

Graded Vector Representations of Immunoglobulins Produced in Response to West Nile Virus.

Trevor Cohen, Dominic Widdows, Jason A. Vander Heiden, Namita T. Gupta, Steven H. Kleinstein

Proceedings of the Quantum Interaction - 10th International Conference, 2016

2015

The center for expanded data annotation and retrieval.

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

J. Am. Medical Informatics Assoc., 2015

Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data.

Namita T. Gupta, Jason A. Vander Heiden, Mohamed Uduman, Daniel Gadala-Maria, Gur Yaari, Steven H. Kleinstein

Bioinform., 2015

Improvement of cytokine annotation using ontology synonym mapping.

Demetrios Sarantis, Steven H. Kleinstein, Kei Cheung

Proceedings of the AMIA 2015, 2015

2014

pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires.

Jason A. Vander Heiden, Gur Yaari, Mohamed Uduman, Joel N. H. Stern, Kevin C. O'Connor, David A. Hafler, Francois Vigneault, Steven H. Kleinstein

Bioinform., 2014

2013

Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection.

Elena Zaslavsky, German Nudelman, Susanna Marquez, Uri Hershberg, Boris M. Hartmann, Juilee Thakar, Stuart C. Sealfon, Steven H. Kleinstein

BMC Bioinform., 2013

2011

Detecting selection in immunoglobulin sequences.

Mohamed Uduman, Gur Yaari, Uri Hershberg, Jacob A. Stern, Mark J. Shlomchik, Steven H. Kleinstein

Nucleic Acids Res., 2011

Activated germinal centre B cells undergo directed migration.

Mark J. O'Connor, Anja E. Hauser, Ann M. Haberman, Steven H. Kleinstein

Int. J. Data Min. Bioinform., 2011

Cell Subset Prediction for Blood Genomic Studies.

Christopher R. Bolen, Mohamed Uduman, Steven H. Kleinstein

BMC Bioinform., 2011

Association between response to brief trastuzumab exposure in cell lines and early stage HER2+ breast tumors.

Emmett Sprecher, Sudipa Sarkar, Steven H. Kleinstein, Murli Narayan, Eric P. Winer, David Tuck, Kimberly Lezon-Geyda, Ian Krop, Lyndsay Harris

Proceedings of the ACM International Conference on Bioinformatics, 2011

2009

Activated Germinal-Center B Cells Undergo Directed Migration.

Mark J. O'Connor, Anja E. Hauser, Ann M. Haberman, Steven H. Kleinstein

Proceedings of the 2009 IEEE International Conference on Bioinformatics and Biomedicine, 2009

2008

Getting Started in Computational Immunology.

Steven H. Kleinstein

PLoS Comput. Biol., 2008

2006

Nonuniform sampling for global optimization of kinetic rate constants in biological pathways.

Steven H. Kleinstein, Dean Bottino, Anna Georgieva, Ramesh Sarangapani, G. Scott Lett

Proceedings of the Winter Simulation Conference WSC 2006, 2006

Mutation parameters from DNA sequence data using graph theoretic measures on lineage trees.

Reuma Magori-Cohen, Yoram Louzoun, Steven H. Kleinstein

Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

2000

Simulating the immune system.

Steven H. Kleinstein, Philip E. Seiden

Comput. Sci. Eng., 2000