Simulating the immune system. - Steven H. Kleinstein; Philip E. Seiden (Comput. Sci. Eng., 2000)

Mutation parameters from DNA sequence data using graph theoretic measures on lineage trees. - Reuma Magori-Cohen; Yoram Louzoun; Steven H. Kleinstein (ISMB (Supplement of Bioinformatics), 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 (WSC, 2006)

Getting Started in Computational Immunology. - Steven H. Kleinstein (PLoS Comput. Biol., 2008)

Activated Germinal-Center B Cells Undergo Directed Migration. - Mark J. O'Connor; Anja E. Hauser; Ann M. Haberman; Steven H. Kleinstein (BIBM, 2009)

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 (BCB, 2011)

Cell Subset Prediction for Blood Genomic Studies. - Christopher R. Bolen; Mohamed Uduman; Steven H. Kleinstein (BMC Bioinform., 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)

Detecting selection in immunoglobulin sequences. - Mohamed Uduman; Gur Yaari; Uri Hershberg; Jacob A. Stern; Mark J. Shlomchik; Steven H. Kleinstein (Nucleic Acids Res., 2011)

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)

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)

Improvement of cytokine annotation using ontology synonym mapping. - Demetrios Sarantis; Steven H. Kleinstein; Kei Cheung (AMIA, 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)

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; et al. (J. Am. Medical Informatics Assoc., 2015)

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 (QI, 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; et al. (BMC Bioinform., 2016)

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)

Formalizing the Representation of Immune Exposures for Human Immunology Studies. - Randi Vita; Bjoern Peters; James A. Overton; Kei-Hoi Cheung; Steven H. Kleinstein (ICBO, 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 B. Graybeal (WWW (Companion Volume), 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 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 B. Graybeal; Mark A. Musen; Kei-Hoi Cheung; Steven H. Kleinstein (BMC Bioinform., 2018)

A linked data graph approach to integration of immunological data. - Syed Ahmad Chan Bukhari; Jeff Mandell; Steven H. Kleinstein; Kei-Hoi Cheung (BIBM, 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)

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)

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)

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)

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)

Phylogenetic analysis of migration, differentiation, and class switching in B cells. - Kenneth B. Hoehn; Oliver G. Pybus; Steven H. Kleinstein (PLoS Comput. Biol., 2022)

Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data. - Xi Chen; Yuan Wang 084; 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; et al. (Nat. Comput. Sci., 2023)

Author Correction: Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data. - Xi Chen; Yuan Wang 084; 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; et al. (Nat. Comput. Sci., 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., 2023)

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; et al. (PLoS Comput. Biol., 2024)

Putting computational models of immunity to the test - An invited challenge to predict B.pertussis vaccination responses. - 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; et al. (PLoS Comput. Biol., 2025)

Supervised fine-tuning of pre-trained antibody language models improves antigen specificity prediction. - Meng Wang; Jonathan Patsenker; Henry Li; Yuval Kluger; Steven H. Kleinstein (PLoS Comput. Biol., 2025)