<tt>nipalsMCIA</tt> : flexible multi-block dimensionality reduction in R via nonlinear iterative partial least squares.

Steven H. Kleinstein

Max Mattessich Joaquin Reyna Edel Aron Ferhat Ay Misha E. Kilmer Steven H. Kleinstein Anna Konstorum <tt>nipalsMCIA</tt> : flexible multi-block dimensionality reduction in R via nonlinear iterative partial least squares. 2025 41 Bioinform. 1 https://doi.org/10.1093/bioinformatics/btaf015 db/journals/bioinformatics/bioinformatics41.html#MattessichRAAKK25

Meng Wang Jonathan Patsenker Henry Li Yuval Kluger Steven H. Kleinstein Supervised fine-tuning of pre-trained antibody language models improves antigen specificity prediction. 1012153 2025 21 PLoS Comput. Biol. 3 https://doi.org/10.1371/journal.pcbi.1012153 db/journals/ploscb/ploscb21.html#WangPLKK25 streams/journals/ploscb

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 Putting computational models of immunity to the test - An invited challenge to predict B.pertussis vaccination responses. 1012927 2025 21 PLoS Comput. Biol. 3 https://doi.org/10.1371/journal.pcbi.1012927 db/journals/ploscb/ploscb21.html#ShindeWAABBCDDEFFGGGGGG25 streams/journals/ploscb

Jeremy P. Gygi Anna Konstorum Shrikant Pawar Edel Aron Steven H. Kleinstein Leying Guan A supervised Bayesian factor model for the identification of multi-omics signatures. 2024 40 Bioinform. 5 https://doi.org/10.1093/bioinformatics/btae202 db/journals/bioinformatics/bioinformatics40.html#GygiKPAKG24

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 nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework. 1012265 2024 20 PLoS Comput. Biol. 7 https://doi.org/10.1371/journal.pcbi.1012265 db/journals/ploscb/ploscb20.html#GabernetMBPMALJLPHHYKNK24 streams/journals/ploscb

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. 292 2023 December 24 BMC Bioinform. 1 https://doi.org/10.1186/s12859-023-05397-8 db/journals/bmcbi/bmcbi24.html#NewtonCKM23

Xi Chen Yuan Wang 0084 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. 644-657 2023 3 Nat. Comput. Sci. 7 https://doi.org/10.1038/s43588-023-00476-5 db/journals/ncs/ncs3.html#ChenWCCZNMRNTTV23

Xi Chen Yuan Wang 0084 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. 805 2023 3 Nat. Comput. Sci. 9 https://doi.org/10.1038/s43588-023-00523-1 db/journals/ncs/ncs3.html#ChenWCCZNMRNTTV23a

Kenneth B. Hoehn Oliver G. Pybus Steven H. Kleinstein Phylogenetic analysis of migration, differentiation, and class switching in B cells. 2022 18 PLoS Comput. Biol. 4 https://doi.org/10.1371/journal.pcbi.1009885 https://www.wikidata.org/entity/Q113308716 db/journals/ploscb/ploscb18.html#HoehnPK22

Syed Ahmad Chan Bukhari Shrikant Pawar Jeff Mandell Steven H. Kleinstein Kei-Hoi Cheung LinkedImm: a linked data graph database for integrating immunological data. 105 2021 22-S BMC Bioinform. 9 https://doi.org/10.1186/s12859-021-04031-9 https://www.wikidata.org/entity/Q112291323 db/journals/bmcbi/bmcbi22S.html#BukhariPMKC21

Randi Vita James A. Overton Patrick Dunn Kei-Hoi Cheung Steven H. Kleinstein Alessandro Sette Bjoern Peters A structured model for immune exposures. 2020 2020 Database J. Biol. Databases Curation https://doi.org/10.1093/database/baaa016 https://www.wikidata.org/entity/Q91866912 db/journals/biodb/biodb2020.html#VitaODCKSP20

Nima Nouri Steven H. Kleinstein Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data. 2020 16 PLoS Comput. Biol. 6 https://doi.org/10.1371/journal.pcbi.1007977 https://www.wikidata.org/entity/Q96646988 db/journals/ploscb/ploscb16.html#NouriK20

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. 259-264 2019 20-S BMC Bioinform. 5 https://doi.org/10.1186/s12859-019-2725-5 https://www.wikidata.org/entity/Q91614095 db/journals/bmcbi/bmcbi20S.html#OvertonVDBBCKDP19

Hailong Meng Gur Yaari Christopher R. Bolen Stefan Avey Steven H. Kleinstein Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE). 2019 15 PLoS Comput. Biol. 4 https://doi.org/10.1371/journal.pcbi.1006899 https://www.wikidata.org/entity/Q64086706 db/journals/ploscb/ploscb15.html#MengYBAK19

Syed Ahmad Chan Bukhari Jeff Mandell Steven H. Kleinstein Kei-Hoi Cheung A linked data graph approach to integration of immunological data. 1742-1749 2019 BIBM https://doi.org/10.1109/BIBM47256.2019.8982986 https://www.wikidata.org/entity/Q112288316 conf/bibm/2019 db/conf/bibm/bibm2019.html#BukhariMKC19

Nima Nouri Steven H. Kleinstein A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data. i341-i349 2018 34 Bioinform. 13 https://doi.org/10.1093/bioinformatics/bty235 https://www.wikidata.org/entity/Q55514140 db/journals/bioinformatics/bioinformatics34.html#NouriK18

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 CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata. 268:1-268:6 2018 19 BMC Bioinform. 1 https://doi.org/10.1186/s12859-018-2247-6 https://www.wikidata.org/entity/Q62608260 db/journals/bmcbi/bmcbi19.html#BukhariROEWGMCK18

Randi Vita Bjoern Peters James A. Overton Kei-Hoi Cheung Steven H. Kleinstein Formalizing the Representation of Immune Exposures for Human Immunology Studies. 2018 ICBO https://ceur-ws.org/Vol-2285/ICBO_2018_paper_41.pdf conf/icbo/2018 db/conf/icbo/icbo2018.html#VitaPOCK18 Mark A. Musen Susanna-Assunta Sansone Kei-Hoi Cheung Steven H. Kleinstein Morgan Crafts Stephan C. Schürer John B. Graybeal CEDAR: Semantic Web Technology to Support Open Science. 427-428 2018 WWW (Companion Volume) https://doi.org/10.1145/3184558.3186200 conf/www/2018c db/conf/www/www2018c.html#MusenSCKCSG18

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. i208-i216 2017 33 Bioinform. 14 https://doi.org/10.1093/bioinformatics/btx260 https://www.wikidata.org/entity/Q40062364 db/journals/bioinformatics/bioinformatics33.html#AveyMWZJSTSK17

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. 333 2016 17 BMC Bioinform. S-13 https://doi.org/10.1186/s12859-016-1214-3 https://www.wikidata.org/entity/Q28843105 db/journals/bmcbi/bmcbi17S.html#TobyLSCBBBCFGHM16

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. 135-148 2016 QI https://doi.org/10.1007/978-3-319-52289-0_11 conf/qi/2016 db/conf/qi/qi2016.html#CohenWHGK16

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. 3356-3358 2015 31 Bioinform. 20 https://doi.org/10.1093/bioinformatics/btv359 https://www.wikidata.org/entity/Q30970597 db/journals/bioinformatics/bioinformatics31.html#GuptaHUGYK15

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. 1148-1152 2015 22 J. Am. Medical Informatics Assoc. 6 https://doi.org/10.1093/jamia/ocv048 https://www.wikidata.org/entity/Q30976796 db/journals/jamia/jamia22.html#MusenBCDDGBKKOP15

Demetrios Sarantis Steven H. Kleinstein Kei Cheung Improvement of cytokine annotation using ontology synonym mapping. 2015 AMIA https://knowledge.amia.org/59310-amia-1.2741865/t001-1.2745946/f001-1.2745947/2244704-1.2746002/2242109-1.2745999 conf/amia/2015 db/conf/amia/amia2015.html#SarantisKC15

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. 1930-1932 2014 30 Bioinform. 13 https://doi.org/10.1093/bioinformatics/btu138 https://www.wikidata.org/entity/Q33807674 db/journals/bioinformatics/bioinformatics30.html#HeidenYUSOHVK14

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. S1 2013 14 BMC Bioinform. S-6 https://doi.org/10.1186/1471-2105-14-S6-S1 https://www.wikidata.org/entity/Q30431448 db/journals/bmcbi/bmcbi14S.html#ZaslavskyNMHHTSK13

Christopher R. Bolen Mohamed Uduman Steven H. Kleinstein Cell Subset Prediction for Blood Genomic Studies. 258 2011 12 BMC Bioinform. https://doi.org/10.1186/1471-2105-12-258 https://www.wikidata.org/entity/Q33942400 db/journals/bmcbi/bmcbi12.html#BolenUK11

Mark J. O'Connor Anja E. Hauser Ann M. Haberman Steven H. Kleinstein Activated germinal centre B cells undergo directed migration. 321-331 2011 5 Int. J. Data Min. Bioinform. 3 https://doi.org/10.1504/IJDMB.2011.040387 https://www.wikidata.org/entity/Q42142851 db/journals/ijdmb/ijdmb5.html#OConnorHHK11

Mohamed Uduman Gur Yaari Uri Hershberg Jacob A. Stern Mark J. Shlomchik Steven H. Kleinstein Detecting selection in immunoglobulin sequences. 499-504 2011 39 Nucleic Acids Res. Web-Server-Issue https://doi.org/10.1093/nar/gkr413 https://www.wikidata.org/entity/Q35075665 db/journals/nar/nar39.html#UdumanYHSSK11

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. 446-450 2011 BCB https://doi.org/10.1145/2147805.2147867 conf/bcb/2011 db/conf/bcb/bcb2011.html#SprecherSKNWTLKH11 Mark J. O'Connor Anja E. Hauser Ann M. Haberman Steven H. Kleinstein Activated Germinal-Center B Cells Undergo Directed Migration. 327-331 2009 BIBM https://doi.org/10.1109/BIBM.2009.61 https://doi.ieeecomputersociety.org/10.1109/BIBM.2009.61 https://www.wikidata.org/entity/Q56973313 conf/bibm/2009 db/conf/bibm/bibm2009.html#OConnorHHK09

Steven H. Kleinstein Getting Started in Computational Immunology. 2008 4 PLoS Comput. Biol. 8 https://doi.org/10.1371/journal.pcbi.1000128 https://www.wikidata.org/entity/Q28757368 db/journals/ploscb/ploscb4.html#Kleinstein08

Reuma Magori-Cohen Yoram Louzoun Steven H. Kleinstein Mutation parameters from DNA sequence data using graph theoretic measures on lineage trees. 332-340 2006 conf/ismb/2006 ISMB (Supplement of Bioinformatics) https://doi.org/10.1093/bioinformatics/btl239 https://www.wikidata.org/entity/Q31050084 db/conf/ismb/ismb2006.html#Magori-CohenLK06 Steven H. Kleinstein Dean Bottino Anna Georgieva Ramesh Sarangapani G. Scott Lett Nonuniform sampling for global optimization of kinetic rate constants in biological pathways. 1611-1616 2006 conf/wsc/2006 WSC https://doi.org/10.1109/WSC.2006.322934 https://doi.ieeecomputersociety.org/10.1109/WSC.2006.322934 http://dl.acm.org/citation.cfm?id=1218405 db/conf/wsc/wsc2006.html#KleinsteinBGSL06

Steven H. Kleinstein Philip E. Seiden Simulating the immune system. 69-77 2000 2 Comput. Sci. Eng. 4 https://doi.org/10.1109/5992.852392 http://doi.ieeecomputersociety.org/10.1109/5992.852392 https://www.wikidata.org/entity/Q113313772 db/journals/cse/cse2.html#KleinsteinS00

Michael Anderson Minori Aoki Edel Aron Stefan Avey Ferhat Ay Saonli Basu Carol A. Bean Sanchita Bhattacharya Robert Bjornson Christopher R. Bolen Dean Bottino Felix Breden Syed Ahmad Chan Bukhari Adam Buntzman Julie G. Burel Antonio Cappuccio David Chartash Daniel G. Chawla Xi Chen Peng Cheng Wan-Sze Cheng Kei Cheung Kei-Hoi Cheung Scott Christley Trevor Cohen Brian Corrie Lindsay G. Cowell Morgan Crafts Michael Dagher Souradipto Ghosh Dastidar Alexander D. Diehl Michel Dumontier Aidan Dunleavy Patrick Dunn Kim A. Durante Attila L. Egyedi Tal Einav John M. Fonner Jamie Forschmiedt Slim Fourati Vance G. Fowler Gisela Gabernet Daniel Gadala-Maria Javier Garcia Mary-Catherine George Anna Georgieva Olivier Gevaert William Gibson Alejandra N. González-Beltrán Barry Grant John B. Graybeal Jason GreenbaumJason A. Greenbaum Leying Guan Weikang Guan Namita T. Gupta Jeremy P. Gygi Brendan Ha Ann M. Haberman David A. Hafler Friederike Hanssen Lyndsay Harris Boris M. Hartmann Anja E. Hauser Jason A. Vander Heiden Uri Hershberg Simon Heumos Kenneth B. Hoehn Joe Hou Jason Hsiao Yunda Huang Rick Jansen Cole G. Jensen Samit R. Joshi Bhargob Kakoty Zhiyu Kang Purvesh Khatri Misha Elena KilmerMisha E. Kilmer Yuval Kluger James J. Kobie Mari Kojima Anna Konstorum Markus C. Kowarik Ian Krop David Ladd Jiyeun Lee Noah Y. Lee Andrew G. Letizia G. Scott Lett Mikhail K. Levin Sloan A. Lewis Kimberly Lezon-Geyda Aixin Li Henry Li Eric F. Lock Yoram Louzoun Reuma Magori-Cohen Jarjapu Mahita Jeff Mandell Susanna Marquez Nishanth Marthandan Max Mattessich Robert A. McDougal Marcus Mendes Hailong Meng Clare M. Miller Subhasis Mohanty Nancy Monson Mark A. Musen Sven Nahnsen Venugopalan D. Nair Murli Narayan Lishomwa C. Ndhlovu Aidan Neher Adam J. H. Newton Somayeh Nili Nima Nouri German Nudelman Kevin C. O'Connor Mark J. O'Connor Martin J. O'Connor Lars Rønn Olsen Shelby Orfield James A. Overton Nidhi Pai Cokie Parker Jonathan Patsenker Shrikant Pawar Alexander Peltzer Björn PetersBjoern Peters Mark Polster Yannick Pouliot Oliver G. Pybus Brian Qian Irene Ramos Mikkel Rasmussen Joaquin Reyna Eve Richardson Philippe Rocca-Serra Marcos Martínez Romero Aaron M. Rosenfeld William Rounds Florian Rubelt Aliza B. Rubenstein Felicia Ruffin Sandra Safo Edward Salinas Susanna-Assunta Sansone Ramesh Sarangapani Demetrios Sarantis Sudipa Sarkar Walter Scarborough Richard H. Scheuermann Stephan C. Schürer Jamie K. Scott Stuart C. Sealfon Robert P. Sebra Philip E. Seiden Alessandro Sette Albert C. Shaw Pramod Shinde Mark J. Shlomchik Barbara Siconolfi Alessandra Soares-Schanoski Josey Sorenson Emmett Sprecher Rachel R. Spurbeck Aparna Srinivasan Jacob A. Stern Joel N. H. Stern Alicja Tadych Juilee Thakar Chandra L. Theesfeld Nicola Thrupp Rashmi Tippalagama Inimary T. Toby Raphael Trevizani Olga G. Troyanskaya Sui Tsang David Tuck Mohamed Uduman Steffen Ventz Francois Vigneault Randi Vita Alexandria Vornholt Jiuzhou Wang Meng Wang Yuan Wang 0084 Dominic Widdows Lisa Willemsen Debra Willrett Jean Wilson Eric P. Winer Jeffrey A. Wiser Christopher W. Woods Cheng-Chang Wu Gur Yaari Frederique Ruf Zamojski Heidi Zapata Elena Zaslavsky