Publications

2024

Host-microbe multiomic profiling reveals age-dependent immune dysregulation associated with COVID-19 immunopathology.Phan HV, Tsitsiklis A, Maguire CP, Haddad EK, Becker PM, Kim-Schulze S, Lee B, Chen J, Hoch A, Pickering H, van Zalm P, Altman MC, Augustine AD, Calfee CS, Bosinger S, Cairns CB, Eckalbar W, Guan L, Jayavelu ND, Kleinstein SH, Krammer F, Maecker HT, Ozonoff A, Peters B, Rouphael N, Montgomery RR, Reed E, Schaenman J, Steen H, Levy O, Diray-Arce J, Langelier CR. Sci Transl Med. 2024 Apr 17; 2024 Apr 17. PMID: 38630846.
A supervised bayesian factor model for the identification of multi-omics signatures.Gygi JP, Konstorum A, Pawar S, Aron E, Kleinstein SH, Guan L. Bioinformatics. 2024 Apr 11; 2024 Apr 11. PMID: 38603606.
Inferring B Cell Phylogenies from Paired H and L Chain BCR Sequences with Dowser.Jensen CG, Sumner JA, Kleinstein SH, Hoehn KB. J Immunol. 2024 Apr 1; 2024 Apr 1. PMID: 38557795.
A multi-omics systems vaccinology resource to develop and test computational models of immunity.Shinde P, Soldevila F, Reyna J, Aoki M, Rasmussen M, Willemsen L, Kojima M, Ha B, Greenbaum JA, Overton JA, Guzman-Orozco H, Nili S, Orfield S, Gygi JP, da Silva Antunes R, Sette A, Grant B, Olsen LR, Konstorum A, Guan L, Ay F, Kleinstein SH, Peters B. Cell Rep Methods. 2024 Mar 25; 2024 Mar 14. PMID: 38490204.
Host-Microbe Multiomic Profiling Reveals Age-Dependent COVID-19 Immunopathology.Van Phan H, Tsitsiklis A, Maguire CP, Haddad EK, Becker PM, Kim-Schulze S, Lee B, Chen J, Hoch A, Pickering H, Van Zalm P, Altman MC, Augustine AD, Calfee CS, Bosinger S, Cairns C, Eckalbar W, Guan L, Jayavelu ND, Kleinstein SH, Krammer F, Maecker HT, Ozonoff A, Peters B, Rouphael N, Montgomery RR, Reed E, Schaenman J, Steen H, Levy O, Diray-Arce J, Langelier CR. medRxiv. 2024 Feb 13; 2024 Feb 13. PMID: 38405760.
CD23(+)IgG1(+) memory B cells are poised to switch to pathogenic IgE production in food allergy.Ota M, Hoehn KB, Fernandes-Braga W, Ota T, Aranda CJ, Friedman S, Miranda-Waldetario MGC, Redes J, Suprun M, Grishina G, Sampson HA, Malbari A, Kleinstein SH, Sicherer SH, Curotto de Lafaille MA. Sci Transl Med. 2024 Feb 7; 2024 Feb 7. PMID: 38324641.
nf-core/airrflow: an adaptive immune receptor repertoire analysis workflow employing the Immcantation framework.Gabernet G, Marquez S, Bjornson R, Peltzer A, Meng H, Aron E, Lee NY, Jensen C, Ladd D, Hanssen F, Heumos S, Yaari G, Kowarik MC, Nahnsen S, Kleinstein SH. bioRxiv. 2024 Jan 28; 2024 Jan 28. PMID: 38293151.
Language model-based B cell receptor sequence embeddings can effectively encode receptor specificity.Wang M, Patsenker J, Li H, Kluger Y, Kleinstein SH. Nucleic Acids Res. 2024 Jan 25. PMID: 38109302.
Features of acute COVID-19 associated with post-acute sequelae of SARS-CoV-2 phenotypes: results from the IMPACC study.Ozonoff A, Jayavelu ND, Liu S, Melamed E, Milliren CE, Qi J, Geng LN, McComsey GA, Cairns CB, Baden LR, Schaenman J, Shaw AC, Samaha H, Seyfert-Margolis V, Krammer F, Rosen LB, Steen H, Syphurs C, Dandekar R, Shannon CP, Sekaly RP, Ehrlich LIR, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Higuita NIA, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Sesma AF, Simon V, van Bakel H, Kim-Schulze S, Hafler DA, Levy O, Kraft M, Bime C, Haddad EK, Calfee CS, Erle DJ, Langelier CR, Eckalbar W, Bosinger SE, Peters B, Kleinstein SH, Reed EF, Augustine AD, Diray-Arce J, Maecker HT, Altman MC, Montgomery RR, Becker PM, Rouphael N. Nat Commun. 2024 Jan 3; 2024 Jan 3. PMID: 38172101.
B cell phylogenetics in the single cell era.Hoehn KB, Kleinstein SH. Trends Immunol. 2024 Jan; 2023 Dec 27. PMID: 38151443.

2023

Early cellular and molecular signatures correlate with severity of West Nile virus infection.Lee HJ, Zhao Y, Fleming I, Mehta S, Wang X, Wyk BV, Ronca SE, Kang H, Chou CH, Fatou B, Smolen KK, Levy O, Clish CB, Xavier RJ, Steen H, Hafler DA, Love JC, Shalek AK, Guan L, Murray KO, Kleinstein SH, Montgomery RR. iScience. 2023 Dec 15; 2023 Nov 2. PMID: 38047068.
Corrigendum to "Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: results from the IMPACC study" [eBioMedicine 83 (2022) 104208].Ozonoff A, Schaenman J, Jayavelu ND, Milliren CE, Calfee CS, Cairns CB, Kraft M, Baden LR, Shaw AC, Krammer F, van Bakel H, Esserman DA, Liu S, Sesma AF, Simon V, Hafler DA, Montgomery RR, Kleinstein SH, Levy O, Bime C, Haddad EK, Erle DJ, Pulendran B, Nadeau KC, Davis MM, Hough CL, Messer WB, Agudelo Higuita NI, Metcalf JP, Atkinson MA, Brakenridge SC, Corry D, Kheradmand F, Ehrlich LIR, Melamed E, McComsey GA, Sekaly R, Diray-Arce J, Peters B, Augustine AD, Reed EF, Altman MC, Becker PM, Rouphael N. EBioMedicine. 2023 Dec; 2023 Nov 1. PMID: 37918220.
Integrated longitudinal multi-omics study identifies immune programs associated with COVID-19 severity and mortality in 1152 hospitalized participants.Gygi JP, Maguire C, Patel RK, Shinde P, Konstorum A, Shannon CP, Xu L, Hoch A, Jayavelu ND, Network I, Haddad EK, Reed EF, Kraft M, McComsey GA, Metcalf J, Ozonoff A, Esserman D, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen LB, van Bakel H, Wilson M, Eckalbar W, Maecker H, Langelier CR, Steen H, Altman MC, Montgomery RR, Levy O, Melamed E, Pulendran B, Diray-Arce J, Smolen KK, Fragiadakis GK, Becker PM, Augustine AD, Sekaly RP, Ehrlich LIR, Fourati S, Peters B, Kleinstein SH, Guan L. bioRxiv. 2023 Nov 6; 2023 Nov 6. PMID: 37986828.
Inferring B cell phylogenies from paired heavy and light chain BCR sequences with Dowser.Jensen CG, Sumner JA, Kleinstein SH, Hoehn KB. bioRxiv. 2023 Oct 2; 2023 Oct 2. PMID: 37873135.
A supervised Bayesian factor model for the identification of multi-omics signatures.Gygi JP, Konstorum A, Pawar S, Aron E, Kleinstein SH, Guan L. bioRxiv. 2023 Sep 27; 2023 Sep 27. PMID: 36747790.
IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data.Peres A, Lees WD, Rodriguez OL, Lee NY, Polak P, Hope R, Kedmi M, Collins AM, Ohlin M, Kleinstein SH, Watson CT, Yaari G. Nucleic Acids Res. 2023 Sep 8. PMID: 37548401.
Author Correction: Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data.Chen X, Wang Y, Cappuccio A, Cheng WS, Zamojski FR, Nair VD, Miller CM, Rubenstein AB, Nudelman G, Tadych A, Theesfeld CL, Vornholt A, George MC, Ruffin F, Dagher M, Chawla DG, Soares-Schanoski A, Spurbeck RR, Ndhlovu LC, Sebra R, Kleinstein SH, Letizia AG, Ramos I, Fowler VG Jr, Woods CW, Zaslavsky E, Troyanskaya OG, Sealfon SC. Nat Comput Sci. 2023 Sep. PMID: 38177788.
A systems vaccinology resource to develop and test computational models of immunity.Shinde P, Soldevila F, Reyna J, Aoki M, Rasmussen M, Willemsen L, Kojima M, Ha B, Greenbaum JA, Overton JA, Guzman-Orozco H, Nili S, Orfield S, Gygi JP, da Silva Antunes R, Sette A, Grant B, Olsen LR, Konstorum A, Guan L, Ay F, Kleinstein SH, Peters B. bioRxiv. 2023 Aug 29; 2023 Aug 29. PMID: 37693565.
Prior cycles of anti-CD20 antibodies affect antibody responses after repeated SARS-CoV-2 mRNA vaccination.Asashima H, Kim D, Wang K, Lele N, Buitrago-Pocasangre NC, Lutz R, Cruz I, Raddassi K, Ruff WE, Racke MK, Wilson JE, Givens TS, Grifoni A, Weiskopf D, Sette A, Kleinstein SH, Montgomery RR, Shaw AC, Li F, Fan R, Hafler DA, Tomayko MM, Longbrake EE. JCI Insight. 2023 Aug 22; 2023 Aug 22. PMID: 37606046.
Antibody gene features associated with binding and functional activity in vaccine-derived human mAbs targeting malaria parasites.Coelho CH, Marquez S, Tentokam BCN, Berhe AD, Miura K, Long CA, Sagara I, Healy S, Kleinstein SH, Duffy PE. bioRxiv. 2023 Aug 3; 2023 Aug 3. PMID: 37781572.
Predictive overfitting in immunological applications: Pitfalls and solutions.Gygi JP, Kleinstein SH, Guan L. Hum Vaccin Immunother. 2023 Aug 1. PMID: 37697867.
Tracking B cell responses to the SARS-CoV-2 mRNA-1273 vaccine.Lopes de Assis F, Hoehn KB, Zhang X, Kardava L, Smith CD, El Merhebi O, Buckner CM, Trihemasava K, Wang W, Seamon CA, Chen V, Schaughency P, Cheung F, Martins AJ, Chiang CI, Li Y, Tsang JS, Chun TW, Kleinstein SH, Moir S. Cell Rep. 2023 Jul 25; 2023 Jul 12. PMID: 37440409.
A pipeline for the retrieval and extraction of domain-specific information with application to COVID-19 immune signatures.Newton AJH, Chartash D, Kleinstein SH, McDougal RA. BMC Bioinformatics. 2023 Jul 20; 2023 Jul 20. PMID: 37474900.
Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data.Chen X, Wang Y, Cappuccio A, Cheng WS, Zamojski FR, Nair VD, Miller CM, Rubenstein AB, Nudelman G, Tadych A, Theesfeld CL, Vornholt A, George MC, Ruffin F, Dagher M, Chawla DG, Soares-Schanoski A, Spurbeck RR, Ndhlovu LC, Sebra R, Kleinstein SH, Letizia AG, Ramos I, Fowler VG Jr, Woods CW, Zaslavsky E, Troyanskaya OG, Sealfon SC. Nat Comput Sci. 2023 Jul; 2023 Jul 25. PMID: 37974651.
High-throughput single-cell profiling of B cell responses following inactivated influenza vaccination in young and older adults.Wang M, Jiang R, Mohanty S, Meng H, Shaw AC, Kleinstein SH. Aging (Albany NY). 2023 Jun 26; 2023 Jun 26. PMID: 37367734.
Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients.Diray-Arce J, Fourati S, Doni Jayavelu N, Patel R, Maguire C, Chang AC, Dandekar R, Qi J, Lee BH, van Zalm P, Schroeder A, Chen E, Konstorum A, Brito A, Gygi JP, Kho A, Chen J, Pawar S, Gonzalez-Reiche AS, Hoch A, Milliren CE, Overton JA, Westendorf K, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen L, Grubaugh ND, van Bakel H, Wilson M, Rajan J, Steen H, Eckalbar W, Cotsapas C, Langelier CR, Levy O, Altman MC, Maecker H, Montgomery RR, Haddad EK, Sekaly RP, Esserman D, Ozonoff A, Becker PM, Augustine AD, Guan L, Peters B, Kleinstein SH. Cell Rep Med. 2023 Jun 20; 2023 May 23. PMID: 37327781.
The Plasma Cell Infiltrate Populating the Muscle Tissue of Patients with Inclusion Body Myositis Features Distinct B Cell Receptor Repertoire Properties.Jiang R, Roy B, Wu Q, Mohanty S, Nowak RJ, Shaw AC, Kleinstein SH, O'Connor KC. Immunohorizons. 2023 May 1. PMID: 37171806.
Age-associated B cells are heterogeneous and dynamic drivers of autoimmunity in mice.Nickerson KM, Smita S, Hoehn KB, Marinov AD, Thomas KB, Kos JT, Yang Y, Bastacky SI, Watson CT, Kleinstein SH, Shlomchik MJ. J Exp Med. 2023 May 1; 2023 Feb 24. PMID: 36828389.
Multiomics integration of 22 immune-mediated monogenic diseases reveals an emergent axis of human immune health.Sparks R, Rachmaninoff N, Hirsch DC, Bansal N, Lau WW, Martins AJ, Chen J, Liu CC, Cheung F, Failla LE, Biancotto A, Fantoni G, Sellers BA, Chawla DG, Howe KN, Mostaghimi D, Farmer R, Kotliarov Y, Calvo KR, Palmer C, Daub J, Foruraghi L, Kreuzburg S, Treat J, Urban AK, Jones A, Romeo T, Deuitch NT, Moura NS, Weinstein B, Moir S, Ferrucci L, Barron KS, Aksentijevich I, Kleinstein SH, Townsley DM, Young NS, Frischmeyer-Guerrerio PA, Uzel G, Pinto-Patarroyo GP, Cudrici CD, Hoffmann P, Stone DL, Ombrello AK, Freeman AF, Zerbe CS, Kastner DL, Holland SM, Tsang JS. Res Sq. 2023 Mar 20; 2023 Mar 20. PMID: 36993430.
Platelet response to influenza vaccination reflects effects of aging.Konstorum A, Mohanty S, Zhao Y, Melillo A, Vander Wyk B, Nelson A, Tsang S, Blevins TP, Belshe RB, Chawla DG, Rondina MT, Gill TM, Montgomery RR, Allore HG, Kleinstein SH, Shaw AC. Aging Cell. 2023 Feb; 2023 Jan 19. PMID: 36656789.
PD-1(high)CXCR5(-)CD4(+) peripheral helper T cells promote CXCR3(+) plasmablasts in human acute viral infection.Asashima H, Mohanty S, Comi M, Ruff WE, Hoehn KB, Wong P, Klein J, Lucas C, Cohen I, Coffey S, Lele N, Greta L, Raddassi K, Chaudhary O, Unterman A, Emu B, Kleinstein SH, Montgomery RR, Iwasaki A, Dela Cruz CS, Kaminski N, Shaw AC, Hafler DA, Sumida TS. Cell Rep. 2023 Jan 31; 2023 Jan 2. PMID: 36596303.
The memory of pathogenic IgE is contained within CD23 (+) IgG1 (+) memory B cells poised to switch to IgE in food allergy.Ota M, Hoehn KB, Ota T, Aranda CJ, Friedman S, Braga WF, Malbari A, Kleinstein SH, Sicherer SH, Curotto de Lafaille MA. bioRxiv. 2023 Jan 25; 2023 Jan 25. PMID: 36747707.
Adaptive immune responses to SARS-CoV-2 persist in the pharyngeal lymphoid tissue of children.Xu Q, Milanez-Almeida P, Martins AJ, Radtke AJ, Hoehn KB, Oguz C, Chen J, Liu C, Tang J, Grubbs G, Stein S, Ramelli S, Kabat J, Behzadpour H, Karkanitsa M, Spathies J, Kalish H, Kardava L, Kirby M, Cheung F, Preite S, Duncker PC, Kitakule MM, Romero N, Preciado D, Gitman L, Koroleva G, Smith G, Shaffer A, McBain IT, McGuire PJ, Pittaluga S, Germain RN, Apps R, Schwartz DM, Sadtler K, Moir S, Chertow DS, Kleinstein SH, Khurana S, Tsang JS, Mudd P, Schwartzberg PL, Manthiram K. Nat Immunol. 2023 Jan; 2022 Dec 19. PMID: 36536106.

2022

Multi-objective optimization identifies a specific and interpretable COVID-19 host response signature.Cappuccio A, Chawla DG, Chen X, Rubenstein AB, Cheng WS, Mao W, Burke TW, Tsalik EL, Petzold E, Henao R, McClain MT, Woods CW, Chikina M, Troyanskaya OG, Sealfon SC, Kleinstein SH, Zaslavsky E. Cell Syst. 2022 Dec 21. PMID: 36549275.
Benchmarking transcriptional host response signatures for infection diagnosis.Chawla DG, Cappuccio A, Tamminga A, Sealfon SC, Zaslavsky E, Kleinstein SH. Cell Syst. 2022 Dec 21. PMID: 36549274.
Pan-vaccine analysis reveals innate immune endotypes predictive of antibody responses to vaccination.Fourati S, Tomalin LE, Mulè MP, Chawla DG, Gerritsen B, Rychkov D, Henrich E, Miller HER, Hagan T, Diray-Arce J, Dunn P, Levy O, Gottardo R, Sarwal MM, Tsang JS, Suárez-Fariñas M, Pulendran B, Kleinstein SH, Sékaly RP. Nat Immunol. 2022 Dec; 2022 Oct 31. PMID: 36316476.
Transcriptional atlas of the human immune response to 13 vaccines reveals a common predictor of vaccine-induced antibody responses.Hagan T, Gerritsen B, Tomalin LE, Fourati S, Mulè MP, Chawla DG, Rychkov D, Henrich E, Miller HER, Diray-Arce J, Dunn P, Lee A, Levy O, Gottardo R, Sarwal MM, Tsang JS, Suárez-Fariñas M, Sékaly RP, Kleinstein SH, Pulendran B. Nat Immunol. 2022 Dec; 2022 Oct 31. PMID: 36316475.
A curated collection of human vaccination response signatures.Smith KC, Chawla DG, Dhillon BK, Ji Z, Vita R, van der Leest EC, Weng JYJ, Tang E, Abid A, Peters B, Hancock REW, Floratos A, Kleinstein SH. Sci Data. 2022 Nov 8; 2022 Nov 8. PMID: 36347894.
Reemergence of pathogenic, autoantibody-producing B cell clones in myasthenia gravis following B cell depletion therapy.Fichtner ML, Hoehn KB, Ford EE, Mane-Damas M, Oh S, Waters P, Payne AS, Smith ML, Watson CT, Losen M, Martinez-Martinez P, Nowak RJ, Kleinstein SH, O'Connor KC. Acta Neuropathol Commun. 2022 Oct 28; 2022 Oct 28. PMID: 36307868.
The Immune Signatures data resource, a compendium of systems vaccinology datasets.Diray-Arce J, Miller HER, Henrich E, Gerritsen B, Mulè MP, Fourati S, Gygi J, Hagan T, Tomalin L, Rychkov D, Kazmin D, Chawla DG, Meng H, Dunn P, Campbell J, Sarwal M, Tsang JS, Levy O, Pulendran B, Sekaly R, Floratos A, Gottardo R, Kleinstein SH, Suárez-Fariñas M. Sci Data. 2022 Oct 20; 2022 Oct 20. PMID: 36266291.
Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: Results from the IMPACC study.Ozonoff A, Schaenman J, Jayavelu ND, Milliren CE, Calfee CS, Cairns CB, Kraft M, Baden LR, Shaw AC, Krammer F, van Bakel H, Esserman DA, Liu S, Sesma AF, Simon V, Hafler DA, Montgomery RR, Kleinstein SH, Levy O, Bime C, Haddad EK, Erle DJ, Pulendran B, Nadeau KC, Davis MM, Hough CL, Messer WB, Higuita NIA, Metcalf JP, Atkinson MA, Brakenridge SC, Corry D, Kheradmand F, Ehrlich LIR, Melamed E, McComsey GA, Sekaly R, Diray-Arce J, Peters B, Augustine AD, Reed EF, Altman MC, Becker PM, Rouphael N. EBioMedicine. 2022 Sep; 2022 Aug 8. PMID: 35952496.
Phylogenetic analysis of migration, differentiation, and class switching in B cells.Hoehn KB, Pybus OG, Kleinstein SH. PLoS Comput Biol. 2022 Apr; 2022 Apr 25. PMID: 35468128.
Robust, persistent adaptive immune responses to SARS-CoV-2 in the oropharyngeal lymphoid tissue of children.Xu Q, Milanez-Almeida P, Martins AJ, Radtke AJ, Hoehn KB, Chen J, Liu C, Tang J, Grubbs G, Stein S, Ramelli S, Kabat J, Behzadpour H, Karkanitsa M, Spathies J, Kalish H, Kardava L, Kirby M, Cheung F, Preite S, Duncker PC, Romero N, Preciado D, Gitman L, Koroleva G, Smith G, Shaffer A, McBain IT, Pittaluga S, Germain RN, Apps R, Sadtler K, Moir S, Chertow DS, Kleinstein SH, Khurana S, Tsang JS, Mudd P, Schwartzberg PL, Manthiram K. Res Sq. 2022 Mar 23; 2022 Mar 23. PMID: 35350206.
Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19.Unterman A, Sumida TS, Nouri N, Yan X, Zhao AY, Gasque V, Schupp JC, Asashima H, Liu Y, Cosme C Jr, Deng W, Chen M, Raredon MSB, Hoehn KB, Wang G, Wang Z, DeIuliis G, Ravindra NG, Li N, Castaldi C, Wong P, Fournier J, Bermejo S, Sharma L, Casanovas-Massana A, Vogels CBF, Wyllie AL, Grubaugh ND, Melillo A, Meng H, Stein Y, Minasyan M, Mohanty S, Ruff WE, Cohen I, Raddassi K, Niklason LE, Ko AI, Montgomery RR, Farhadian SF, Iwasaki A, Shaw AC, van Dijk D, Zhao H, Kleinstein SH, Hafler DA, Kaminski N, Dela Cruz CS. Nat Commun. 2022 Jan 21; 2022 Jan 21. PMID: 35064122.

2021

Intranasal priming induces local lung-resident B cell populations that secrete protective mucosal antiviral IgA.Oh JE, Song E, Moriyama M, Wong P, Zhang S, Jiang R, Strohmeier S, Kleinstein SH, Krammer F, Iwasaki A. Sci Immunol. 2021 Dec 10; 2021 Dec 10. PMID: 34890255.
Human B cell lineages associated with germinal centers following influenza vaccination are measurably evolving.Hoehn KB, Turner JS, Miller FI, Jiang R, Pybus OG, Ellebedy AH, Kleinstein SH. Elife. 2021 Nov 17; 2021 Nov 17. PMID: 34787567.
Elevated N-Linked Glycosylation of IgG V Regions in Myasthenia Gravis Disease Subtypes.Mandel-Brehm C, Fichtner ML, Jiang R, Winton VJ, Vazquez SE, Pham MC, Hoehn KB, Kelleher NL, Nowak RJ, Kleinstein SH, Wilson MR, DeRisi JL, O'Connor KC. J Immunol. 2021 Oct 15; 2021 Sep 20. PMID: 34544801.
B Cell Mobilization, Dissemination, Fine Tuning of Local Antigen Specificity and Isotype Selection in Asthma.Ohm-Laursen L, Meng H, Hoehn KB, Nouri N, Jiang Y, Clouser C, Johnstone TG, Hause R, Sandhar BS, Upton NEG, Chevretton EB, Lakhani R, Corrigan CJ, Kleinstein SH, Gould HJ. Front Immunol. 2021; 2021 Oct 14. PMID: 34721376.
Mind the gap from research laboratory to clinic: Challenges and opportunities for next-generation assays in human diseases.D'Souza MP, Palin AC, Calder T, Golding H, Kleinstein SH, Milliken EL, O'Connor D, Tomaras G, Warren J, Boggiano C. Vaccine. 2021 Aug 31; 2021 Aug 6. PMID: 34366145.
LinkedImm: a linked data graph database for integrating immunological data.Bukhari SAC, Pawar S, Mandell J, Kleinstein SH, Cheung KH. BMC Bioinformatics. 2021 Aug 25; 2021 Aug 25. PMID: 34433410.
Heterogeneity of meningeal B cells reveals a lymphopoietic niche at the CNS borders.Brioschi S, Wang WL, Peng V, Wang M, Shchukina I, Greenberg ZJ, Bando JK, Jaeger N, Czepielewski RS, Swain A, Mogilenko DA, Beatty WL, Bayguinov P, Fitzpatrick JAJ, Schuettpelz LG, Fronick CC, Smirnov I, Kipnis J, Shapiro VS, Wu GF, Gilfillan S, Cella M, Artyomov MN, Kleinstein SH, Colonna M. Science. 2021 Jul 23; 2021 Jun 3. PMID: 34083450.
Comparing Host Module Activation Patterns and Temporal Dynamics in Infection by Influenza H1N1 Viruses.Nudelman I, Kudrin D, Nudelman G, Deshpande R, Hartmann BM, Kleinstein SH, Myers CL, Sealfon SC, Zaslavsky E. Front Immunol. 2021; 2021 Jul 14. PMID: 34335598.
Single-cell immunophenotyping of the skin lesion erythema migrans identifies IgM memory B cells.Jiang R, Meng H, Raddassi K, Fleming I, Hoehn KB, Dardick KR, Belperron AA, Montgomery RR, Shalek AK, Hafler DA, Kleinstein SH, Bockenstedt LK. JCI Insight. 2021 Jun 22; 2021 Jun 22. PMID: 34061047.
Cutting Edge: Distinct B Cell Repertoires Characterize Patients with Mild and Severe COVID-19.Hoehn KB, Ramanathan P, Unterman A, Sumida TS, Asashima H, Hafler DA, Kaminski N, Dela Cruz CS, Sealfon SC, Bukreyev A, Kleinstein SH. J Immunol. 2021 Jun 15; 2021 May 28. PMID: 34049971.
Divergent and self-reactive immune responses in the CNS of COVID-19 patients with neurological symptoms.Song E, Bartley CM, Chow RD, Ngo TT, Jiang R, Zamecnik CR, Dandekar R, Loudermilk RP, Dai Y, Liu F, Sunshine S, Liu J, Wu W, Hawes IA, Alvarenga BD, Huynh T, McAlpine L, Rahman NT, Geng B, Chiarella J, Goldman-Israelow B, Vogels CBF, Grubaugh ND, Casanovas-Massana A, Phinney BS, Salemi M, Alexander JR, Gallego JA, Lencz T, Walsh H, Wapniarski AE, Mohanty S, Lucas C, Klein J, Mao T, Oh J, Ring A, Spudich S, Ko AI, Kleinstein SH, Pak J, DeRisi JL, Iwasaki A, Pleasure SJ, Wilson MR, Farhadian SF. Cell Rep Med. 2021 May 18; 2021 May 3. PMID: 33969321.
Immune dysregulation and autoreactivity correlate with disease severity in SARS-CoV-2-associated multisystem inflammatory syndrome in children.Ramaswamy A, Brodsky NN, Sumida TS, Comi M, Asashima H, Hoehn KB, Li N, Liu Y, Shah A, Ravindra NG, Bishai J, Khan A, Lau W, Sellers B, Bansal N, Guerrerio P, Unterman A, Habet V, Rice AJ, Catanzaro J, Chandnani H, Lopez M, Kaminski N, Dela Cruz CS, Tsang JS, Wang Z, Yan X, Kleinstein SH, van Dijk D, Pierce RW, Hafler DA, Lucas CL. Immunity. 2021 May 11; 2021 Apr 13. PMID: 33891889.
Post-infectious inflammatory disease in MIS-C features elevated cytotoxicity signatures and autoreactivity that correlates with severity.Ramaswamy A, Brodsky NN, Sumida TS, Comi M, Asashima H, Hoehn KB, Li N, Liu Y, Shah A, Ravindra NG, Bishai J, Khan A, Lau W, Sellers B, Bansal N, Guerrerio P, Unterman A, Habet V, Rice AJ, Catanzaro J, Chandnani H, Lopez M, Kaminski N, Dela Cruz CS, Tsang JS, Wang Z, Yan X, Kleinstein SH, van Dijk D, Pierce RW, Hafler DA, Lucas CL. medRxiv. 2021 Apr 3; 2021 Apr 3. PMID: 33300011.
CD4+ follicular regulatory T cells optimize the influenza virus-specific B cell response.Lu Y, Jiang R, Freyn AW, Wang J, Strohmeier S, Lederer K, Locci M, Zhao H, Angeletti D, O'Connor KC, Kleinstein SH, Nachbagauer R, Craft J. J Exp Med. 2021 Mar 1. PMID: 33326020.
Alignment free identification of clones in B cell receptor repertoires.Lindenbaum O, Nouri N, Kluger Y, Kleinstein SH. Nucleic Acids Res. 2021 Feb 26. PMID: 33330933.
Sex-Biased Aging Effects on Ig Somatic Hypermutation Targeting.Cui A, Chawla DG, Kleinstein SH. J Immunol. 2021 Jan 1; 2020 Dec 7. PMID: 33288546.

2020

Position-Dependent Differential Targeting of Somatic Hypermutation.Zhou JQ, Kleinstein SH. J Immunol. 2020 Dec 15; 2020 Nov 13. PMID: 33188076.
Exploratory neuroimmune profiling identifies CNS-specific alterations in COVID-19 patients with neurological involvement.Song E, Bartley CM, Chow RD, Ngo TT, Jiang R, Zamecnik CR, Dandekar R, Loudermilk RP, Dai Y, Liu F, Hawes IA, Alvarenga BD, Huynh T, McAlpine L, Rahman NT, Geng B, Chiarella J, Goldman-Israelow B, Vogels CBF, Grubaugh ND, Casanovas-Massana A, Phinney BS, Salemi M, Alexander J, Gallego JA, Lencz T, Walsh H, Lucas C, Klein J, Mao T, Oh J, Ring A, Spudich S, Ko AI, Kleinstein SH, DeRisi JL, Iwasaki A, Pleasure SJ, Wilson MR, Farhadian SF. bioRxiv. 2020 Dec 9; 2020 Dec 9. PMID: 32935102.
Thymus-derived B cell clones persist in the circulation after thymectomy in myasthenia gravis.Jiang R, Hoehn KB, Lee CS, Pham MC, Homer RJ, Detterbeck FC, Aban I, Jacobson L, Vincent A, Nowak RJ, Kaminski HJ, Kleinstein SH, O'Connor KC. Proc Natl Acad Sci U S A. 2020 Dec 1; 2020 Nov 16. PMID: 33199596.
Human germinal centres engage memory and naive B cells after influenza vaccination.Turner JS, Zhou JQ, Han J, Schmitz AJ, Rizk AA, Alsoussi WB, Lei T, Amor M, McIntire KM, Meade P, Strohmeier S, Brent RI, Richey ST, Haile A, Yang YR, Klebert MK, Suessen T, Teefey S, Presti RM, Krammer F, Kleinstein SH, Ward AB, Ellebedy AH. Nature. 2020 Oct; 2020 Aug 31. PMID: 32866963.
A Potently Neutralizing Antibody Protects Mice against SARS-CoV-2 Infection.Alsoussi WB, Turner JS, Case JB, Zhao H, Schmitz AJ, Zhou JQ, Chen RE, Lei T, Rizk AA, McIntire KM, Winkler ES, Fox JM, Kafai NM, Thackray LB, Hassan AO, Amanat F, Krammer F, Watson CT, Kleinstein SH, Fremont DH, Diamond MS, Ellebedy AH. J Immunol. 2020 Aug 15; 2020 Jun 26. PMID: 32591393.
Single-cell repertoire tracing identifies rituximab-resistant B cells during myasthenia gravis relapses.Jiang R, Fichtner ML, Hoehn KB, Pham MC, Stathopoulos P, Nowak RJ, Kleinstein SH, O'Connor KC. JCI Insight. 2020 Jul 23; 2020 Jul 23. PMID: 32573488.
Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data.Nouri N, Kleinstein SH. PLoS Comput Biol. 2020 Jun; 2020 Jun 23. PMID: 32574157.
Mutant EZH2 Induces a Pre-malignant Lymphoma Niche by Reprogramming the Immune Response.Béguelin W, Teater M, Meydan C, Hoehn KB, Phillip JM, Soshnev AA, Venturutti L, Rivas MA, Calvo-Fernández MT, Gutierrez J, Camarillo JM, Takata K, Tarte K, Kelleher NL, Steidl C, Mason CE, Elemento O, Allis CD, Kleinstein SH, Melnick AM. Cancer Cell. 2020 May 11. PMID: 32396861.
Seasonal Variability and Shared Molecular Signatures of Inactivated Influenza Vaccination in Young and Older Adults.Avey S, Mohanty S, Chawla DG, Meng H, Bandaranayake T, Ueda I, Zapata HJ, Park K, Blevins TP, Tsang S, Belshe RB, Kaech SM, Shaw AC, Kleinstein SH. J Immunol. 2020 Mar 15; 2020 Feb 14. PMID: 32060136.
Single cell immune profiling of dengue virus patients reveals intact immune responses to Zika virus with enrichment of innate immune signatures.Zhao Y, Amodio M, Vander Wyk B, Gerritsen B, Kumar MM, van Dijk D, Moon K, Wang X, Malawista A, Richards MM, Cahill ME, Desai A, Sivadasan J, Venkataswamy MM, Ravi V, Fikrig E, Kumar P, Kleinstein SH, Krishnaswamy S, Montgomery RR. PLoS Negl Trop Dis. 2020 Mar; 2020 Mar 9. PMID: 32150565.
A structured model for immune exposures.Vita R, Overton JA, Dunn P, Cheung KH, Kleinstein SH, Sette A, Peters B. Database (Oxford). 2020 Jan 1. PMID: 32283555.

2019

Overexpression of T-bet in HIV infection is associated with accumulation of B cells outside germinal centers and poor affinity maturation.Austin JW, Buckner CM, Kardava L, Wang W, Zhang X, Melson VA, Swanson RG, Martins AJ, Zhou JQ, Hoehn KB, Fisk JN, Dimopoulos Y, Chassiakos A, O'Dell S, Smelkinson MG, Seamon CA, Kwan RW, Sneller MC, Pittaluga S, Doria-Rose NA, McDermott A, Li Y, Chun TW, Kleinstein SH, Tsang JS, Petrovas C, Moir S. Sci Transl Med. 2019 Nov 27. PMID: 31776286.
Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination.Hoehn KB, Vander Heiden JA, Zhou JQ, Lunter G, Pybus OG, Kleinstein SH. Proc Natl Acad Sci U S A. 2019 Nov 5; 2019 Oct 21. PMID: 31636219.
A linked data graph approach to integration of immunological data.Bukhari SAC, Mandell J, Kleinstein SH, Cheung KH. Proceedings (IEEE Int Conf Bioinformatics Biomed). 2019 Nov; 2020 Feb 6. PMID: 34707915.
Cutting Edge: Ig H Chains Are Sufficient to Determine Most B Cell Clonal Relationships.Zhou JQ, Kleinstein SH. J Immunol. 2019 Oct 1; 2019 Sep 4. PMID: 31484734.
Phenotypic and Ig Repertoire Analyses Indicate a Common Origin of IgD(-)CD27(-) Double Negative B Cells in Healthy Individuals and Multiple Sclerosis Patients.Fraussen J, Marquez S, Takata K, Beckers L, Montes Diaz G, Zografou C, Van Wijmeersch B, Villar LM, O'Connor KC, Kleinstein SH, Somers V. J Immunol. 2019 Sep 15; 2019 Aug 7. PMID: 31391234.
Migrant memory B cells secrete luminal antibody in the vagina.Oh JE, Iijima N, Song E, Lu P, Klein J, Jiang R, Kleinstein SH, Iwasaki A. Nature. 2019 Jul; 2019 Jun 12. PMID: 31189952.
Early B cell tolerance defects in neuromyelitis optica favour anti-AQP4 autoantibody production.Cotzomi E, Stathopoulos P, Lee CS, Ritchie AM, Soltys JN, Delmotte FR, Oe T, Sng J, Jiang R, Ma AK, Vander Heiden JA, Kleinstein SH, Levy M, Bennett JL, Meffre E, O'Connor KC. Brain. 2019 Jun 1. PMID: 31056665.
Reporting and connecting cell type names and gating definitions through ontologies.Overton JA, Vita R, Dunn P, Burel JG, Bukhari SAC, Cheung KH, Kleinstein SH, Diehl AD, Peters B. BMC Bioinformatics. 2019 Apr 25; 2019 Apr 25. PMID: 31272390.
Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE).Meng H, Yaari G, Bolen CR, Avey S, Kleinstein SH. PLoS Comput Biol. 2019 Apr; 2019 Apr 2. PMID: 30939133.
Inferred Allelic Variants of Immunoglobulin Receptor Genes: A System for Their Evaluation, Documentation, and Naming.Ohlin M, Scheepers C, Corcoran M, Lees WD, Busse CE, Bagnara D, Thörnqvist L, Bürckert JP, Jackson KJL, Ralph D, Schramm CA, Marthandan N, Breden F, Scott J, Matsen Iv FA, Greiff V, Yaari G, Kleinstein SH, Christley S, Sherkow JS, Kossida S, Lefranc MP, van Zelm MC, Watson CT, Collins AM. Front Immunol. 2019; 2019 Mar 18. PMID: 30936866.
Identification of Subject-Specific Immunoglobulin Alleles From Expressed Repertoire Sequencing Data.Gadala-Maria D, Gidoni M, Marquez S, Vander Heiden JA, Kos JT, Watson CT, O'Connor KC, Yaari G, Kleinstein SH. Front Immunol. 2019; 2019 Feb 13. PMID: 30814994.

2018

AIRR Community Standardized Representations for Annotated Immune Repertoires.Vander Heiden JA, Marquez S, Marthandan N, Bukhari SAC, Busse CE, Corrie B, Hershberg U, Kleinstein SH, Matsen Iv FA, Ralph DK, Rosenfeld AM, Schramm CA, Christley S, Laserson U. Front Immunol. 2018; 2018 Sep 28. PMID: 30323809.
Affinity Maturation Is Impaired by Natural Killer Cell Suppression of Germinal Centers.Rydyznski CE, Cranert SA, Zhou JQ, Xu H, Kleinstein SH, Singh H, Waggoner SN. Cell Rep. 2018 Sep 25. PMID: 30257198.
Spatiotemporal segregation of human marginal zone and memory B cell populations in lymphoid tissue.Zhao Y, Uduman M, Siu JHY, Tull TJ, Sanderson JD, Wu YB, Zhou JQ, Petrov N, Ellis R, Todd K, Chavele KM, Guesdon W, Vossenkamper A, Jassem W, D'Cruz DP, Fear DJ, John S, Scheel-Toellner D, Hopkins C, Moreno E, Woodman NL, Ciccarelli F, Heck S, Kleinstein SH, Bemark M, Spencer J. Nat Commun. 2018 Sep 21; 2018 Sep 21. PMID: 30242242.
Local Clonal Diversification and Dissemination of B Lymphocytes in the Human Bronchial Mucosa.Ohm-Laursen L, Meng H, Chen J, Zhou JQ, Corrigan CJ, Gould HJ, Kleinstein SH. Front Immunol. 2018; 2018 Sep 7. PMID: 30245687.
The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information Repositories.Bukhari SAC, O'Connor MJ, Martínez-Romero M, Egyedi AL, Willrett D, Graybeal J, Musen MA, Rubelt F, Cheung KH, Kleinstein SH. Front Immunol. 2018; 2018 Aug 16. PMID: 30166985.
Optimized Threshold Inference for Partitioning of Clones From High-Throughput B Cell Repertoire Sequencing Data.Nouri N, Kleinstein SH. Front Immunol. 2018; 2018 Jul 26. PMID: 30093903.
CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata.Bukhari SAC, Martínez-Romero M, O' Connor MJ, Egyedi AL, Willrett D, Graybeal J, Musen MA, Cheung KH, Kleinstein SH. BMC Bioinformatics. 2018 Jul 16; 2018 Jul 16. PMID: 30012108.
A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data.Nouri N, Kleinstein SH. Bioinformatics. 2018 Jul 1. PMID: 29949968.

2017

Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data.Rubelt F, Busse CE, Bukhari SAC, Bürckert JP, Mariotti-Ferrandiz E, Cowell LG, Watson CT, Marthandan N, Faison WJ, Hershberg U, Laserson U, Corrie BD, Davis MM, Peters B, Lefranc MP, Scott JK, Breden F, Luning Prak ET, Kleinstein SH. Nat Immunol. 2017 Nov 16. PMID: 29144493.
Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data.Breden F, Luning Prak ET, Peters B, Rubelt F, Schramm CA, Busse CE, Vander Heiden JA, Christley S, Bukhari SAC, Thorogood A, Matsen Iv FA, Wine Y, Laserson U, Klatzmann D, Douek DC, Lefranc MP, Collins AM, Bubela T, Kleinstein SH, Watson CT, Cowell LG, Scott JK, Kepler TB. Front Immunol. 2017; 2017 Nov 1. PMID: 29163494.
Interleukin-10 from CD4(+) follicular regulatory T cells promotes the germinal center response.Laidlaw BJ, Lu Y, Amezquita RA, Weinstein JS, Vander Heiden JA, Gupta NT, Kleinstein SH, Kaech SM, Craft J. Sci Immunol. 2017 Oct 20. PMID: 29054998.
Multiple network-constrained regressions expand insights into influenza vaccination responses.Avey S, Mohanty S, Wilson J, Zapata H, Joshi SR, Siconolfi B, Tsang S, Shaw AC, Kleinstein SH. Bioinformatics. 2017 Jul 15. PMID: 28881994.
Comment on "A Database of Human Immune Receptor Alleles Recovered from Population Sequencing Data".Watson CT, Matsen FA 4th, Jackson KJL, Bashir A, Smith ML, Glanville J, Breden F, Kleinstein SH, Collins AM, Busse CE. J Immunol. 2017 May 1. PMID: 28416712.
Polycomb Repressive Complex 2-Mediated Chromatin Repression Guides Effector CD8(+) T Cell Terminal Differentiation and Loss of Multipotency.Gray SM, Amezquita RA, Guan T, Kleinstein SH, Kaech SM. Immunity. 2017 Apr 18; 2017 Apr 11. PMID: 28410989.
Hierarchical Clustering Can Identify B Cell Clones with High Confidence in Ig Repertoire Sequencing Data.Gupta NT, Adams KD, Briggs AW, Timberlake SC, Vigneault F, Kleinstein SH. J Immunol. 2017 Mar 15; 2017 Feb 8. PMID: 28179494.
Dysregulation of B Cell Repertoire Formation in Myasthenia Gravis Patients Revealed through Deep Sequencing.Vander Heiden JA, Stathopoulos P, Zhou JQ, Chen L, Gilbert TJ, Bolen CR, Barohn RJ, Dimachkie MM, Ciafaloni E, Broering TJ, Vigneault F, Nowak RJ, Kleinstein SH, O'Connor KC. J Immunol. 2017 Feb 15; 2017 Jan 13. PMID: 28087666.
Solving Immunology?Vodovotz Y, Xia A, Read EL, Bassaganya-Riera J, Hafler DA, Sontag E, Wang J, Tsang JS, Day JD, Kleinstein SH, Butte AJ, Altman MC, Hammond R, Sealfon SC. Trends Immunol. 2017 Feb; 2016 Dec 13. PMID: 27986392.

2016

Recurrent genetic defects in classical Hodgkin lymphoma cell lines.Hudnall SD, Meng H, Lozovatsky L, Li P, Strout M, Kleinstein SH. Leuk Lymphoma. 2016 Dec; 2016 Apr 27. PMID: 27121023.

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