Publications

• MTHFR allele and one-carbon metabolic profile predict severity of COVID-19.Petrova B, Syphurs C, Culhane AJ, Chen J, Chen E, Cotsapas C, Esserman D, Montgomery RR, Kleinstein SH, Smolen KK, Mendez K, Lasky-Su J, Steen H, Levy O, Diray-Arce J, Kanarek N. Proc Natl Acad Sci U S A. 2025 Dec 23; 2025 Dec 18. PMID: 41410771.
• Sequential class switching generates antigen-specific gut IgA from IgG1 B cells.Siniscalco ER, Meng H, Gabernet G, Pacheco GA, Saghaei S, Ramirez SI, Hills LB, Faraji F, Chen S, Yin X, Dien C, Hoyt LR, Liu EG, Barrett A, Briggs N, Williams A, Shukla V, Crotty S, Wesemann DR, Kleinstein SH, Craft J, Eisenbarth SC. Immunity. 2025 Dec 9; 2025 Nov 17. PMID: 41253159.
• Evaluating COVID-19 severity prediction and immune dynamics with NULISAseq: Insights from the IMPACC study.Abe K, Holmes TH, Nguyen TT, Kim-Schulze S, Levy O, Baden LR, Melamed E, Ehrlich LIR, McComsey GA, Sekaly RP, Cairns CB, Haddad EK, Shaw AC, Hafler DA, Montgomery RR, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Agudelo Higuita NI, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Fernandez-Sesma A, Simon V, Kraft M, Bime C, Calfee CS, Erle DJ, Schaenman J, Reed EF, Ozonoff A, Peters B, Kleinstein SH, Augustine AD, Diray-Arce J, Becker PM, Rouphael N, Maecker HT. J Immunol. 2025 Dec 1. PMID: 41166719.
• Minimalistic transcriptomic signatures permit accurate early prediction of COVID-19 mortality.Narendra R, Lydon EC, Phan HV, Spottiswoode N, Neyton LP, Diray-Arce J, Becker PM, Kim-Schulze S, Hoch A, Pickering H, van Zalm P, Cairns CB, Altman MC, Augustine AD, Bosinger S, Eckalbar W, Guan L, Doni Jayavelu N, Kleinstein SH, Krammer F, Maecker HT, Ozonoff A, Peters B, Rouphael N, Montgomery RR, Reed E, Schaenman J, Steen H, Levy O, Haller SC, Erle D, Hendrickson CM, Krummel MF, Matthay MA, Woodruff P, Haddad EK, Calfee CS, Langelier CR. JCI Insight. 2025 Nov 10; 2025 Nov 10. PMID: 41212055.
• A multiomics recovery factor predicts long COVID in the IMPACC study.Gabernet G, Maciuch J, Gygi JP, Moore JF, Hoch A, Syphurs C, Chu T, Doni Jayavelu N, Corry DB, Kheradmand F, Baden LR, Sekaly RP, McComsey GA, Haddad EK, Cairns CB, Rouphael N, Fernandez-Sesma A, Simon V, Metcalf JP, Agudelo Higuita NI, Hough CL, Messer WB, Davis MM, Nadeau KC, Pulendran B, Kraft M, Bime C, Reed EF, Schaenman J, Erle DJ, Calfee CS, Atkinson MA, Brakenridge SC, Melamed E, Shaw AC, Hafler DA, Augustine AD, Becker PM, Ozonoff A, Bosinger SE, Eckalbar W, Maecker HT, Kim-Schulze S, Steen H, Krammer F, Westendorf K, Peters B, Fourati S, Altman MC, Levy O, Smolen KK, Montgomery RR, Diray-Arce J, Kleinstein SH, Guan L, Ehrlich LI. J Clin Invest. 2025 Nov 3; 2025 Sep 9. PMID: 40924481.
• Innate immune molecular landscape following controlled human influenza virus infection.Thistlethwaite W, Vangeti S, Cheng WS, Agarwal P, Cappuccio A, Wang W, Wei B, Myers R, Rubenstein AB, Chawla D, Hariharan M, McClain MT, Burke TW, Kleinstein SH, Ecker JR, Woods CW, Greenleaf WJ, Chen X, Ramos I, Zaslavsky E, Evans TG, Troyanskaya OG, Sealfon SC. Cell Rep. 2025 Oct 28; 2025 Sep 16. PMID: 40966076.
• Circulating endothelial signatures correlate with worse outcomes in COVID-19, respiratory failure and ARDS.Costa Monteiro AC, Pickering H, Sarma A, Taylor CS, Jenkins MM, Hsu FM, Nadel B, Levy O, Baden LR, Melamed E, Ehrlich LIR, McComsey GA, Sekaly RP, Cairns CB, Haddad EK, Shaw AC, Hafler DA, Montgomery RR, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Higuita NIA, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Geng LN, Fernandez-Sesma A, Simon V, Krammer F, Kraft M, Bime C, Calfee CS, Erle DJ, Bosinger S, Eckalbar W, Maecker H, Rahman A, Guan L, Peters B, Kleinstein SH, Augustine AD, Diray-Arce J, Becker PM, Rouphael N, Agus M, Kulkarni H, Schaenmann JM, Salehi-Rad R, Matthay MA, Reed EF, Sapru A. Crit Care. 2025 Oct 14; 2025 Oct 14. PMID: 41088445.
• MICBG406A polymorphism reduces risk of mechanical ventilation and death during viral acute lung injury.Pickering H, Alipanah-Lechner N, Chen E, Duchen D, Maecker HT, Kim-Schulze S, Montgomery RR, Cotsapas C, Steen H, Krammer F, Langelier CR, Levy O, Baden LR, Melamed E, Ehrlich LI, McComsey GA, Sekaly RP, Cairns CB, Haddad EK, Shaw AC, Hafler DA, 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, Kraft M, Bime C, Erle DJ, Schaenmann J, Ozonoff A, Peters B, Kleinstein SH, Augustine AD, Diray-Arce J, Becker PM, Rouphael N, Altman MC, Bosinger S, Eckalbar W, Calfee CS, Aguilar OA, Reed EF, Greenland JR, Calabrese DR. JCI Insight. 2025 Aug 8; 2025 Jul 3. PMID: 40608426.
• Mapping of human monoclonal antibody responses to XBB.1.5 COVID-19 monovalent vaccines: a B cell analysis.Fantin RF, Clark JJ, Cohn H, Jaiswal D, Bozarth B, Rao V, Civljak A, Lobo I, Nardulli JR, Srivastava K, Yong JS, Andreata-Santos R, Bushfield K, Lee ES, Singh G, Kleinstein SH, Krammer F, Simon V, Bajic G, Coelho CH. Lancet Microbe. 2025 Aug; 2025 May 30. PMID: 40456237.
• BLIMP1 controls GC B cell expansion and exit through regulating cell cycle progression and key transcription factors BCL6 and IRF4.Conter L, Smita S, Callahan D, Wu S, Brown A, Nickerson KM, Elsner RA, Meng W, Peres A, Yaari G, Kleinstein SH, Luning Prak ET, Luo W, Shlomchik M. Cell Rep. 2025 Jul 22; 2025 Jul 10. PMID: 40650910.
• High-affinity CD16A polymorphism associated with reduced risk ofsevere COVID-19.Qualls AE, Tsao T, Lui I, Lim SA, Su Y, Chen E, Duchen D, Maecker HT, Kim-Schulze S, Montgomery RR, Krammer F, Langelier CR, Levy O, Baden LR, Melamed E, Ehrlich LI, McComsey GA, Sekaly RP, Cairns CB, Haddad EK, Shaw AC, Hafler DA, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Higuita NIA, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Fernandez-Sesma A, Simon V, Kraft M, Bime C, Calfee CS, Erle DJ, Schaenmann J, Ozonoff A, Peters B, Kleinstein SH, Augustine AD, Diray-Arce J, Becker PM, Rouphael N, Goldman JD, Calabrese DR, Heath JR, Wells JA, Reed EF, Lanier LL, Pickering H, Aguilar OA. JCI Insight. 2025 Jul 8; 2025 May 22. PMID: 40402577.
• Baseline predictors for 28-day COVID-19 severity and mortality among hospitalized patients: results from the IMPACC study.Hou J, Haslund-Gourley B, Diray-Arce J, Hoch A, Rouphael N, Becker PM, Augustine AD, Ozonoff A, Guan L, Kleinstein SH, Peters B, Reed E, Altman M, Langelier CR, Maecker H, Kim S, Montgomery RR, Krammer F, Wilson M, Eckalbar W, Bosinger SE, Levy O, Steen H, Rosen LB, Baden LR, Melamed E, Ehrlich LIR, McComsey GA, Sekaly RP, Schaenman J, Shaw AC, Hafler DA, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Agudelo Higuita NI, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Fernandez Sesma A, Simon V, Kraft M, Bime C, Calfee CS, Erle DJ, Impacc Network, Robinson LF, Cairns CB, Haddad EK, Comunale MA. Front Med (Lausanne). 2025; 2025 Jul 4. PMID: 40687705.
• Single cell immunophenotyping identifies CD8(+) GZMK(+) IFNG(+) T cells as a key immune population in cutaneous Lyme disease.Aron E, Meng H, Filippidis P, Belperron AA, Kleinstein SH, Bockenstedt LK. bioRxiv. 2025 Jun 12; 2025 Jun 12. PMID: 40661371.
• Germline-encoded recognition of peanut underlies development of convergent antibodies in humans.Marini-Rapoport O, Andrieux L, Keswani T, Zong G, Duchen D, Yaari G, Min J, Lytle IR, Rosenberg AF, Fucile C, Kobie JJ, Piepenbrink MS, Sun T, Martin VM, Yuan Q, Shreffler WG, Seppo AE, Järvinen KM, Loeffler JR, Ward AB, Kleinstein SH, Pedersen LC, Fernández-Quintero ML, Mueller GA, Patil SU. Sci Transl Med. 2025 Jun 11; 2025 Jun 11. PMID: 40498852.
• Minimalistic Transcriptomic Signatures Permit Accurate Early Prediction of COVID-19 Mortality.Narendra R, Lydon EC, Van Phan H, Spottiswoode N, Neyton LP, Diray-Arce J, Becker PM, Kim-Schulze S, Hoch A, Pickering H, van Zalm P, Cairns CB, Altman MC, Augustine AD, Bosinger S, 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, Carillo SA, Erle D, Hendrickson CM, Krummel MF, Matthay MA, Woodruff P, Haddad EK, Calfee CS, Langelier CR. medRxiv. 2025 May 19; 2025 May 19. PMID: 40475132.
• Partially characterized topology guides reliable anchor-free scRNA-integration.He C, Filippidis P, Kleinstein SH, Guan L. Commun Biol. 2025 Apr 4; 2025 Apr 4. PMID: 40185996.
• Putting computational models of immunity to the test-An invited challenge to predict B.pertussis vaccination responses.Shinde P, Willemsen L, Anderson M, Aoki M, Basu S, Burel JG, Cheng P, Ghosh Dastidar S, Dunleavy A, Einav T, Forschmiedt J, Fourati S, Garcia J, Gibson W, Greenbaum JA, Guan L, Guan W, Gygi JP, Ha B, Hou J, Hsiao J, Huang Y, Jansen R, Kakoty B, Kang Z, Kobie JJ, Kojima M, Konstorum A, Lee J, Lewis SA, Li A, Lock EF, Mahita J, Mendes M, Meng H, Neher A, Nili S, Olsen LR, Orfield S, Overton JA, Pai N, Parker C, Qian B, Rasmussen M, Reyna J, Richardson E, Safo S, Sorenson J, Srinivasan A, Thrupp N, Tippalagama R, Trevizani R, Ventz S, Wang J, Wu CC, Ay F, Grant B, Kleinstein SH, Peters B. PLoS Comput Biol. 2025 Mar; 2025 Mar 31. PMID: 40163550.
• Supervised fine-tuning of pre-trained antibody language models improves antigen specificity prediction.Wang M, Patsenker J, Li H, Kluger Y, Kleinstein SH. PLoS Comput Biol. 2025 Mar; 2025 Mar 31. PMID: 40163503.
• AMULETY: A Python package to embed adaptive immune receptor sequences.Wang M, Kluger Y, Kleinstein SH, Gabernet G. bioRxiv. 2025 Mar 25; 2025 Mar 25. PMID: 40196678.
• A single-cell atlas of circulating immune cells over the first 2 months of age in extremely premature infants.Olaloye O, Gu W, Gehlhaar A, Sabuwala B, Eke CK, Li Y, Kehoe T, Farmer R, Gabernet G, Lucas CL, Tsang JS, Lakhani SA, Taylor SN, Tseng G, Kleinstein SH, Konnikova L. Sci Transl Med. 2025 Mar 5; 2025 Mar 5. PMID: 40043141.
• Identification of a multi-omics factor predictive of long COVID in the IMPACC study.Gabernet G, Maciuch J, Gygi JP, Moore JF, Hoch A, Syphurs C, Chu T, Jayavelu ND, Corry DB, Kheradmand F, Baden LR, Sekaly RP, McComsey GA, Haddad EK, Cairns CB, Rouphael N, Fernandez-Sesma A, Simon V, Metcalf JP, Agudelo Higuita NI, Hough CL, Messer WB, Davis MM, Nadeau KC, Pulendran B, Kraft M, Bime C, Reed EF, Schaenman J, Erle DJ, Calfee CS, Atkinson MA, Brackenridge SC, Melamed E, Shaw AC, Hafler DA, Ozonoff A, Bosinger SE, Eckalbar W, Maecker HT, Kim-Schulze S, Steen H, Krammer F, Westendorf K, Peters B, Fourati S, Altman MC, Levy O, Smolen KK, Montgomery RR, Diray-Arce J, Kleinstein SH, Guan L, Ehrlich LIR. bioRxiv. 2025 Feb 14; 2025 Feb 14. PMID: 39990442.
• Machine learning models predict long COVID outcomes based on baseline clinical and immunologic factors.Jayavelu ND, Samaha H, Wimalasena ST, Hoch A, Gygi JP, Gabernet G, Ozonoff A, Liu S, Milliren CE, Levy O, Baden LR, Melamed E, Ehrlich LIR, McComsey GA, Sekaly RP, Cairns CB, Haddad EK, Schaenman J, Shaw AC, Hafler DA, Montgomery RR, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Higuita NIA, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Geng LN, Sesma AF, Simon V, Krammer F, Kraft M, Bime C, Calfee CS, Erle DJ, Langelier CR, Guan L, Maecker HT, Peters B, Kleinstein SH, Reed EF, Diray-Arce J, Rouphael N, Altman MC. medRxiv. 2025 Feb 13; 2025 Feb 13. PMID: 39990570.
• Host-microbe multiomic profiling identifies distinct COVID-19 immune dysregulation in solid organ transplant recipients.Pickering H, Schaenman J, Phan HV, Maguire C, Tsitsiklis A, Rouphael N, Higuita NIA, Atkinson MA, Brakenridge S, Fung M, Messer W, Salehi-Rad R, Altman MC, Becker PM, Bosinger SE, Eckalbar W, Hoch A, Doni Jayavelu N, Kim-Schulze S, Jenkins M, Kleinstein SH, Krammer F, Maecker HT, Ozonoff A, Diray-Arce J, Shaw A, Baden L, Levy O, Reed EF, Langelier CR. Nat Commun. 2025 Jan 10; 2025 Jan 10. PMID: 39794319.
• nipalsMCIA: flexible multi-block dimensionality reduction in R via nonlinear iterative partial least squares.Mattessich M, Reyna J, Aron E, Ay F, Kilmer M, Kleinstein SH, Konstorum A. Bioinformatics. 2024 Dec 26. PMID: 39799512.
• Unraveling SARS-CoV-2 Host-Response Heterogeneity through Longitudinal Molecular Subtyping.Wang K, Nie Y, Maguire C, Syphurs C, Sheen H, Karoly M, Lapp L, Gygi JP, Jayavelu ND, Patel RK, Hoch A, Corry D, Kheradmand F, McComsey GA, Fernandez-Sesma A, Simon V, Metcalf JP, Higuita NIA, Messer WB, Davis MM, Nadeau KC, Kraft M, Bime C, Schaenman J, Erle D, Calfee CS, Atkinson MA, Brackenridge SC, Hafler DA, Shaw A, Rahman A, Hough CL, Geng LN, Ozonoff A, Haddad EK, Reed EF, van Bakel H, Kim-Schultz S, Krammer F, Wilson M, Eckalbar W, Bosinger S, Langelier CR, Sekaly RP, Montgomery RR, Maecker HT, Krumholz H, Melamed E, Steen H, Pulendran B, Augustine AD, Cairns CB, Rouphael N, Becker PM, Fourati S, Shannon CP, Smolen KK, Peters B, Kleinstein SH, Levy O, Altman MC, Iwasaki A, Diray-Arce J, Ehrlich LIR, Guan L. bioRxiv. 2024 Nov 25; 2024 Nov 25. PMID: 39651165.
• Chronic Viral Reactivation and Associated Host Immune Response and Clinical Outcomes in Acute COVID-19 and Post-Acute Sequelae of COVID-19.Maguire C, Chen J, Rouphael N, Pickering H, Phan HV, Glascock A, Chu V, Dandekar R, Corry D, Kheradmand F, Baden LR, Selaky R, McComsey GA, Haddad EK, Cairns CB, Pulendran B, Fernandez-Sesma A, Simon V, Metcalf JP, Higuita NIA, Messer WB, David MM, Nadeau KC, Kraft M, Bime C, Schaenman J, Erle D, Calfee CS, Atkinson MA, Brackenridge SC, Ehrlich LIR, Montgomery RR, Shaw AC, Hough CL, Geng LN, Hafler DA, Augustine AD, Becker PM, Peters B, Ozonoff A, Kim-Schulze SH, Krammer F, Bosinger S, Eckalbar W, Altman MC, Wilson M, Guan L, Kleinstein SH, Smolen KK, Reed EF, Levy O, Maecker H, Hunt P, Steen H, Diray-Arce J, Langelier CR, Melamed E. bioRxiv. 2024 Nov 16; 2024 Nov 16. PMID: 39605478.
• Putting computational models of immunity to the test - an invited challenge to predict B. pertussis vaccination outcomes.Shinde P, Willemsen L, Anderson M, Aoki M, Basu S, Burel JG, Cheng P, Dastidar SG, Dunleavy A, Einav T, Forschmiedt J, Fourati S, Garcia J, Gibson W, Greenbaum JA, Guan L, Guan W, Gygi JP, Ha B, Hou J, Hsiao J, Huang Y, Jansen R, Kakoty B, Kang Z, Kobie JJ, Kojima M, Konstorum A, Lee J, Lewis SA, Li A, Lock EF, Mahita J, Mendes M, Meng H, Neher A, Nili S, Olsen LR, Orfield S, Overton JA, Pai N, Parker C, Qian B, Rasmussen M, Reyna J, Richardson E, Safo S, Sorenson J, Srinivasan A, Thrupp N, Tippalagama R, Trevizani R, Ventz S, Wang J, Wu CC, Ay F, Grant B, Kleinstein SH, Peters B. bioRxiv. 2024 Sep 8; 2024 Sep 8. PMID: 39282381.
• A unified metric of human immune health.Sparks R, Rachmaninoff N, Lau WW, Hirsch DC, Bansal N, 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 JD, 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. Nat Med. 2024 Sep; 2024 Jul 3. PMID: 38961223.
• Antibody gene features associated with binding and functional activity in malaria vaccine-derived human mAbs.Coelho CH, Marquez S, Nguemwo Tentokam BC, Berhe AD, Miura K, Rao VN, Long CA, Doumbo OK, Sagara I, Healy S, Kleinstein SH, Duffy PE. NPJ Vaccines. 2024 Aug 10; 2024 Aug 10. PMID: 39127706.
• Maturation of germinal center B cells after influenza virus vaccination in humans.McIntire KM, Meng H, Lin TH, Kim W, Moore NE, Han J, McMahon M, Wang M, Malladi SK, Mohammed BM, Zhou JQ, Schmitz AJ, Hoehn KB, Carreño JM, Yellin T, Suessen T, Middleton WD, Teefey SA, Presti RM, Krammer F, Turner JS, Ward AB, Wilson IA, Kleinstein SH, Ellebedy AH. J Exp Med. 2024 Aug 5; 2024 Jun 27. PMID: 38935072.
• PI3Kγ in B cells promotes antibody responses and generation of antibody-secreting cells.Lanahan SM, Yang L, Jones KM, Qi Z, Cabrera EC, Cominsky LY, Ramaswamy A, Barmada A, Gabernet G, Uthaya Kumar DB, Xu L, Shan P, Wymann MP, Kleinstein SH, Rao VK, Mustillo P, Romberg N, Abraham RS, Lucas CL. Nat Immunol. 2024 Aug; 2024 Jul 3. PMID: 38961274.
• 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 CG, Ladd D, Polster M, Hanssen F, Heumos S, Yaari G, Kowarik MC, Nahnsen S, Kleinstein SH. PLoS Comput Biol. 2024 Jul; 2024 Jul 26. PMID: 39058741.
• Dissecting human monoclonal antibody responses from mRNA- and protein-based XBB.1.5 COVID-19 monovalent vaccines.Fantin RF, Clark JJ, Cohn H, Jaiswal D, Bozarth B, Civljak A, Rao V, Lobo I, Nardulli JR, Srivastava K, Yong J, Andreata-Santos R, Bushfield K, Lee ES, Singh G, Kleinstein SH, Krammer F, Simon V, Bajic G, Coelho CH. bioRxiv. 2024 Jul 16; 2024 Jul 16. PMID: 39071292.
• nipalsMCIA: Flexible Multi-Block Dimensionality Reduction in R via Non-linear Iterative Partial Least Squares.Mattessich M, Reyna J, Aron E, Ay F, Kilmer M, Kleinstein SH, Konstorum A. bioRxiv. 2024 Jun 10; 2024 Jun 10. PMID: 38915554.
• 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 May 15. PMID: 38557795.
• Supervised fine-tuning of pre-trained antibody language models improves antigen specificity prediction.Wang M, Patsenker J, Li H, Kluger Y, Kleinstein SH. bioRxiv. 2024 May 13; 2024 May 13. PMID: 38798340.
• 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 May 2. PMID: 38603606.
• Integrated longitudinal multiomics study identifies immune programs associated with acute COVID-19 severity and mortality.Gygi JP, Maguire C, Patel RK, Shinde P, Konstorum A, Shannon CP, Xu L, Hoch A, Jayavelu ND, Haddad EK, Reed EF, Kraft M, McComsey GA, Metcalf JP, Ozonoff A, Esserman D, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen LB, van Bakel H, Wilson M, Eckalbar WL, Maecker HT, Langelier CR, Steen H, Altman MC, Montgomery RR, Levy O, Melamed E, Pulendran B, Diray-Arce J, Smolen KK, Fragiadakis GK, Becker PM, Sekaly RP, Ehrlich LI, Fourati S, Peters B, Kleinstein SH, Guan L. J Clin Invest. 2024 May 1; 2024 May 1. PMID: 38690733.
• 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 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.
• 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.
• 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.
• 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.
• 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.