Publications

1. Zaslavsky ME, Craig E, Michuda JK, Sehgal N, Ram-Mohan N, Lee JY, Nguyen KD, Hoh RA, Pham TD, Röltgen K, Lam B, Parsons ES, Macwana SR, DeJager W, Drapeau EM, Roskin KM, Cunningham-Rundles C, Moody MA, Haynes BF, Goldman JD, Heath JR, Chinthrajah RS, Nadeau KC, Pinsky BA, Blish CA, Hensley SE, Jensen K, Meyer E, Balboni I, Utz PJ, Merrill JT, Guthridge JM, James JA, Yang S, Tibshirani R, Kundaje A, Boyd SD. Disease diagnostics using machine learning of B cell and T cell receptor sequences. Science. 2025 Feb 21;387(6736):eadp2407. doi: 10.1126/science.adp2407. Epub 2025 Feb 21. PMID: 39977494.  Link to pdf

1.     Sarin KY, Zheng H, Chaichian Y, Arunachalam PS, Swaminathan G, Eschholz A, Gao F, Wirz OF, Lam B, Yang E, Lee LW, Feng A, Lewis MA, Lin J, Maecker HT, Boyd SD, Davis MM, Nadeau KC, Pulendran B, Khatri P, Utz PJ, Zaba LC. Impaired innate and adaptive immune responses to BNT162b2 SARS-CoV-2 vaccination in systemic lupus erythematosus. JCI Insight. 2024 Mar 8;9(5):e176556. doi: 10.1172/jci.insight.176556. PMID: 38456511; PMCID: PMC10972586.

2.     Liu S, Ezran C, Wang MFZ, Li Z, Awayan K; Tabula Microcebus Consortium; Long JZ, De Vlaminck I, Wang S, Epelbaum J, Kuo CS, Terrien J, Krasnow MA, Ferrell JE Jr. An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome. Nat Commun. 2024 Mar 11;15(1):2188. doi: 10.1038/s41467-024-46070-9. PMID: 38467625; PMCID: PMC10928088.

3.     Tajima T, Martinez OM, Bernstein D, Boyd SD, Gratzinger D, Lum G, Sasaki K, Tan B, Twist CJ, Weinberg K, Armstrong B, Desai DM, Mazariegos GV, Chin C, Fishbein TM, Tekin A, Venick RS, Krams SM, Esquivel CO. Epstein-Barr virus-associated post-transplant lymphoproliferative disorders in pediatric transplantation: A prospective multicenter study in the United States. Pediatr Transplant. 2024 Jun;28(4):e14763. doi: 10.1111/petr.14763. PMID: 38682750; PMCID: PMC11115376.

4.     Satitsuksanoa P, van de Veen W, Tan G, Lopez JF, Wirz O, Jansen K, Sokolowska M, Mirer D, Globinska A, Boonpiyathad T, Schneider SR, Barletta E, Spits H, Chang I, Babayev H, Tahralı İ, Deniz G, Yücel EÖ, Kıykım A, Boyd SD, Akdis CA, Nadeau K, Akdis M. Allergen-specific B cell responses in oral immunotherapy-induced desensitization, remission, and natural outgrowth in cow's milk allergy. Allergy. 2024 Jul 11. doi: 10.1111/all.16220. Epub ahead of print. PMID: 38989779.

5.     Shah MM, Layhadi JA, Hourcade DE, Fulton WT, Tan TJ, Dunham D, Chang I, Vel MS, Fernandes A, Lee AS, Liu J, Arunachalam PS, Galli SJ, Boyd SD, Pulendran B, Davis MM, O'Hara R, Park H, Mitchell LM, Akk A, Patterson A, Jerath MR, Monroy JM, Ren Z, Kendall PL, Durham SR, Fedina A, Gibbs BF, Agache I, Chinthrajah S, Sindher SB, Heider A, Akdis CA, Shamji MH, Pham CTN, Nadeau KC. Elucidating allergic reaction mechanisms in response to SARS-CoV-2 mRNA vaccination in adults. Allergy. 2024 Jul 20. doi: 10.1111/all.16231. Epub ahead of print. PMID: 39033312.

6.     Seastedt H, Han X, Fernandes A, Galli SJ, Boyd SD, Nadeau KC, Manohar M, Chinthrajah S. Association of cytotoxic effector memory CD8⁺ T cells with sustained unresponsiveness after peanut oral immunotherapy. Allergy. 2024 Sep 7. doi: 10.1111/all.16307. Epub ahead of print. PMID: 39244697.

7.     Jacobson KB, Röltgen K, Lam B, Nayebare P, Kakuru A, Kizza J, Aguti M, Nankya F, Briggs J, Takahashi S, Greenhouse B, Rodriguez-Barraquer I, van der Ploeg K, Wohlstadter JN, Sigal GB, Roh ME, Nankabirwa JI, Cuu G, Gaw SL, Rosenthal PJ, Kamya MR, Ssewanyana I, Dorsey G, Boyd SD, Jagannathan P. Gestational SARS-CoV-2 Infection in a Ugandan Birth Cohort: High Incidence, Mild Maternal Disease, and Evidence of Association with Transient Infant Stunting. Am J Trop Med Hyg. 2024 Sep 17;111(5):1107-1117. doi: 10.4269/ajtmh.23-0801. PMID: 39288758; PMCID: PMC11542540.

8.     Zhou X, Dunham D, Sindher SB, Long A, Fernandes A, Chang I, Assa'ad A, Pongracic J, Spergel JM, Tam J, Tilles S, Wang J, Boyd SD, Chinthrajah RS, Nadeau KC. HLA-DR⁺ regulatory T cells and IL-10 are associated with success or failure of desensitization outcomes. Allergy. 2024 Sep 18. doi: 10.1111/all.16311. Epub ahead of print. PMID: 39291303.

9.     Mikelov A, Nefedev G, Tashkeev A, Rodriguez OL, Ortmans DA, Skatova V, Izraelson M, Davydov AN, Poslavsky S, Rahmouni S, Watson CT, Chudakov DM, Boyd SD, Bolotin DA. Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR. Genome Res. 2024 Oct 21:gr.278775.123. doi: 10.1101/gr.278775.123. Epub ahead of print. PMID: 39433438.

1.     Martinez OM, Krams SM, Robien MA, Lapasaran MG, Arvedson MP, Reitsma A, Balachandran Y, Harris-Arnold A, Weinberg K, Boyd SD, Armstrong B, Trickey A, Twist CJ, Gratzinger D, Tan B, Brown M, Chin C, Desai DM, Fishbein TM, Mazariegos GV, Tekin A, Venick RS, Bernstein D, Esquivel CO. Mutations in latent membrane protein 1 of Epstein-Barr virus are associated with increased risk of posttransplant lymphoproliferative disorder in children. Am J Transplant. 2023 May;23(5):611-618. doi: 10.1016/j.ajt.2023.02.014. Epub 2023 Feb 15. PMID: 36796762; PMCID: PMC10159954.

2.     Hoh RA, Thörnqvist L, Yang F, Godzwon M, King JJ, Lee JY, Greiff L, Boyd SD, Ohlin M. Clonal evolution and stereotyped sequences of human IgE lineages in aeroallergen-specific immunotherapy. J Allergy Clin Immunol. 2023 Feb 23:S0091-6749(23)00223-3. doi: 10.1016/j.jaci.2023.02.009. Epub ahead of print. PMID: 36828082.

3.     Gao F, Mallajoysula V, Arunachalam PS, van der Ploeg K, Manohar M, Röltgen K, Yang F, Wirz O, Hoh R, Haraguchi E, Lee JY, Willis R, Ramachandiran V, Li J, Kathuria KR, Li C, Lee AS, Shah MM, Sindher SB, Gonzalez J, Altman JD, Wang TT, Boyd SD, Pulendran B, Jagannathan P, Nadeau KC, Davis MM. Spheromers reveal robust T cell responses to the Pfizer/BioNTech vaccine and attenuated peripheral CD8⁺ T cell responses post SARS-CoV-2 infection. Immunity. 2023 Apr 11;56(4):864-878.e4. doi: 10.1016/j.immuni.2023.03.005. Epub 2023 Mar 16. PMID: 36996809; PMCID: PMC10017386.

4.     Rodriguez OL, Safonova Y, Silver CA, Shields K, Gibson WS, Kos JT, Tieri D, Ke H, Jackson KJL, Boyd SD, Smith ML, Marasco WA, Watson CT. Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire. Nat Commun. 2023 Jul 21;14(1):4419. doi: 10.1038/s41467-023-40070-x. PMID: 37479682; PMCID: PMC10362067.

5.     Vieira MC, Palm AE, Stamper CT, Tepora ME, Nguyen KD, Pham TD, Boyd SD, Wilson PC, Cobey S. Germline-encoded specificities and the predictability of the B cell response. PLoS Pathog. 2023 Aug 25;19(8):e1011603. doi: 10.1371/journal.ppat.1011603. PMID: 37624867; PMCID: PMC10484431.

6.     Ugale SS, Holmes TH, Maysel-Auslender S, Boyd SD, Dekker CL, Davis MM, Maecker HT. Acute Respiratory Illness Is Associated with Memory T Cell Differentiation and Other Immune Cell Changes in an Age-Associated Manner. Immunohorizons. 2023 Sep 1;7(9):611-618. doi: 10.4049/immunohorizons.2300050. PMID: 37707792; PMCID: PMC10590771.

1.     Pillet S, Arunachalam PS, Andreani G, Golden N, Fontenot J, Aye PP, Röltgen K, Lehmicke G, Gobeil P, Dubé C, Trépanier S, Charland N, D'Aoust MA, Russell-Lodrigue K, Monjure C, Blair RV, Boyd SD, Bohm RP, Rappaport J, Villinger F, Landry N, Pulendran B, Ward BJ. Safety, immunogenicity, and protection provided by unadjuvanted and adjuvanted formulations of a recombinant plant-derived virus-like particle vaccine candidate for COVID-19 in nonhuman primates. Cellular and Molecular Immunology. 2022 Feb;19(2):222-233. doi: 10.1038/s41423-021-00809-2. Epub 2022 Jan 5. PMID: 34983950; PMCID: PMC8727235.

2.     Sievers BL, Chakraborty S, Xue Y, Gelbart T, Gonzalez JC, Cassidy AG, Golan Y, Prahl M, Gaw SL, Arunachalam PS, Blish CA, Boyd SD, Davis MM, Jagannathan P, Nadeau KC, Pulendran B, Singh U, Scheuermann RH, Frieman MB, Vashee S, Wang TT, Tan GS. Antibodies elicited by SARS-CoV-2 infection or mRNA vaccines have reduced neutralizing activity against Beta and Omicron pseudoviruses. Science Translational Medicine. 2022 Mar 2;14(634):eabn7842. doi: 10.1126/scitranslmed.abn7842. Epub 2022 Mar 2. PMID: 35025672.

3.     Chakraborty S, Gonzalez JC, Sievers BL, Mallajosyula V, Chakraborty S, Dubey M, Ashraf U, Cheng BY, Kathale N, Tran KQT, Scallan C, Sinnott A, Cassidy A, Chen ST, Gelbart T, Gao F, Golan Y, Ji X, Kim-Schulze S, Prahl M, Gaw SL, Gnjatic S, Marron TU, Merad M, Arunachalam PS, Boyd SD, Davis MM, Holubar M, Khosla C, Maecker HT, Maldonado Y, Mellins ED, Nadeau KC, Pulendran B, Singh U, Subramanian A, Utz PJ, Sherwood R, Zhang S, Jagannathan P, Tan GS, Wang TT. Early non-neutralizing, afucosylated antibody responses are associated with COVID-19 severity. Science Translational Medicine. 2022 Jan 18:eabm7853. doi: 10.1126/scitranslmed.abm7853. Epub ahead of print. PMID: 35040666.

4.     Ghosh D, Pham TD, Nanaware PP, Sengupta D, Adler LN, Li CG, He X, O'Mara ME, Kantor AB, Nguyen KD, Yang Y, Eisenlohr LC, Jensen PE, Herzenberg LA, Stern LJ, Boyd SD, Ghosn EEB, Mellins ED. Regulation of the BCR signalosome by the class II peptide editor, H2-M, affects the development and repertoire of innate-like B cells. Cell Reports. 2022 Jan 25;38(4):110200. doi: 10.1016/j.celrep.2021.110200. PMID: 35081339.

5.     Zhang W, Dhondalay GK, Liu TA, Kaushik A, Hoh R, Kwok S, Kambham N, Fernandez-Becker NQ, Andorf S, Desai M, Galli SJ, Boyd SD, Nadeau KC, Manohar M, DeKruyff RH, Chinthrajah RS. Gastrointestinal γδ T cells reveal differentially expressed transcripts and enriched pathways during peanut oral immunotherapy. Allergy. 2022 Feb 10. doi: 10.1111/all.15250. Epub ahead of print. PMID: 35143054.

6.     Röltgen K, Nielsen SCA, Silva O, Younes SF, Zaslavsky M, Costales C, Yang F, Wirz OF, Solis D, Hoh RA, Wang A, Arunachalam PS, Colburg D, Zhao S, Haraguchi E, Lee AS, Shah MM, Manohar M, Chang I, Gao F, Mallajosyula V, Li C, Liu J, Shoura MJ, Sindher SB, Parsons E, Dashdorj NJ, Dashdorj ND, Monroe R, Serrano GE, Beach TG, Chinthrajah RS, Charville GW, Wilbur JL, Wohlstadter JN, Davis MM, Pulendran B, Troxell ML, Sigal GB, Natkunam Y, Pinsky BA, Nadeau KC, Boyd SD. Immune imprinting, breadth of variant recognition, and germinal center response in human SARS-CoV-2 infection and vaccination. Cell. 2022 Jan 25:S0092-8674(22)00076-9. doi: 10.1016/j.cell.2022.01.018. Epub ahead of print. PMID: 35148837; PMCID: PMC8786601.

7.     Auladell M, Phuong HVM, Mai LTQ, Tseng YY, Carolan L, Wilks S, Thai PQ, Price D, Duong NT, Hang NLK, Thanh LT, Thuong NTH, Huong TTK, Diep NTN, Bich VTN, Khvorov A, Hensen L, Duong TN, Kedzierska K, Anh DD, Wertheim H, Boyd SD, Good-Jacobson KL, Smith D, Barr I, Sullivan S, van Doorn HR, Fox A. Influenza virus infection history shapes antibody responses to influenza vaccination. Nature Medicine. 2022 Feb;28(2):363-372. doi: 10.1038/s41591-022-01690-w. Epub 2022 Feb 17. PMID: 35177857.

8.     Suthar MS, Arunachalam PS, Hu M, Reis N, Trisal M, Raeber O, Chinthrajah S, Davis-Gardner ME, Manning K, Mudvari P, Boritz E, Godbole S, Henry AR, Douek DC, Halfmann P, Kawaoka Y, Boyd SD, Davis MM, Zarnitsyna VI, Nadeau K, Pulendran B. Durability of immune responses to the BNT162b2 mRNA vaccine. Med (N Y). 2022 Jan 14;3(1):25-27. doi: 10.1016/j.medj.2021.12.005. PMID: 35590141.

9.     Su Y, Yuan D, Chen DG, Ng RH, Wang K, Choi J, Li S, Hong S, Zhang R, Xie J, Kornilov SA, Scherler K, Pavlovitch-Bedzyk AJ, Dong S, Lausted C, Lee I, Fallen S, Dai CL, Baloni P, Smith B, Duvvuri VR, Anderson KG, Li J, Yang F, Duncombe CJ, McCulloch DJ, Rostomily C, Troisch P, Zhou J, Mackay S, DeGottardi Q, May DH, Taniguchi R, Gittelman RM, Klinger M, Snyder TM, Roper R, Wojciechowska G, Murray K, Edmark R, Evans S, Jones L, Zhou Y, Rowen L, Liu R, Chour W, Algren HA, Berrington WR, Wallick JA, Cochran RA, Micikas ME; ISB-Swedish COVID-19 Biobanking Unit, Wrin T, Petropoulos CJ, Cole HR, Fischer TD, Wei W, Hoon DSB, Price ND, Subramanian N, Hill JA, Hadlock J, Magis AT, Ribas A, Lanier LL, Boyd SD, Bluestone JA, Chu H, Hood L, Gottardo R, Greenberg PD, Davis MM, Goldman JD, Heath JR. Multiple early factors anticipate post-acute COVID-19 sequelae. Cell. 2022 Jan 25:S0092-8674(22)00072-1. doi: 10.1016/j.cell.2022.01.014. Epub ahead of print. PMID: 35216672; PMCID: PMC8786632.

10.  Yang LM, Costales C, Ramanathan M, Bulterys PL, Murugesan K, Schroers-Martin J, Alizadeh AA, Boyd SD, Brown JM, Nadeau KC, Nadimpalli SS, Wang AX, Busque S, Pinsky BA, Banaei N. Cellular and humoral immune response to SARS-CoV-2 vaccination and booster dose in immunosuppressed patients: An observational cohort study. J Clin Virol. 2022 Aug;153:105217. doi: 10.1016/j.jcv.2022.105217. Epub 2022 Jun 11. PMID: 35714462; PMCID: PMC9188451.

11.  Jia X, Cao S, Lee AS, Manohar M, Sindher SB, Ahuja N, Artandi M, Blish CA, Blomkalns AL, Chang I, Collins WJ, Desai M, Din HN, Do E, Fernandes A, Geng LN, Rosenberg-Hasson Y, Mahoney MR, Glascock AL, Chan LY, Fong SY; CLIAHUB Consortium; Chan Zuckerberg Biohub; Phelps M, Raeber O; Stanford COVID-19 Biobank Study Group; Purington N, Röltgen K, Rogers AJ, Snow T, Wang TT, Solis D, Vaughan L, Verghese M, Maecker H, Wittman R, Puri R, Kistler A, Yang S, Boyd SD, Pinsky BA, Chinthrajah S, Nadeau KC. Anti-nucleocapsid antibody levels and pulmonary comorbid conditions are linked to post-COVID-19 syndrome. JCI Insight. 2022 Jul 8;7(13):e156713. doi: 10.1172/jci.insight.156713. PMID: 35801588; PMCID: PMC9310538.

12.  Serrano GE, Walker JE, Tremblay C, Piras IS, Huentelman MJ, Belden CM, Goldfarb D, Shprecher D, Atri A, Adler CH, Shill HA, Driver-Dunckley E, Mehta SH, Caselli R, Woodruff BK, Haarer CF, Ruhlen T, Torres M, Nguyen S, Schmitt D, Rapscak SZ, Bime C, Peters JL, Alevritis E, Arce RA, Glass MJ, Vargas D, Sue LI, Intorcia AJ, Nelson CM, Oliver J, Russell A, Suszczewicz KE, Borja CI, Cline MP, Hemmingsen SJ, Qiji S, Hobgood HM, Mizgerd JP, Sahoo MK, Zhang H, Solis D, Montine TJ, Berry GJ, Reiman EM, Röltgen K, Boyd SD, Pinsky BA, Zehnder JL, Talbot P, Desforges M, DeTure M, Dickson DW, Beach TG. SARS-CoV-2 Brain Regional Detection, Histopathology, Gene Expression, and Immunomodulatory Changes in Decedents with COVID-19. J Neuropathol Exp Neurol. 2022 Aug 16;81(9):666-695. doi: 10.1093/jnen/nlac056. PMID: 35818336; PMCID: PMC9278252.

13.  Feyaerts D, Hédou J, Gillard J, Chen H, Tsai ES, Peterson LS, Ando K, Manohar M, Do E, Dhondalay GKR, Fitzpatrick J, Artandi M, Chang I, Snow TT, Chinthrajah RS, Warren CM, Wittman R, Meyerowitz JG, Ganio EA, Stelzer IA, Han X, Verdonk F, Gaudillière DK, Mukherjee N, Tsai AS, Rumer KK, Jacobsen DR, Bjornson-Hooper ZB, Jiang S, Saavedra SF, Valdés Ferrer SI, Kelly JD, Furman D, Aghaeepour N, Angst MS, Boyd SD, Pinsky BA, Nolan GP, Nadeau KC, Gaudillière B, McIlwain DR. Integrated plasma proteomic and single-cell immune signaling network signatures demarcate mild, moderate, and severe COVID-19. Cell Rep Med. 2022 Jul 19;3(7):100680. doi: 10.1016/j.xcrm.2022.100680. Epub 2022 Jun 28. PMID: 35839768; PMCID: PMC9238057.

14.  Frank HK, Enard D, Boyd SD. Exceptional diversity and selection pressure on coronavirus host receptors in bats compared to other mammals. Proc Biol Sci. 2022 Jul 27;289(1979):20220193. doi: 10.1098/rspb.2022.0193. Epub 2022 Jul 27. PMID: 35892217; PMCID: PMC9326293.

15.  Sen A, Enriquez J, Rao M, Glass M, Balachandran Y, Syed S, Twist CJ, Weinberg K, Boyd SD, Bernstein D, Trickey AW, Gratzinger D, Tan B, Lapasaran MG, Robien MA, Brown M, Armstrong B, Desai D, Mazariegos G, Chin C, Fishbein TM, Venick RS, Tekin A, Zimmermann H, Trappe RU, Anagnostopoulos I, Esquivel CO, Martinez OM, Krams SM. Host microRNAs are decreased in pediatric solid-organ transplant recipients during EBV+ Post-transplant Lymphoproliferative Disorder. Front Immunol. 2022 Oct 7;13:994552. doi: 10.3389/fimmu.2022.994552. PMID: 36304469; PMCID: PMC9595046.

16.  Kaushik A, Dunham D, Han X, Do E, Andorf S, Gupta S, Fernandes A, Kost LE, Sindher SB, Yu W, Tsai M, Tibshirani R, Boyd SD, Desai M, Maecker HT, Galli SJ, Chinthrajah RS, DeKruyff RH, Manohar M, Nadeau KC. CD8⁺ T cell differentiation status correlates with the feasibility of sustained unresponsiveness following oral immunotherapy. Nat Commun. 2022 Nov 4;13(1):6646. doi: 10.1038/s41467-022-34222-8. PMID: 36333296; PMCID: PMC9636180.

17.  Goldman JD, Wang K, Röltgen K, Nielsen SCA, Roach JC, Naccache SN, Yang F, Wirz OF, Yost KE, Lee JY, Chun K, Wrin T, Petropoulos CJ, Lee I, Fallen S, Manner PM, Wallick JA, Algren HA, Murray KM, Hadlock J, Chen D, Dai CL, Yuan D, Su Y, Jeharajah J, Berrington WR, Pappas GP, Nyatsatsang ST, Greninger AL, Satpathy AT, Pauk JS, Boyd SD, Heath JR. Reinfection with SARS-CoV-2 and Waning Humoral Immunity: A Case Report. Vaccines (Basel). 2022 Dec 20;11(1):5. doi: 10.3390/vaccines11010005. PMID: 36679852; PMCID: PMC9861578.

1. Chakraborty S, Gonzalez J, Edwards K, Mallajosyula V, Buzzanco AS, Sherwood R, Buffone C, Kathale N, Providenza S, Xie MM, Andrews JR, Blish CA, Singh U, Dugan H, Wilson PC, Pham TD, Boyd SD, Nadeau KC, Pinsky BA, Zhang S, Memoli MJ, Taubenberger JK, Morales T, Schapiro JM, Tan GS, Jagannathan P, Wang TT. Proinflammatory IgG Fc structures in patients with severe COVID-19. Nature Immunology 2021 Jan;22(1):67-73. doi: 10.1038/s41590-020-00828-7. Epub 2020 Nov 9. PMID: 33169014. Link

2. Hogan CA, Gombar S, Wang H, Röltgen K, Shi RZ, Holubar M, Chang SI, Lee GM, Boyd SD, Zehnder J, Pinsky BA. Large-Scale Testing of Asymptomatic Healthcare Personnel for Severe Acute Respiratory Syndrome Coronavirus 2. Emerging Infectious Disease. 2021 Jan;27(1):250–4. doi: 10.3201/eid2701.203892. Epub 2020 Nov 30. PMID: 33256889; PMCID: PMC7774535. Link

3.    Wagar LE, Salahudeen A, Constantz CM, Wendel BS, Lyons MM, Mallajosyula V, Jatt LP, Adamska JZ, Blum LK, Gupta N, Jackson KJL, Yang F, Röltgen K, Roskin KM, Blaine KM, Meister KD, Ahmad IN, Cortese M, Dora EG, Tucker SN, Sperling AI, Jain A, Davies DH, Felgner PL, Hammer GB, Kim PS, Robinson WH, Boyd SD, Kuo CJ, Davis MM. Modeling human adaptive immune responses with tonsil organoids. Nature Medicine. 2021 Jan;27(1):125-135. doi: 10.1038/s41591-020-01145-0. Epub 2021 Jan 11. PMID: 33432170; PMCID: PMC7891554. Link

4.    Aguilera-Lizarraga J, Florens MV, Viola MF, Jain P, Decraecker L, Appeltans I, Cuende-Estevez M, Fabre N, Van Beek K, Perna E, Balemans D, Stakenborg N, Theofanous S, Bosmans G, Mondelaers SU, Matteoli G, Ibiza Martínez S, Lopez-Lopez C, Jaramillo-Polanco J, Talavera K, Alpizar YA, Feyerabend TB, Rodewald HR, Farre R, Redegeld FA, Si J, Raes J, Breynaert C, Schrijvers R, Bosteels C, Lambrecht BN, Boyd SD, Hoh RA, Cabooter D, Nelis M, Augustijns P, Hendrix S, Strid J, Bisschops R, Reed DE, Vanner SJ, Denadai-Souza A, Wouters MM, Boeckxstaens GE. Local immune response to food antigens drives meal-induced abdominal pain. Nature. 2021 Feb;590(7844):151-156. doi: 10.1038/s41586-020-03118-2. Epub 2021 Jan 13. PMID: 33442055. Link

5.    Wang H, Wiredja D, Yang L, Bulterys PL, Costales C, Röltgen K, Manalac J, Yee J, Zehnder J, Shi RZ, Boyd SD, Pinsky BA. Case-Control Study of Individuals with Discrepant Nucleocapsid and Spike Protein SARS-CoV-2 IgG Results. Clinical Chemistry. 2021 Mar 15:hvab045. doi: 10.1093/clinchem/hvab045. Epub ahead of print. PMID: 33720347; PMCID: PMC7989591. Link

6.    Manohar M, Dunham D, Gupta S, Yan Z, Zhang W, Minnicozzi S, Kirkey M, Bunning B, Chowdhury RR, Galli SJ, Boyd SD, Kost LE, Chinthrajah RS, Desai M, Oettgen HC, Maecker HT, Yu W, DeKruyff RH, Andorf S, Nadeau KC. Immune Changes Beyond Th2 Pathways During Rapid Multifood Immunotherapy enabled with Omalizumab. Allergy. 2021 Mar 30. doi: 10.1111/all.14833. Epub ahead of print. PMID: 33782956. Link

7.    Newberry JA, Gautreau M, Staats K, Carrillo E, Mulkerin W, Yang S, Kohn MA, Matheson L, Boyd SD, Pinsky BA, Blomkalns AL, Strehlow MC, D'Souza PA. SARS-CoV-2 IgG Seropositivity and Acute Asymptomatic Infection Rate Among Firefighter First Responders in an Early Outbreak County in California. Prehospital Emergency Care. 2021 Apr 5:1-10. doi: 10.1080/10903127.2021.1912227. Epub ahead of print. PMID: 33819128. Link

8.    Yang F, Nielsen SCA, Hoh RA, Röltgen K, Wirz OF, Haraguchi E, Jean GH, Lee JY, Pham TD, Jackson KJL, Roskin KM, Liu Y, Nguyen K, Ohgami RS, Osborne EM, Nadeau KC, Niemann CU, Parsonnet J, Boyd SD. Shared B cell memory to coronaviruses and other pathogens varies in human age groups and tissues. Science. 2021 Apr 12:eabf6648. doi: 10.1126/science.abf6648. Epub ahead of print. PMID: 33846272. Link

9.    Lawrence L, Stevens BA, Sahoo MK, Huang C, Yamamoto F, Röltgen K, Wirz O, Zehnder J, Shi RZ, Boyd SD, Schoolnik G, Pinsky BA, Hogan CA. Plasma as an alternative COVID-19 diagnostic specimen in a hospitalized patient negative for SARS-CoV-2 by nasopharyngeal swab. Diagnostic Microbiology Infectious Disease. 2021 Mar 4;100(3):115365. doi: 10.1016/j.diagmicrobio.2021.115365. Epub ahead of print. PMID: 33865070; PMCID: PMC7930728. Link

10.    Arunachalam PS, Walls AC, Golden N, Atyeo C, Fischinger S, Li C, Aye P, Navarro MJ, Lai L, Edara VV, Röltgen K, Rogers K, Shirreff L, Ferrell DE, Wrenn S, Pettie D, Kraft JC, Miranda MC, Kepl E, Sydeman C, Brunette N, Murphy M, Fiala B, Carter L, White AG, Trisal M, Hsieh CL, Russell-Lodrigue K, Monjure C, Dufour J, Spencer S, Doyle-Meyer L, Bohm RP, Maness NJ, Roy C, Plante JA, Plante KS, Zhu A, Gorman MJ, Shin S, Shen X, Fontenot J, Gupta S, O'Hagan DT, Van Der Most R, Rappuoli R, Coffman RL, Novack D, McLellan JS, Subramaniam S, Montefiori D, Boyd SD, Flynn JL, Alter G, Villinger F, Kleanthous H, Rappaport J, Suthar MS, King NP, Veesler D, Pulendran B. Adjuvanting a subunit COVID-19 vaccine to induce protective immunity. Nature. 2021 Apr 19. doi: 10.1038/s41586-021-03530-2. Epub ahead of print. PMID: 33873199. Link

11.     Truong TT, Ryutov A, Pandey U, Yee R, Goldberg L, Bhojwani D, Aguayo-Hiraldo P, Pinsky BA, Pekosz A, Shen L, Boyd SD, Wirz OF, Röltgen K, Bootwalla M, Maglinte DT, Ostrow D, Ruble D, Han JH, Biegel JA, Li M, Huang C, Sahoo MK, Pannaraj PS, O'Gorman M, Judkins AR, Gai X, Dien Bard J. Increased viral variants in children and young adults with impaired humoral immunity and persistent SARS-CoV-2 infection: A consecutive case series. EBioMedicine. 2021 May;67:103355. doi: 10.1016/j.ebiom.2021.103355. Epub 2021 Apr 26. PMID: 33915337; PMCID: PMC8072072.

12.     Sibai M, Solis D, Röltgen K, Stevens BA, Mfuh KO, Sahoo MK, Shi RZ, Zehnder J, Boyd SD, Pinsky BA. Evaluation of SARS-CoV-2 total antibody detection via a lateral flow nanoparticle fluorescence immunoassay. Journal of Clinical Virology 2021 Jun;139:104818. doi: 10.1016/j.jcv.2021.104818. Epub 2021 Apr 1. PMID: 33932848; PMCID: PMC8015349.

13.     Anand S, Montez-Rath ME, Han J, Garcia P, Cadden L, Hunsader P, Kerschmann R, Beyer P, Boyd SD, Chertow GM, Parsonnet J. Serial SARS-CoV-2 Receptor-Binding Domain Antibody Responses in Patients Receiving Dialysis. Annals of Internal Medicine. 2021 May 18:M21-0256. doi: 10.7326/M21-0256. Epub ahead of print. PMID: 34000201; PMCID: PMC8252842.

14. Nguyen KD, Wirz OF, Röltgen K, Pandey S, Tolentino L, Boyd SD^*, Pham TD^*. Efficient Identification of High-Titer Anti-Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Antibody Plasma Samples by Pooling Method. Archives of Pathology and Laboratory Medicine. 2021 Jun 8. doi: 10.5858/arpa.2021-0215-SA. Epub ahead of print. PMID: 34101801. [* = equal contribution]

15. Anand S, Montez-Rath ME, Han J, Garcia P, Cadden L, Hunsader P, Kerschmann R, Beyer P, Dittrich M, Block GA, Boyd SD, Parsonnet J, Chertow GM. Antibody Response to COVID-19 Vaccination in Patients Receiving Dialysis. Journal of the American Society for Nephrology. 2021 Oct;32(10):2435-2438. doi: 10.1681/ASN.2021050611. Epub 2021 Jun 11. PMID: 34117129; PMCID: PMC8722791.

16.  Anand S, Montez-Rath M, Han J, Cadden L, Hunsader P, Kerschmann R, Beyer P, Boyd SD, Garcia P, Dittrich M, Block GA, Parsonnet J, Chertow GM. Estimated SARS-CoV-2 Seroprevalence in US Patients Receiving Dialysis 1 Year After the Beginning of the COVID-19 Pandemic. JAMA Network Open. 2021 Jul 1;4(7):e2116572. doi: 10.1001/jamanetworkopen.2021.16572. PMID: 34251441; PMCID: PMC8276082.

17.     Arunachalam PS, Scott MKD, Hagan T, Li C, Feng Y, Wimmers F, Grigoryan L, Trisal M, Edara VV, Lai L, Chang SE, Feng A, Dhingra S, Shah M, Lee AS, Chinthrajah S, Sindher SB, Mallajosyula V, Gao F, Sigal N, Kowli S, Gupta S, Pellegrini K, Tharp G, Maysel-Auslender S, Hamilton S, Aoued H, Hrusovsky K, Roskey M, Bosinger SE, Maecker HT, Boyd SD, Davis MM, Utz PJ, Suthar MS, Khatri P, Nadeau KC, Pulendran B. Systems vaccinology of the BNT162b2 mRNA vaccine in humans. Nature. 2021 Aug;596(7872):410-416. doi: 10.1038/s41586-021-03791-x. Epub 2021 Jul 12. PMID: 34252919; PMCID: PMC8761119.

18.     Baker MC, Mallajosyula V, Davis MM, Boyd SD, Nadeau KC, Robinson WH. Effective viral vector response to SARS-CoV-2 booster vaccination in a patient with rheumatoid arthritis after initial ineffective response to messenger RNA vaccine. Arthritis and Rheumatology. 2022 Mar;74(3):541-542. doi: 10.1002/art.41978. Epub 2022 Jan 18. PMID: 34514750; PMCID: PMC8652858.

19.     Wirz OF, Röltgen K, Stevens BA, Pandey S, Sahoo MK, Tolentino L, Verghese M, Nguyen K, Hunter M, Snow TT, Singh AR, Blish CA, Cochran JR, Zehnder JL, Nadeau KC, Pinsky BA, Pham TD, Boyd SD. Use of Outpatient-Derived COVID-19 Convalescent Plasma in COVID-19 Patients Before Seroconversion. Frontiers in Immunology. 2021 Sep 14;12:739037. doi: 10.3389/fimmu.2021.739037. PMID: 34594341; PMCID: PMC8477649.

20.  Wang H, Hogan CA, Verghese M, Solis D, Sibai M, Huang C, Röltgen K, Stevens BA, Yamamoto F, Sahoo MK, Zehnder J, Boyd SD, Pinsky BA. SARS-CoV-2 Nucleocapsid Plasma Antigen for Diagnosis and Monitoring of COVID-19. Clinical Chemistry. 2021 Dec 30;68(1):204-213. doi: 10.1093/clinchem/hvab216. PMID: 34605900; PMCID: PMC8522398.

21.  Le BL, Sper R, Nielsen SCA, Pineda S, Nguyen QH, Lee JY, Boyd SD, MacKenzie TC, Sirota M. Maternal and Infant Immune Repertoire Sequencing Analysis Identifies Distinct Ig and TCR Development in Term and Preterm Infants. Journal of Immunology. 2021 Nov 15;207(10):2445-2455. doi: 10.4049/jimmunol.2100566. Epub 2021 Oct 15. PMID: 34654689; PMCID: PMC8578401.

22.  Dashdorj NJ, Wirz OF, Röltgen K, Haraguchi E, Buzzanco AS 3rd, Sibai M, Wang H, Miller JA, Solis D, Sahoo MK, Arunachalam PS, Lee AS, Shah MM, Liu J, Byambabaatar S, Bat-Ulzii P, Enkhbat A, Batbold E, Zulkhuu D, Ochirsum B, Khurelsukh T, Dalantai G, Burged N, Baatarsuren U, Ariungerel N, Oidovsambuu O, Bungert AS, Genden Z, Yagaanbuyant D, Mordorj A, Pulendran B, Chinthrajah S, Nadeau KC, Jardetzky T, Wilbur JL, Wohlstadter JN, Sigal GB, Pinsky BA, Boyd SD*, Dashdorj ND*. Direct comparison of antibody responses to four SARS-CoV-2 vaccines in Mongolia. Cell Host & Microbe. 2021 Dec 8;29(12):1738-1743.e4. doi: 10.1016/j.chom.2021.11.004. Epub 2021 Nov 12. PMID: 34861167; PMCID: PMC8585611. [*=equal contribution]

1. Roskin KM, Jackson KJL, Lee J-Y, Hoh RA, Joshi SA, Hwang K-K, Bonsignori M, Pedroza-Pacheco I, Liao H, Moody MA, Fire AZ, Borrow P, Haynes BF, Boyd SD. Aberrant B cell repertoire selection associated with HIV neutralizing antibody breadth. Nature Immunology.  2020 Jan 20. doi: 10.1038/s41590-019-0581-0. PubMed PMID: 31959979. Link

2. Hoh RA, Joshi SA, Lee J-Y, Martin BA, Varma S, Kwok S, Nielsen SCA, Nejad P, Haraguchi E, Dixit PS, Shutthanandan SV, Roskin KM, Zhang W, Tupa D, Bunning BJ, Manohar M, Tibshirani R, Fernandez-Becker NQ, Kambham N, West RB, Hamilton RG, Tsai M, Galli SJ, Chinthrajah RS, Nadeau KC, Boyd SD. Origins and clonal convergence of gastrointestinal IgE+ B cells in human peanut allergy. Science Immunology. 2020 Mar 6;5(45):eaay4209. doi: 10.1126/sciimmunol.aay4209. PMID: 32139586. Link

3. Wright BL, Fernandez-Becker NQ, Kambham N, Purington N, Cao S, Tupa D, Zhang W, Sindher SB, Rank MA, Kita H, Katzka DA, Shim KP, Bunning BJ, Doyle AD, Jacobsen EA, Tsai M, Boyd SD, Manohar M, Chinthrajah RS. Gastrointestinal Eosinophil Responses in a Longitudinal, Randomized Trial of Peanut Oral Immunotherapy. Clinics in Gastroenterology and  Hepatology. 2020 May 17:S1542-3565(20)30676-5. doi: 10.1016/j.cgh.2020.05.019. PMID: 32434067 Link

4. Scott GD, Kumar J, Oak JS, Boyd SD, Raess PW, Gratzinger DA. Histology-Independent Signature Distinguishes Kikuchi-Fujimoto Disease/Systemic Lupus Erythematosus-Associated Lymphadenitis From Benign and Malignant Lymphadenopathies. American Journal of Clinical Pathology. 2020 Jul 7;154(2):215-224. doi: 10.1093/ajcp/aqaa036. PMID: 32367142 Link

5. Ellebedy AH, Nachbagauer R, Jackson KJL, Dai YN, Han J, Alsoussi WB, Davis CW, Stadlbauer D, Rouphael N, Chromikova V, McCausland M, Chang CY, Cortese M, Bower M, Chennareddy C, Schmitz AJ, Zarnitsyna VI, Lai L, Rajabhathor A, Kazemian C, Antia R, Mulligan MJ, Ward AB, Fremont DH, Boyd SD, Pulendran B, Krammer F, Ahmed R. Adjuvanted H5N1 influenza vaccine enhances both cross-reactive memory B cell and strain-specific naive B cell responses in humans. Proceedings of the National Academy of Sciences U S A. 2020 Jul 13:201906613. doi: 10.1073/pnas.1906613117. PMID: 32661157 Link

6. Pham TD, Huang C, Wirz OF, Röltgen K, Sahoo MK, Layon A, Pandey S, Foung SK, Boyd SD, Pinsky BA. SARS-CoV-2 RNAemia in a Healthy Blood Donor 40 Days After Respiratory Illness Resolution. Annals of Internal Medicine. 2020 Jul 17. doi: 10.7326/L20-0725. PMID: 32678685 Link

7. Davis CW, Jackson KJL, McCausland MM, Darce J, Chang C, Linderman SL, Chennareddy C, Gerkin R, Brown SJ, Wrammert J, Mehta AK, Cheung WC, Boyd SD, Waller EK, Ahmed R. Influenza vaccine-induced human bone marrow plasma cells decline within a year after vaccination. Science. 2020 Aug 13:eaaz8432. doi: 10.1126/science.aaz8432. Online ahead of print. PMID: 32792465 Link

8. Nielsen SCA, Yang F, Jackson KJL, Hoh RA, Röltgen K,Jean GH, Stevens BA, Lee J, Rustagi A, Rogers AJ, Powell AE, Hunter M, Najeeb J, Otrelo-Cardoso AR, Yost KE, Daniel B, Nadeau KC, Chang HY, Satpathy AT, Jardetzky TS, Kim PS, Wang TT, Pinsky BA, Blish CA, Boyd SD. Human B cell clonal expansion and convergent antibody responses to SARS-CoV-2. Cell Host and Microbe. Published online:September 03, 2020 DOI:https://doi.org/10.1016/j.chom.2020.09.002. PMID: 32941787. Link

9. Wang W, Lyu SC, Ji X, Gupta S, Manohar M, Dhondalay GKR, Chinthrajah S, Andorf S, Boyd SD, Tibshirani R, Galli SJ, Nadeau KC, Maecker HT. Transcriptional changes in peanut-specific CD4+ T cells over the course of oral immunotherapy. Clinical Immunology. 2020 Oct;219:108568. doi: 10.1016/j.clim.2020.108568. Epub 2020 Aug 9. PMID: 32783912 Link

10. Röltgen K, Powell AE, Wirz OF, Stevens BA, Hogan CA, Najeeb J, Hunter M, Wang H, Sahoo MK, Huang C, Yamamoto F, Manohar M, Manalac J, Otrelo-Cardoso AR, Pham TD, Rustagi A, Rogers AJ, Shah NH, Blish CA, Cochran JR, Jardetzky TS, Zehnder JL, Wang TT, Narasimhan B, Gombar S, Tibshirani R, Nadeau KC, Kim PS, Pinsky BA, Boyd SD. Defining the features and duration of antibody responses to SARS-CoV-2 infection associated with disease severity and outcome. Science Immunology. 2020 Dec 7;5(54):eabe0240. doi: 10.1126/sciimmunol.abe0240. PMID: 33288645; PMCID: PMC7857392. Link

12. Rosser JI, Röltgen K, Dymock M, Shepard J, Martin A, Hogan CA, Blomkalns A, Mathew R, Parsonnet J, Pinsky BA, Maldonado YA, Boyd SD, Chang SI, Holubar M; Stanford Healthcare COVID-19 Workforce Response Group. Severe acute respiratory coronavirus virus 2 (SARS-CoV-2) seroprevalence in healthcare personnel in northern California early in the coronavirus disease 2019 (COVID-19) pandemic. Infection Control and Hospital Epidemiology. 2020 Dec 9:1-7. doi: 10.1017/ice.2020.1358. Epub ahead of print. PMID: 33292895; PMCID: PMC7783083. Link

13.    Satitsuksanoa P, Daanje M, Akdis M, Boyd SD, van de Veen W. Biology and dynamics of B cells in the context of IgE-mediated food allergy. Allergy. 2020 Dec 3. doi: 10.1111/all.14684. Epub ahead of print. PMID: 33274454 Link

14.    Paranjape A, Tsai M, Mukai K, Hoh RA, Joshi SA, Chinthrajah RS, Nadeau KC, Boyd SD, Galli SJ. Oral Immunotherapy and Basophil and Mast Cell Reactivity in Food Allergy. Frontiers in Immunology. 2020 Dec 14;11:602660. doi: 10.3389/fimmu.2020.602660. PMID: 33381123; PMCID: PMC7768812. Link

1. Nielsen SCA, Roskin KM, Jackson KJL, Joshi SA, Nejad P, Lee JY, Wagar LE, Pham TD, Hoh RA, Nguyen KD, Tsunemoto HY, Patel SB, Tibshirani R, Ley C, Davis MM, Parsonnet J, Boyd SD. Shaping of infant B cell receptor repertoires by environmental factors and infectious disease. Science Translational Medicine 2019 Feb 27;11(481). pii: eaat2004. doi: 10.1126/scitranslmed.aat2004. PubMed PMID: 30814336. Link

2. Nielsen SCA, Boyd SD. New technologies and applications in infant B cell immunology. Current Opinions in Immunology 2019 Apr;57:53-57. doi: 10.1016/j.coi.2018.12.005. Epub 2019 Feb 27. Review. PubMed PMID: 30825678; PubMed Central PMCID: PMC6511472. Link

3. Tian L, Liu Y, Fire AZ, Boyd SD, Olshen RA. Clonality: Point Estimation. Annals of Applied Statistics. Volume 13, Number 1 (March 2019), 113-131. Link

4. Davis CW, Jackson KJL, McElroy AK, Halfmann P, Huang J, Chennareddy C, Piper AE, Leung Y, Albariño CG, Crozier I, Ellebedy AH, Sidney J, Sette A, Yu T, Nielsen SCA, Goff AJ, Spiropoulou CF, Saphire EO, Cavet G, Kawaoka Y, Mehta AK, Glass PJ, Boyd SD, Ahmed R. Longitudinal Analysis of the Human B Cell Response to Ebola Virus Infection. Cell. 2019 May 30;177(6):1566-1582.e17. doi: 10.1016/j.cell.2019.04.036. Epub 2019 May 16. PubMed PMID: 31104840. Link

5. Chinthrajah RS, Purington N, Andorf S, Long A, O'Laughlin KL, Lyu SC, Manohar M, Boyd SD, Tibshirani R, Maecker H, Plaut M, Mukai K, Tsai M, Desai M, Galli SJ, Nadeau KC. Sustained outcomes in oral immunotherapy for peanut allergy (POISED study): a large, randomised, double-blind, placebo-controlled, phase 2 study. Lancet. 2019 Sep 12. pii: S0140-6736(19)31793-3. doi:10.1016/S0140-6736(19)31793-3. PubMed PMID: 31522849. Link

6.  Omer A, Shemesh O, Peres A, Polak P, Shepherd AJ, Watson CT, Boyd SD, Collins AM, Lees W, Yaari G. VDJbase: an adaptive immune receptor genotype and haplotype database. Nucleic Acids Research. 2019 Oct 11. pii: gkz872. doi: 10.1093/nar/gkz872. PubMed PMID: 31602484. Link

1: Kaul V, Weinberg KI, Boyd SD, Bernstein D, Esquivel CO, Martinez OM, Krams SM. Dynamics of Viral and Host Immune Cell MicroRNA Expression during Acute Infectious Mononucleosis. Frontiers in Microbiology. 2018 Jan 15;8:2666. doi: 10.3389/fmicb. 2017.02666. eCollection 2017. PubMed PMID: 29379474; PubMed Central PMCID: PMC5775229. Link

2. Nielsen SCA, Boyd SD. Human adaptive immune receptor repertoire analysis- Past, present, and future. Immunological Reviews. 2018 Jul;284(1):9-23. doi: 10.1111/imr.12667. PubMed PMID: 29944765. Link

3. Dhondalay GK, Rael E, Acharya S, Zhang W, Sampath V, Galli SJ, Tibshirani R, Boyd SD, Maecker H, Nadeau KC, Andorf S. Food allergy and omics. Journal of Allergy and Clinical Immunology. 2018 Jan;141(1):20-29. doi: 10.1016/j.jaci.2017.11.007. PubMed PMID: 29307411.

4. Hoh RA, Boyd SD. Gut Mucosal Antibody Responses and Implications for Food Allergy. Frontiers in Immunology 2018 Sep 27;9:2221. doi: 10.3389/fimmu.2018.02221. eCollection 2018. Review. PubMed PMID: 30319658; PubMed Central PMCID:PMC6170638. Link

5. Frank HK, Boyd SD, Hadly EA. Global fingerprint of humans on the distribution of Bartonella bacteria in mammals. PLoS Neglected Tropical Diseases 2018 Nov 15;12(11):e0006865. doi: 10.1371/journal.pntd.0006865. eCollection 2018 Nov. PubMed PMID: 30439961; PubMed Central PMCID: PMC6237287. Link

6. Wright BL, Fernandez-Becker NQ, Kambham N, Purington N, Tupa D, Zhang W, Rank MA, Kita H, Shim KP, Bunning BJ, Doyle AD, Jacobsen EA, Boyd SD, Tsai M, Maecker H, Manohar M, Galli SJ, Nadeau KC, Chinthrajah RS. Baseline Gastrointestinal Eosinophilia Is Common in Oral Immunotherapy Subjects With IgE-Mediated Peanut Allergy. Frontiers in Immunology 2018 Nov 22;9:2624. doi: 10.3389/fimmu.2018.02624. eCollection 2018. PubMed PMID: 30524424; PubMed Central PMCID: PMC6261984. Link

1: Pham TD, Chng MHY, Roskin KM, Jackson KJL, Nguyen KD, Glanville J, Lee JY, Engleman EG, Boyd SD. High-fat diet induces systemic B-cell repertoire changes associated with insulin resistance. Mucosal Immunol. 2017 Apr 19. doi:10.1038/mi.2017.25. [Epub ahead of print] PubMed PMID: 28422186. Link


2: Glanville J, Huang H, Nau A, Hatton O, Wagar LE, Rubelt F, Ji X, Han A, Krams SM, Pettus C, Haas N, Arlehamn CSL, Sette A, Boyd SD, Scriba TJ, Martinez OM, Davis MM. Identifying specificity groups in the T cell receptor repertoire. Nature. 2017 Jun 21. doi: 10.1038/nature22976. [Epub ahead of print] PubMed PMID: 28636589. Link

1: Ellebedy AH*, Jackson KJ*, Kissick HT, Nakaya HI, Davis CW, Roskin KM, McElroy AK, Oshansky CM, Elbein R, Thomas S, Lyon GM, Spiropoulou CF, Mehta AK, Thomas PG, Boyd SD*, Ahmed R*. Defining antigen-specific plasmablast and memory B cell subsets in human blood after viral infection or vaccination. Nat Immunol. 2016 Oct;17(10):1226-34. doi: 10.1038/ni.3533. Epub 2016 Aug 15. PubMed PMID: 27525369. [*= equal contribution] Link


2: Bradley T, Trama A, Tumba N, Gray E, Lu X, Madani N, Jahanbakhsh F, Eaton A, Xia SM, Parks R, Lloyd KE, Sutherland LL, Scearce RM, Bowman CM, Barnett S, Abdool-Karim SS, Boyd SD, Melillo B, Smith AB 3rd, Sodroski J, Kepler TB, Alam SM, Gao F, Bonsignori M, Liao HX, Moody MA, Montefiori D, Santra S, Morris L, Haynes BF. Amino Acid Changes in the HIV-1 gp41 Membrane Proximal Region Control Virus Neutralization Sensitivity. EBioMedicine. 2016 Aug 31. pii: S2352-3964(16)30402-9. doi: 10.1016/j.ebiom.2016.08.045. [Epub ahead of print] PubMed PMID: 27612593. Link


3: Jackson KJ, Boyd SD. Broadening Horizons: New Antibodies Against Influenza. Cell. 2016 Jul 28;166(3):532-3. doi: 10.1016/j.cell.2016.07.023. PubMed PMID: 27471961. Link


4: Boyd SD, Crowe JE Jr. Deep sequencing and human antibody repertoire analysis. Curr Opin Immunol. 2016 Jun;40:103-9. doi: 10.1016/j.coi.2016.03.008. Epub 2016 Apr 8. Review. PubMed PMID: 27065089. Link


5: Levin M, King JJ, Glanville J, Jackson KJ, Looney TJ, Hoh RA, Mari A, Andersson M, Greiff L, Fire AZ, Boyd SD, Ohlin M. Persistence and evolution of allergen-specific IgE repertoires during subcutaneous specific immunotherapy. J Allergy Clin Immunol. 2016 May;137(5):1535-44. doi: 10.1016/j.jaci.2015.09.027. Epub 2015 Nov 11. PubMed PMID: 26559321; PubMed Central PMCID: PMC5010428. Link


6: Bonsignori M, Zhou T, Sheng Z, Chen L, Gao F, Joyce MG, Ozorowski G, Chuang GY, Schramm CA, Wiehe K, Alam SM, Bradley T, Gladden MA, Hwang KK, Iyengar S, Kumar A, Lu X, Luo K, Mangiapani MC, Parks RJ, Song H, Acharya P, Bailer RT, Cao A, Druz A, Georgiev IS, Kwon YD, Louder MK, Zhang B, Zheng A, Hill BJ, Kong R, Soto C; NISC Comparative Sequencing Program, Mullikin JC, Douek DC, Montefiori DC, Moody MA, Shaw GM, Hahn BH, Kelsoe G, Hraber PT, Korber BT, Boyd SD, Fire AZ, Kepler TB, Shapiro L, Ward AB, Mascola JR, Liao HX, Kwong PD, Haynes BF. Maturation Pathway from Germline to Broad HIV-1 Neutralizer of a CD4-Mimic Antibody. Cell. 2016 Apr 7;165(2):449-63. doi: 10.1016/j.cell.2016.02.022. Epub 2016 Mar 3. PubMed PMID: 26949186; PubMed Central PMCID: PMC4826291. Link


7: Chinthrajah RS, Hernandez JD, Boyd SD, Galli SJ, Nadeau KC. Molecular and cellular mechanisms of food allergy and food tolerance. J Allergy Clin Immunol. 2016 Apr;137(4):984-97. doi: 10.1016/j.jaci.2016.02.004. Review. PubMed PMID: 27059726; PubMed Central PMCID: PMC5030841. Link


8: Qi Q, Cavanagh MM, Le Saux S, NamKoong H, Kim C, Turgano E, Liu Y, Wang C, Mackey S, Swan GE, Dekker CL, Olshen RA, Boyd SD, Weyand CM, Tian L, Goronzy JJ. Diversification of the antigen-specific T cell receptor repertoire after varicella zoster vaccination. Sci Transl Med. 2016 Mar 30;8(332):332ra46. doi: 10.1126/scitranslmed.aaf1725. PubMed PMID: 27030598; PubMed Central PMCID: PMC4878824. Link


9: Ryan JF, Hovde R, Glanville J, Lyu SC, Ji X, Gupta S, Tibshirani RJ, Jay DC, Boyd SD, Chinthrajah RS, Davis MM, Galli SJ, Maecker HT, Nadeau KC. Successful immunotherapy induces previously unidentified allergen-specific CD4+ T-cell subsets. Proc Natl Acad Sci U S A. 2016 Mar 1;113(9):E1286-95. doi: 10.1073/pnas.1520180113. Epub 2016 Jan 25. PubMed PMID: 26811452; PubMed Central PMCID: PMC4780622. Link


10: Looney TJ, Lee JY, Roskin KM, Hoh RA, King J, Glanville J, Liu Y, Pham TD, Dekker CL, Davis MM, Boyd SD. Human B-cell isotype switching origins of IgE. J Allergy Clin Immunol. 2016 Feb;137(2):579-586.e7. doi: 10.1016/j.jaci.2015.07.014. Epub 2015 Aug 22. PubMed PMID: 26309181; PubMed Central PMCID: PMC4747810. Link


11: Kidd MJ, Jackson KJ, Boyd SD, Collins AM. DJ Pairing during VDJ Recombination Shows Positional Biases That Vary among Individuals with Differing IGHD Locus Immunogenotypes. J Immunol. 2016 Feb 1;196(3):1158-64. doi: 10.4049/jimmunol.1501401. Epub 2015 Dec 23. PubMed PMID: 26700767; PubMed Central PMCID: PMC4724508. Link


12: Hoh RA, Joshi SA, Liu Y, Wang C, Roskin KM, Lee JY, Pham T, Looney TJ, Jackson KJ, Dixit VP, King J, Lyu SC, Jenks J, Hamilton RG, Nadeau KC, Boyd SD. Single B-cell deconvolution of peanut-specific antibody responses in allergic patients. J Allergy Clin Immunol. 2016 Jan;137(1):157-67. doi: 10.1016/j.jaci.2015.05.029. Epub 2015 Jul 4. PubMed PMID: 26152318; PubMed Central PMCID: PMC4699867. Link

1: Roskin KM, Simchoni N, Liu Y, Lee JY, Seo K, Hoh RA, Pham T, Park JH, Furman D, Dekker CL, Davis MM, James JA, Nadeau KC, Cunningham-Rundles C, Boyd SD. IgH sequences in common variable immune deficiency reveal altered B cell development and selection. Sci Transl Med. 2015 Aug 26;7(302):302ra135. doi: 10.1126/scitranslmed.aab1216. PubMed PMID: 26311730; PubMed Central PMCID: PMC4584259. Link


2: Laudadio J, McNeal JL, Boyd SD, Le LP, Lockwood C, McCloskey CB, Sharma G, Voelkerding KV, Haspel RL. Design of a Genomics Curriculum: Competencies for Practicing Pathologists. Arch Pathol Lab Med. 2015 Jul;139(7):894-900. doi: 10.5858/arpa.2014-0253-CP. PubMed PMID: 26125429. Link


3: Boyd SD, Jackson KJ. Predicting vaccine responsiveness. Cell Host Microbe. 2015 Mar 11;17(3):301-7. doi: 10.1016/j.chom.2015.02.015. Review. PubMed PMID: 25766292. Link


4: Wang C, Liu Y, Cavanagh MM, Le Saux S, Qi Q, Roskin KM, Looney TJ, Lee JY, Dixit V, Dekker CL, Swan GE, Goronzy JJ, Boyd SD. B-cell repertoire responses to varicella-zoster vaccination in human identical twins. Proc Natl Acad Sci U S A. 2015 Jan 13;112(2):500-5. doi: 10.1073/pnas.1415875112. Epub 2014 Dec 22. PubMed PMID: 25535378; PubMed Central PMCID: PMC4299233. Link


5: Wang C, Liu Y, Roskin KM, Jackson KJ, Boyd SD. Laboratory and Data Analysis Methods for Characterization of Human B Cell Repertoires by High-Throughput DNA Sequencing. Methods Mol Biol. 2015;1343:219-33. doi:10.1007/978-1-4939-2963-4_17. PubMed PMID: 26420720. Link

1: Boyd SD, Joshi SA. High-Throughput DNA Sequencing Analysis of Antibody Repertoires. Microbiol Spectr. 2014 Oct;2(5). doi: 10.1128/microbiolspec.AID-0017-2014. Review. PubMed PMID: 26104353. Link


2: Kepler TB, Liao HX, Alam SM, Bhaskarabhatla R, Zhang R, Yandava C, Stewart S, Anasti K, Kelsoe G, Parks R, Lloyd KE, Stolarchuk C, Pritchett J, Solomon E, Friberg E, Morris L, Karim SS, Cohen MS, Walter E, Moody MA, Wu X, Altae-Tran HR, Georgiev IS, Kwong PD, Boyd SD, Fire AZ, Mascola JR, Haynes BF. Immunoglobulin gene insertions and deletions in the affinity maturation of HIV-1 broadly reactive neutralizing antibodies. Cell Host Microbe. 2014 Sep 10;16(3):304-13. doi: 10.1016/j.chom.2014.08.006. PubMed PMID: 25211073; PubMed Central PMCID: PMC4163498. Link


3: Qi Q, Liu Y, Cheng Y, Glanville J, Zhang D, Lee JY, Olshen RA, Weyand CM, Boyd SD, Goronzy JJ. Diversity and clonal selection in the human T-cell repertoire. Proc Natl Acad Sci U S A. 2014 Sep 9;111(36):13139-44. doi: 10.1073/pnas.1409155111. Epub 2014 Aug 25. PubMed PMID: 25157137; PubMed Central PMCID: PMC4246948. Link


4: Boyd SD, Galli SJ, Schrijver I, Zehnder JL, Ashley EA, Merker JD. A Balanced Look at the Implications of Genomic (and Other "Omics") Testing for Disease Diagnosis and Clinical Care. Genes (Basel). 2014 Sep 1;5(3):748-66. doi: 10.3390/genes5030748. PubMed PMID: 25257203; PubMed Central PMCID: PMC4198929. Link


5: Trama AM, Moody MA, Alam SM, Jaeger FH, Lockwood B, Parks R, Lloyd KE, Stolarchuk C, Scearce R, Foulger A, Marshall DJ, Whitesides JF, Jeffries TL Jr, Wiehe K, Morris L, Lambson B, Soderberg K, Hwang KK, Tomaras GD, Vandergrift N, Jackson KJ, Roskin KM, Boyd SD, Kepler TB, Liao HX, Haynes BF. HIV-1 envelope gp41 antibodies can originate from terminal ileum B cells that share cross-reactivity with commensal bacteria. Cell Host Microbe. 2014 Aug 13;16(2):215-26. doi: 10.1016/j.chom.2014.07.003. PubMed PMID: 25121750; PubMed Central PMCID: PMC4294419. Link


6: Jackson KJ, Liu Y, Roskin KM, Glanville J, Hoh RA, Seo K, Marshall EL, Gurley TC, Moody MA, Haynes BF, Walter EB, Liao HX, Albrecht RA, García-Sastre A, Chaparro-Riggers J, Rajpal A, Pons J, Simen BB, Hanczaruk B, Dekker CL, Laserson J, Koller D, Davis MM, Fire AZ, Boyd SD. Human responses to influenza vaccination show seroconversion signatures and convergent antibody rearrangements. Cell Host  Microbe. 2014 Jul 9;16(1):105-14. doi: 10.1016/j.chom.2014.05.013. Epub 2014 Jun 26. PubMed PMID: 24981332; PubMed Central PMCID: PMC4158033. Link


7: Bonsignori M, Wiehe K, Grimm SK, Lynch R, Yang G, Kozink DM, Perrin F, Cooper AJ, Hwang KK, Chen X, Liu M, McKee K, Parks RJ, Eudailey J, Wang M, Clowse M, Criscione-Schreiber LG, Moody MA, Ackerman ME, Boyd SD, Gao F, Kelsoe G, Verkoczy L, Tomaras GD, Liao HX, Kepler TB, Montefiori DC, Mascola JR, Haynes BF. An autoreactive antibody from an SLE/HIV-1 individual broadly neutralizes HIV-1. J Clin Invest. 2014 Apr;124(4):1835-43. doi: 10.1172/JCI73441. Epub 2014 Mar 10. PubMed PMID: 24614107; PubMed Central PMCID: PMC3973118. Link


8: Wang C, Liu Y, Xu LT, Jackson KJ, Roskin KM, Pham TD, Laserson J, Marshall EL, Seo K, Lee JY, Furman D, Koller D, Dekker CL, Davis MM, Fire AZ, Boyd SD. Effects of aging, cytomegalovirus infection, and EBV infection on human B cell repertoires. J Immunol. 2014 Jan 15;192(2):603-11. doi: 10.4049/jimmunol.1301384. Epub 2013 Dec 11. PubMed PMID: 24337376; PubMed Central PMCID: PMC3947124. Link

1: Merker JD, Roskin KM, Ng D, Pan C, Fisk DG, King JJ, Hoh R, Stadler M, Okumoto LM, Abidi P, Hewitt R, Jones CD, Gojenola L, Clark MJ, Zhang B, Cherry AM, George TI, Snyder M, Boyd SD, Zehnder JL, Fire AZ, Gotlib J. Comprehensive whole-genome sequencing of an early-stage primary myelofibrosis patient defines low mutational burden and non-recurrent candidate genes. Haematologica. 2013 Nov;98(11):1689-96. doi: 10.3324/haematol.2013.092379. Epub 2013 Jul 19. PubMed PMID: 23872309; PubMed Central PMCID: PMC3815168. Link


2: Boyd SD, Liu Y, Wang C, Martin V, Dunn-Walters DK. Human lymphocyte repertoires in ageing. Curr Opin Immunol. 2013 Aug;25(4):511-5. doi: 10.1016/j.coi.2013.07.007. Epub 2013 Aug 28. Review. PubMed PMID: 23992996; PubMed Central PMCID: PMC4811628. Link


3: Parameswaran P, Liu Y, Roskin KM, Jackson KK, Dixit VP, Lee JY, Artiles KL, Zompi S, Vargas MJ, Simen BB, Hanczaruk B, McGowan KR, Tariq MA, Pourmand N, Koller D, Balmaseda A, Boyd SD*, Harris E*, Fire AZ*. Convergent antibody signatures in human dengue. Cell Host Microbe. 2013 Jun 12;13(6):691-700. doi: 10.1016/j.chom.2013.05.008. PubMed PMID: 23768493; PubMed Central PMCID: PMC4136508. [*=co-senior authors] Link


4: Liao HX, Lynch R, Zhou T, Gao F, Alam SM, Boyd SD, Fire AZ, Roskin KM, Schramm CA, Zhang Z, Zhu J, Shapiro L; NISC Comparative Sequencing Program, Mullikin JC, Gnanakaran S, Hraber P, Wiehe K, Kelsoe G, Yang G, Xia SM, Montefiori DC, Parks R, Lloyd KE, Scearce RM, Soderberg KA, Cohen M, Kamanga G, Louder MK, Tran LM, Chen Y, Cai F, Chen S, Moquin S, Du X, Joyce MG, Srivatsan S, Zhang B, Zheng A, Shaw GM, Hahn BH, Kepler TB, Korber BT, Kwong PD, Mascola JR, Haynes BF. Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. Nature. 2013 Apr 25;496(7446):469-76. doi: 10.1038/nature12053. Epub 2013 Apr 3. PubMed PMID: 23552890; PubMed Central PMCID: PMC3637846. Link


5: Boyd SD, Natkunam Y, Allen JR, Warnke RA. Selective immunophenotyping for diagnosis of B-cell neoplasms: immunohistochemistry and flow cytometry strategies and results. Appl Immunohistochem Mol Morphol. 2013 Mar;21(2):116-31. doi: 10.1097/PAI.0b013e31825d550a. Review. PubMed PMID: 22820658; PubMed Central PMCID: PMC4993814. Link


6: Schrijver I, Natkunam Y, Galli S, Boyd SD. Integration of genomic medicine into pathology residency training: the stanford open curriculum. J Mol Diagn. 2013 Mar;15(2):141-8. doi: 10.1016/j.jmoldx.2012.11.003. Epub 2013 Jan 10. PubMed PMID: 23313248. Link


7: Boyd SD. Diagnostic applications of high-throughput DNA sequencing. Annu Rev Pathol. 2013 Jan 24;8:381-410. doi: 10.1146/annurev-pathol-020712-164026. Epub 2012 Nov 1. Review. PubMed PMID: 23121054. Link

1: Maecker HT, Lindstrom TM, Robinson WH, Utz PJ, Hale M, Boyd SD, Shen-Orr SS, Fathman CG. New tools for classification and monitoring of autoimmune diseases. Nat Rev Rheumatol. 2012 May 31;8(6):317-28. doi: 10.1038/nrrheum.2012.66. Review. PubMed PMID: 22647780; PubMed Central PMCID: PMC3409841. Link


2: Kidd MJ, Chen Z, Wang Y, Jackson KJ, Zhang L, Boyd SD, Fire AZ, Tanaka MM, Gaëta BA, Collins AM. The inference of phased haplotypes for the immunoglobulin H chain V region gene loci by analysis of VDJ gene rearrangements. J Immunol. 2012 Feb 1;188(3):1333-40. doi: 10.4049/jimmunol.1102097. Epub 2011 Dec 28. PubMed PMID: 22205028; PubMed Central PMCID: PMC4734744. Link

1: Logan AC, Gao H, Wang C, Sahaf B, Jones CD, Marshall EL, Buño I, Armstrong R, Fire AZ, Weinberg KI, Mindrinos M, Zehnder JL, Boyd SD, Xiao W, Davis RW, Miklos DB. High-throughput VDJ sequencing for quantification of minimal residual disease in chronic lymphocytic leukemia and immune reconstitution assessment. Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):21194-9. doi: 10.1073/pnas.1118357109. Epub 2011 Dec 12. PubMed PMID: 22160699; PubMed Central PMCID: PMC3248502. Link


2: Liao HX, Chen X, Munshaw S, Zhang R, Marshall DJ, Vandergrift N, Whitesides JF, Lu X, Yu JS, Hwang KK, Gao F, Markowitz M, Heath SL, Bar KJ, Goepfert PA, Montefiori DC, Shaw GC, Alam SM, Margolis DM, Denny TN, Boyd SD, Marshal E, Egholm M, Simen BB, Hanczaruk B, Fire AZ, Voss G, Kelsoe G, Tomaras GD, Moody MA, Kepler TB, Haynes BF. Initial antibodies binding to HIV-1 gp41 in acutely infected subjects are polyreactive and highly mutated. J Exp Med. 2011 Oct 24;208(11):2237-49. doi: 10.1084/jem.20110363. Epub 2011 Oct 10. PubMed PMID: 21987658; PubMed Central PMCID: PMC3201211. Link


3: Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ, Sidow A. Determinants of nucleosome organization in primary human cells. Nature. 2011 May 22;474(7352):516-20. doi: 10.1038/nature10002. PubMed PMID: 21602827; PubMed Central PMCID: PMC3212987. Link

1: Boyd SD, Gaëta BA, Jackson KJ, Fire AZ, Marshall EL, Merker JD, Maniar JM, Zhang LN, Sahaf B, Jones CD, Simen BB, Hanczaruk B, Nguyen KD, Nadeau KC, Egholm M, Miklos DB, Zehnder JL, Collins AM. Individual variation in the germline Ig gene repertoire inferred from variable region gene rearrangements. J Immunol. 2010 Jun 15;184(12):6986-92. doi: 10.4049/jimmunol.1000445. Epub 2010 May 21. PubMed PMID: 20495067; PubMed Central PMCID: PMC4281569. Link

1: Boyd SD, Marshall EL, Merker JD, Maniar JM, Zhang LN, Sahaf B, Jones CD, Simen BB, Hanczaruk B, Nguyen KD, Nadeau KC, Egholm M, Miklos DB, Zehnder JL, Fire AZ. Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing. Sci Transl Med. 2009 Dec 23;1(12):12ra23. PubMed PMID: 20161664; PubMed Central PMCID: PMC2819115. Link


2: Ahn JY, Seo K, Weinberg O, Boyd SD, Arber DA. A comparison of two methods for screening CEBPA mutations in patients with acute myeloid leukemia. J Mol Diagn. 2009 Jul;11(4):319-23. doi: 10.2353/jmoldx.2009.080121. Epub 2009 Jun 12. PubMed PMID: 19525338; PubMed Central PMCID: PMC2710708. Link


3: Boyd SD, Mobley BC, Regula DP, Arber DA. Features of hemolysis due to Clostridium perfringens infection. Int J Lab Hematol. 2009 Jun;31(3):364-7. doi: 10.1111/j.1751-553X.2007.01018.x. Epub 2007 Dec 20. PubMed PMID: 18177433. Link

1: Boyd SD. Everything you wanted to know about small RNA but were afraid to ask. Lab Invest. 2008 Jun;88(6):569-78. doi: 10.1038/labinvest.2008.32. Epub 2008 Apr 21. Review. PubMed PMID: 18427554. Link


2: Boyd SD, Stenard F, Lee DK, Goodnough LT, Esquivel CO, Fontaine MJ. Alloimmunization to red blood cell antigens affects clinical outcomes in liver transplant patients. Liver Transpl. 2007 Dec;13(12):1654-61. PubMed PMID: 18044783. Link


3: Boyd SD, Tsai KY, Jacks T. An intact HDM2 RING-finger domain is required for nuclear exclusion of p53. Nat Cell Biol. 2000 Sep;2(9):563-8. PubMed PMID: 10980695. Link


4: Oosterwegel MA, Mandelbrot DA, Boyd SD, Lorsbach RB, Jarrett DY, Abbas AK, Sharpe AH. The role of CTLA-4 in regulating Th2 differentiation. J Immunol. 1999 Sep 1;163(5):2634-9. PubMed PMID: 10453003. Link


5: Brugarolas J, Moberg K, Boyd SD, Taya Y, Jacks T, Lees JA. Inhibition of cyclin-dependent kinase 2 by p21 is necessary for retinoblastoma protein-mediated G1 arrest after gamma-irradiation. Proc Natl Acad Sci U S A. 1999 Feb 2;96(3):1002-7. PubMed PMID: 9927683; PubMed Central PMCID: PMC15340. Link


6: Tivol EA, Boyd SD, McKeon S, Borriello F, Nickerson P, Strom TB, Sharpe AH. CTLA4Ig prevents lymphoproliferation and fatal multiorgan tissue destruction in CTLA-4-deficient mice. J Immunol. 1997 Jun 1;158(11):5091-4. PubMed PMID: 9164923. Link


7: Borriello F, Sethna MP, Boyd SD, Schweitzer AN, Tivol EA, Jacoby D, Strom TB, Simpson EM, Freeman GJ, Sharpe AH. B7-1 and B7-2 have overlapping, critical roles in immunoglobulin class switching and germinal center formation. Immunity. 1997 Mar;6(3):303-13. PubMed PMID: 9075931. Link