Publications

2017

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

2016

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

2015

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

2014

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

2013

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

2012

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

2011

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

2010

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

2009

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

Pre-2009

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