My Bibliography

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Safonova Y, Shin SB, Kramer L, Reecy J, Watson CT, Smith TPL, Pevzner PA. Variations in antibody repertoires correlate with vaccine responses. Genome Res. 2022 Apr;32(4):791-804. doi: 10.1101/gr.276027.121. Epub 2022 Mar 31. PubMed PMID: 35361626; PubMed Central PMCID: PMC8997358.

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Geller AE, Shrestha R, Woeste MR, Guo H, Hu X, Ding C, Andreeva K, Chariker JH, Zhou M, Tieri D, Watson CT, Mitchell RA, Zhang HG, Li Y, Martin Ii RCG, Rouchka EC, Yan J. The induction of peripheral trained immunity in the pancreas incites anti-tumor activity to control pancreatic cancer progression. Nat Commun. 2022 Feb 9;13(1):759. doi: 10.1038/s41467-022-28407-4. PubMed PMID: 35140221; PubMed Central PMCID: PMC8828725.

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Omer A, Peres A, Rodriguez OL, Watson CT, Lees W, Polak P, Collins AM, Yaari G. T cell receptor beta germline variability is revealed by inference from repertoire data. Genome Med. 2022 Jan 7;14(1):2. doi: 10.1186/s13073-021-01008-4. PubMed PMID: 34991709; PubMed Central PMCID: PMC8740489.

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Rodriguez OL, Sharp AJ, Watson CT. Limitations of lymphoblastoid cell lines for establishing genetic reference datasets in the immunoglobulin loci. PLoS One. 2021;16(12):e0261374. doi: 10.1371/journal.pone.0261374. eCollection 2021. PubMed PMID: 34898642; PubMed Central PMCID: PMC8668129.

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Collins AM, Peres A, Corcoran MM, Watson CT, Yaari G, Lees WD, Ohlin M. Commentary on Population matched (pm) germline allelic variants of immunoglobulin (IG) loci: relevance in infectious diseases and vaccination studies in human populations. Genes Immun. 2021 Dec;22(7-8):335-338. doi: 10.1038/s41435-021-00152-6. Epub 2021 Oct 19. PubMed PMID: 34667305; PubMed Central PMCID: PMC8674141.

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Morrissey SM, Zhang F, Ding C, Montoya-Durango DE, Hu X, Yang C, Wang Z, Yuan F, Fox M, Zhang HG, Guo H, Tieri D, Kong M, Watson CT, Mitchell RA, Zhang X, McMasters KM, Huang J, Yan J. Tumor-derived exosomes drive immunosuppressive macrophages in a pre-metastatic niche through glycolytic dominant metabolic reprogramming. Cell Metab. 2021 Oct 5;33(10):2040-2058.e10. doi: 10.1016/j.cmet.2021.09.002. Epub 2021 Sep 23. PubMed PMID: 34559989; PubMed Central PMCID: PMC8506837.

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Zhou M, Dascani P, Ding C, Kos JT, Tieri D, Lin X, Caster D, Powell D, Wen C, Watson CT, Yan J. Integrin CD11b Negatively Regulates B Cell Receptor Signaling to Shape Humoral Response during Immunization and Autoimmunity. J Immunol. 2021 Oct 1;207(7):1785-1797. doi: 10.4049/jimmunol.2100070. Epub 2021 Sep 1. PubMed PMID: 34470858; PubMed Central PMCID: PMC8455437.

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Lee JH, Toy L, Kos JT, Safonova Y, Schief WR, Havenar-Daughton C, Watson CT, Crotty S. Vaccine genetics of IGHV1-2 VRC01-class broadly neutralizing antibody precursor naïve human B cells. NPJ Vaccines. 2021 Sep 6;6(1):113. doi: 10.1038/s41541-021-00376-7. PubMed PMID: 34489473; PubMed Central PMCID: PMC8421370.

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Peng K, Safonova Y, Shugay M, Popejoy AB, Rodriguez OL, Breden F, Brodin P, Burkhardt AM, Bustamante C, Cao-Lormeau VM, Corcoran MM, Duffy D, Fuentes-Guajardo M, Fujita R, Greiff V, Jönsson VD, Liu X, Quintana-Murci L, Rossetti M, Xie J, Yaari G, Zhang W, Abedalthagafi MS, Adekoya KO, Ahmed RA, Chang WC, Gray C, Nakamura Y, Lees WD, Khatri P, Alachkar H, Scheepers C, Watson CT, Karlsson Hedestam GB, Mangul S. Diversity in immunogenomics: the value and the challenge. Nat Methods. 2021 Jun;18(6):588-591. doi: 10.1038/s41592-021-01169-5. PubMed PMID: 34002093; PubMed Central PMCID: PMC8842483.

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Kenter AL, Watson CT, Spille JH. Igh Locus Polymorphism May Dictate Topological Chromatin Conformation and V Gene Usage in the Ig Repertoire. Front Immunol. 2021;12:682589. doi: 10.3389/fimmu.2021.682589. eCollection 2021. Review. PubMed PMID: 34084176; PubMed Central PMCID: PMC8167033.

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Morrissey SM, Geller AE, Hu X, Tieri D, Ding C, Klaes CK, Cooke EA, Woeste MR, Martin ZC, Chen O, Bush SE, Zhang HG, Cavallazzi R, Clifford SP, Chen J, Ghare S, Barve SS, Cai L, Kong M, Rouchka EC, McLeish KR, Uriarte SM, Watson CT, Huang J, Yan J. A specific low-density neutrophil population correlates with hypercoagulation and disease severity in hospitalized COVID-19 patients. JCI Insight. 2021 May 10;6(9). doi: 10.1172/jci.insight.148435. PubMed PMID: 33986193; PubMed Central PMCID: PMC8262329.

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Waide ML, Polidoro R, Powell WL, Denny JE, Kos J, Tieri DA, Watson CT, Schmidt NW. Gut Microbiota Composition Modulates the Magnitude and Quality of Germinal Centers during Plasmodium Infections. Cell Rep. 2020 Dec 15;33(11):108503. doi: 10.1016/j.celrep.2020.108503. PubMed PMID: 33326773; PubMed Central PMCID: PMC7772993.

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Collins AM, Yaari G, Shepherd AJ, Lees W, Watson CT. Germline immunoglobulin genes: disease susceptibility genes hidden in plain sight?. Current opinion in systems biology. 2020 December; 24:100-108.

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Rodriguez OL, Gibson WS, Parks T, Emery M, Powell J, Strahl M, Deikus G, Auckland K, Eichler EE, Marasco WA, Sebra R, Sharp AJ, Smith ML, Bashir A, Watson CT. A Novel Framework for Characterizing Genomic Haplotype Diversity in the Human Immunoglobulin Heavy Chain Locus. Front Immunol. 2020;11:2136. doi: 10.3389/fimmu.2020.02136. eCollection 2020. PubMed PMID: 33072076; PubMed Central PMCID: PMC7539625.

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Alsoussi WB, Turner JS, Case JB, Zhao H, Schmitz AJ, Zhou JQ, Chen RE, Lei T, Rizk AA, McIntire KM, Winkler ES, Fox JM, Kafai NM, Thackray LB, Hassan AO, Amanat F, Krammer F, Watson CT, Kleinstein SH, Fremont DH, Diamond MS, Ellebedy AH. A Potently Neutralizing Antibody Protects Mice against SARS-CoV-2 Infection. J Immunol. 2020 Aug 15;205(4):915-922. doi: 10.4049/jimmunol.2000583. Epub 2020 Jun 26. PubMed PMID: 32591393; PubMed Central PMCID: PMC7566074.

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Christley S, Aguiar A, Blanck G, Breden F, Bukhari SAC, Busse CE, Jaglale J, Harikrishnan SL, Laserson U, Peters B, Rocha A, Schramm CA, Taylor S, Vander Heiden JA, Zimonja B, Watson CT, Corrie B, Cowell LG. The ADC API: A Web API for the Programmatic Query of the AIRR Data Commons. Front Big Data. 2020;3:22. doi: 10.3389/fdata.2020.00022. eCollection 2020. PubMed PMID: 33693395; PubMed Central PMCID: PMC7931935.

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Do AN, Watson CT, Cohain AT, Griffin RS, Grishin A, Wood RA, Wesley Burks A, Jones SM, Scurlock A, Leung DYM, Sampson HA, Sicherer SH, Sharp AJ, Schadt EE, Bunyavanich S. Dual transcriptomic and epigenomic study of reaction severity in peanut-allergic children. J Allergy Clin Immunol. 2020 Apr;145(4):1219-1230. doi: 10.1016/j.jaci.2019.10.040. Epub 2019 Dec 12. PubMed PMID: 31838046; PubMed Central PMCID: PMC7192362.

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Ford M, Haghshenas E, Watson CT, Sahinalp SC. Genotyping and Copy Number Analysis of Immunoglobin Heavy Chain Variable Genes Using Long Reads. iScience. 2020 Mar 27;23(3):100883. doi: 10.1016/j.isci.2020.100883. Epub 2020 Feb 4. PubMed PMID: 32109676; PubMed Central PMCID: PMC7044747.

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Snyder KE, Pittard CM, Fowler A, Watson CT. “Epic-Genetics”: An exploration of pre-service helping professionals’ (mis)understanding of epigenetic influences on human development. Teaching and Learning Inquiry. 2020 March; 8:122-137.

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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 Res. 2020 Jan 8;48(D1):D1051-D1056. doi: 10.1093/nar/gkz872. PubMed PMID: 31602484; PubMed Central PMCID: PMC6943044.

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Lees W, Busse CE, Corcoran M, Ohlin M, Scheepers C, Matsen FA, Yaari G, Watson CT, Collins A, Shepherd AJ. OGRDB: a reference database of inferred immune receptor genes. Nucleic Acids Res. 2020 Jan 8;48(D1):D964-D970. doi: 10.1093/nar/gkz822. PubMed PMID: 31566225; PubMed Central PMCID: PMC6943078.

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Busse CE, Jackson KJL, Watson CT, Collins AM. A Proposed New Nomenclature for the Immunoglobulin Genes of Mus musculus. Front Immunol. 2019;10:2961. doi: 10.3389/fimmu.2019.02961. eCollection 2019. PubMed PMID: 31921202; PubMed Central PMCID: PMC6930147.

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Watson CT, Kos JT, Gibson WS, Newman L, Deikus G, Busse CE, Smith ML, Jackson KJ, Collins AM. A comparison of immunoglobulin IGHV, IGHD and IGHJ genes in wild-derived and classical inbred mouse strains. Immunol Cell Biol. 2019 Nov;97(10):888-901. doi: 10.1111/imcb.12288. Epub 2019 Oct 6. PubMed PMID: 31441114.

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Cirelli KM, Carnathan DG, Nogal B, Martin JT, Rodriguez OL, Upadhyay AA, Enemuo CA, Gebru EH, Choe Y, Viviano F, Nakao C, Pauthner MG, Reiss S, Cottrell CA, Smith ML, Bastidas R, Gibson W, Wolabaugh AN, Melo MB, Cossette B, Kumar V, Patel NB, Tokatlian T, Menis S, Kulp DW, Burton DR, Murrell B, Schief WR, Bosinger SE, Ward AB, Watson CT, Silvestri G, Irvine DJ, Crotty S. Slow Delivery Immunization Enhances HIV Neutralizing Antibody and Germinal Center Responses via Modulation of Immunodominance. Cell. 2019 May 16;177(5):1153-1171.e28. doi: 10.1016/j.cell.2019.04.012. Epub 2019 May 9. PubMed PMID: 31080066; PubMed Central PMCID: PMC6619430.

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Castro K, Ntranos A, Amatruda M, Petracca M, Kosa P, Chen EY, Morstein J, Trauner D, Watson CT, Kiebish MA, Bielekova B, Inglese M, Katz Sand I, Casaccia P. Body Mass Index in Multiple Sclerosis modulates ceramide-induced DNA methylation and disease course. EBioMedicine. 2019 May;43:392-410. doi: 10.1016/j.ebiom.2019.03.087. Epub 2019 Apr 10. PubMed PMID: 30981648; PubMed Central PMCID: PMC6557766.

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Hardesty JE, Wahlang B, Falkner KC, Shi H, Jin J, Zhou Y, Wilkey DW, Merchant ML, Watson CT, Feng W, Morris AJ, Hennig B, Prough RA, Cave MC. Proteomic Analysis Reveals Novel Mechanisms by Which Polychlorinated Biphenyls Compromise the Liver Promoting Diet-Induced Steatohepatitis. J Proteome Res. 2019 Apr 5;18(4):1582-1594. doi: 10.1021/acs.jproteome.8b00886. Epub 2019 Mar 15. PubMed PMID: 30807179; PubMed Central PMCID: PMC7059562.

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Ohlin M, Scheepers C, Corcoran M, Lees WD, Busse CE, Bagnara D, Thörnqvist L, Bürckert JP, Jackson KJL, Ralph D, Schramm CA, Marthandan N, Breden F, Scott J, Matsen Iv FA, Greiff V, Yaari G, Kleinstein SH, Christley S, Sherkow JS, Kossida S, Lefranc MP, van Zelm MC, Watson CT, Collins AM. Inferred Allelic Variants of Immunoglobulin Receptor Genes: A System for Their Evaluation, Documentation, and Naming. Front Immunol. 2019;10:435. doi: 10.3389/fimmu.2019.00435. eCollection 2019. Review. PubMed PMID: 30936866; PubMed Central PMCID: PMC6431624.

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Ntranos A, Ntranos V, Bonnefil V, Liu J, Kim-Schulze S, He Y, Zhu Y, Brandstadter R, Watson CT, Sharp AJ, Katz Sand I, Casaccia P. Fumarates target the metabolic-epigenetic interplay of brain-homing T cells in multiple sclerosis. Brain. 2019 Mar 1;142(3):647-661. doi: 10.1093/brain/awy344. PubMed PMID: 30698680; PubMed Central PMCID: PMC6821213.

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Gadala-Maria D, Gidoni M, Marquez S, Vander Heiden JA, Kos JT, Watson CT, O'Connor KC, Yaari G, Kleinstein SH. Identification of Subject-Specific Immunoglobulin Alleles From Expressed Repertoire Sequencing Data. Front Immunol. 2019;10:129. doi: 10.3389/fimmu.2019.00129. eCollection 2019. PubMed PMID: 30814994; PubMed Central PMCID: PMC6381938.

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Hardesty JE, Wahlang B, Falkner KC, Shi H, Jin J, Wilkey D, Merchant M, Watson C, Prough RA, Cave MC. Hepatic signalling disruption by pollutant Polychlorinated biphenyls in steatohepatitis. Cell Signal. 2019 Jan;53:132-139. doi: 10.1016/j.cellsig.2018.10.004. Epub 2018 Oct 6. PubMed PMID: 30300668; PubMed Central PMCID: PMC6289731.

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Collins AM, Watson CT. Immunoglobulin Light Chain Gene Rearrangements, Receptor Editing and the Development of a Self-Tolerant Antibody Repertoire. Front Immunol. 2018;9:2249. doi: 10.3389/fimmu.2018.02249. eCollection 2018. Review. PubMed PMID: 30349529; PubMed Central PMCID: PMC6186787.

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Garg P, Joshi RS, Watson C, Sharp AJ. A survey of inter-individual variation in DNA methylation identifies environmentally responsive co-regulated networks of epigenetic variation in the human genome. PLoS Genet. 2018 Oct;14(10):e1007707. doi: 10.1371/journal.pgen.1007707. eCollection 2018 Oct. PubMed PMID: 30273333; PubMed Central PMCID: PMC6181428.

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Cobb CA, Watson CT, Ellis SR. Establishing Best Practices for Effective Online Learning Modules: a Single Institution Study. Medical Science Educator. 2018 August; 28:683-691. doi: 10.1007/s40670-018-0613-7.

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Barbosa M, Joshi RS, Garg P, Martin-Trujillo A, Patel N, Jadhav B, Watson CT, Gibson W, Chetnik K, Tessereau C, Mei H, De Rubeis S, Reichert J, Lopes F, Vissers LELM, Kleefstra T, Grice DE, Edelmann L, Soares G, Maciel P, Brunner HG, Buxbaum JD, Gelb BD, Sharp AJ. Identification of rare de novo epigenetic variations in congenital disorders. Nat Commun. 2018 May 25;9(1):2064. doi: 10.1038/s41467-018-04540-x. PubMed PMID: 29802345; PubMed Central PMCID: PMC5970273.

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Watson CT, Cohain AT, Griffin RS, Chun Y, Grishin A, Hacyznska H, Hoffman GE, Beckmann ND, Shah H, Dawson P, Henning A, Wood R, Burks AW, Jones SM, Leung DYM, Sicherer S, Sampson HA, Sharp AJ, Schadt EE, Bunyavanich S. Integrative transcriptomic analysis reveals key drivers of acute peanut allergic reactions. Nat Commun. 2017 Dec 5;8(1):1943. doi: 10.1038/s41467-017-02188-7. PubMed PMID: 29203772; PubMed Central PMCID: PMC5715016.

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Rubelt F, Busse CE, Bukhari SAC, Bürckert JP, Mariotti-Ferrandiz E, Cowell LG, Watson CT, Marthandan N, Faison WJ, Hershberg U, Laserson U, Corrie BD, Davis MM, Peters B, Lefranc MP, Scott JK, Breden F, Luning Prak ET, Kleinstein SH. Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data. Nat Immunol. 2017 Nov 16;18(12):1274-1278. doi: 10.1038/ni.3873. PubMed PMID: 29144493; PubMed Central PMCID: PMC5790180.

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Breden F, Luning Prak ET, Peters B, Rubelt F, Schramm CA, Busse CE, Vander Heiden JA, Christley S, Bukhari SAC, Thorogood A, Matsen Iv FA, Wine Y, Laserson U, Klatzmann D, Douek DC, Lefranc MP, Collins AM, Bubela T, Kleinstein SH, Watson CT, Cowell LG, Scott JK, Kepler TB. Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data. Front Immunol. 2017;8:1418. doi: 10.3389/fimmu.2017.01418. eCollection 2017. PubMed PMID: 29163494; PubMed Central PMCID: PMC5671925.

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Sandkam BA, Joy JB, Watson CT, Breden F. Genomic Environment Impacts Color Vision Evolution in a Family with Visually Based Sexual Selection. Genome Biol Evol. 2017 Nov 1;9(11):3100-3107. doi: 10.1093/gbe/evx228. PubMed PMID: 29121209; PubMed Central PMCID: PMC5714168.

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Watson CT, Glanville J, Marasco WA. The Individual and Population Genetics of Antibody Immunity. Trends Immunol. 2017 Jul;38(7):459-470. doi: 10.1016/j.it.2017.04.003. Epub 2017 May 20. Review. PubMed PMID: 28539189; PubMed Central PMCID: PMC5656258.

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Watson CT, Matsen FA 4th, Jackson KJL, Bashir A, Smith ML, Glanville J, Breden F, Kleinstein SH, Collins AM, Busse CE. Comment on "A Database of Human Immune Receptor Alleles Recovered from Population Sequencing Data". J Immunol. 2017 May 1;198(9):3371-3373. doi: 10.4049/jimmunol.1700306. PubMed PMID: 28416712.

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Breden F, Watson CT. Using High-Throughput Sequencing to Characterize the Development of the Antibody Repertoire During Infections: A Case Study of HIV-1. Adv Exp Med Biol. 2017;1053:245-263. doi: 10.1007/978-3-319-72077-7_12. Review. PubMed PMID: 29549643.

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Joshi RS, Garg P, Zaitlen N, Lappalainen T, Watson CT, Azam N, Ho D, Li X, Antonarakis SE, Brunner HG, Buiting K, Cheung SW, Coffee B, Eggermann T, Francis D, Geraedts JP, Gimelli G, Jacobson SG, Le Caignec C, de Leeuw N, Liehr T, Mackay DJ, Montgomery SB, Pagnamenta AT, Papenhausen P, Robinson DO, Ruivenkamp C, Schwartz C, Steiner B, Stevenson DA, Surti U, Wassink T, Sharp AJ. DNA Methylation Profiling of Uniparental Disomy Subjects Provides a Map of Parental Epigenetic Bias in the Human Genome. Am J Hum Genet. 2016 Sep 1;99(3):555-566. doi: 10.1016/j.ajhg.2016.06.032. Epub 2016 Aug 25. PubMed PMID: 27569549; PubMed Central PMCID: PMC5011056.

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Avnir Y, Watson CT, Glanville J, Peterson EC, Tallarico AS, Bennett AS, Qin K, Fu Y, Huang CY, Beigel JH, Breden F, Zhu Q, Marasco WA. IGHV1-69 polymorphism modulates anti-influenza antibody repertoires, correlates with IGHV utilization shifts and varies by ethnicity. Sci Rep. 2016 Feb 16;6:20842. doi: 10.1038/srep20842. PubMed PMID: 26880249; PubMed Central PMCID: PMC4754645.

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Watson CT, Roussos P, Garg P, Ho DJ, Azam N, Katsel PL, Haroutunian V, Sharp AJ. Genome-wide DNA methylation profiling in the superior temporal gyrus reveals epigenetic signatures associated with Alzheimer's disease. Genome Med. 2016 Jan 19;8(1):5. doi: 10.1186/s13073-015-0258-8. PubMed PMID: 26803900; PubMed Central PMCID: PMC4719699.

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Watson CT, Szutorisz H, Garg P, Martin Q, Landry JA, Sharp AJ, Hurd YL. Genome-Wide DNA Methylation Profiling Reveals Epigenetic Changes in the Rat Nucleus Accumbens Associated With Cross-Generational Effects of Adolescent THC Exposure. Neuropsychopharmacology. 2015 Dec;40(13):2993-3005. doi: 10.1038/npp.2015.155. Epub 2015 Jun 5. PubMed PMID: 26044905; PubMed Central PMCID: PMC4864634.

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Watson CT, Steinberg KM, Graves TA, Warren RL, Malig M, Schein J, Wilson RK, Holt RA, Eichler EE, Breden F. Sequencing of the human IG light chain loci from a hydatidiform mole BAC library reveals locus-specific signatures of genetic diversity. Genes Immun. 2015 Jan-Feb;16(1):24-34. doi: 10.1038/gene.2014.56. Epub 2014 Oct 23. PubMed PMID: 25338678; PubMed Central PMCID: PMC4304971.

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Watson CT, Marques-Bonet T, Sharp AJ, Mefford HC. The genetics of microdeletion and microduplication syndromes: an update. Annu Rev Genomics Hum Genet. 2014;15:215-244. doi: 10.1146/annurev-genom-091212-153408. Epub 2014 Apr 16. Review. PubMed PMID: 24773319; PubMed Central PMCID: PMC4476258.

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Bala Tannan N, Brahmachary M, Garg P, Borel C, Alnefaie R, Watson CT, Thomas NS, Sharp AJ. DNA methylation profiling in X;autosome translocations supports a role for L1 repeats in the spread of X chromosome inactivation. Hum Mol Genet. 2014 Mar 1;23(5):1224-36. doi: 10.1093/hmg/ddt553. Epub 2013 Nov 1. PubMed PMID: 24186870; PubMed Central PMCID: PMC3919006.

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Disanto G, Kjetil Sandve G, Ricigliano VA, Pakpoor J, Berlanga-Taylor AJ, Handel AE, Kuhle J, Holden L, Watson CT, Giovannoni G, Handunnetthi L, Ramagopalan SV. DNase hypersensitive sites and association with multiple sclerosis. Hum Mol Genet. 2014 Feb 15;23(4):942-8. doi: 10.1093/hmg/ddt489. Epub 2013 Oct 2. PubMed PMID: 24092328.

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Watson CT, Steinberg KM, Huddleston J, Warren RL, Malig M, Schein J, Willsey AJ, Joy JB, Scott JK, Graves TA, Wilson RK, Holt RA, Eichler EE, Breden F. Complete haplotype sequence of the human immunoglobulin heavy-chain variable, diversity, and joining genes and characterization of allelic and copy-number variation. Am J Hum Genet. 2013 Apr 4;92(4):530-46. doi: 10.1016/j.ajhg.2013.03.004. Epub 2013 Mar 28. PubMed PMID: 23541343; PubMed Central PMCID: PMC3617388.