2017

  1. Integrative Genetic and Epigenetic Analysis Uncovers Regulatory Mechanisms of Autoimmune Disease. Shooshtari P, Huang H, Cotsapas C. American journal of human genetics. 2017; 101(1):75-86. PMID: 28686857.
  2. Large-Scale trans-eQTLs Affect Hundreds of Transcripts and Mediate Patterns of Transcriptional Co-regulation. Brynedal B, Choi J, Raj T, Bjornson R, Stranger BE, Neale BM, Voight BF, Cotsapas C. American journal of human genetics. 2017; 100(4):581-591. PMID: 28285767 PMCID: PMC5384037
  3. Limited statistical evidence for shared genetic effects of eQTLs and autoimmune-disease-associated loci in three major immune-cell types. Chun S, Casparino A, Patsopoulos NA, Croteau-Chonka DC, Raby BA, De Jager PL, Sunyaev SR, Cotsapas C. Nature genetics. 2017; 49(4):600-605. PMID: 28218759 PMCID: PMC5374036
  4. Novel determinants of mammalian primary microRNA processing revealed by systematic evaluation of hairpin-containing transcripts and human genetic variation. Roden C, Gaillard J, Kanoria S, Rennie W, Barish S, Cheng J, Pan W, Liu J, Cotsapas C, Ding Y, Lu J. Genome research. 2017; 27(3):374-384. PMID: 28087842 PMCID: PMC5340965

2016

  1. NR1H3 p.Arg415Gln Is Not Associated to Multiple Sclerosis Risk. Cotsapas C, on behalf of International MS Genetics Consortium. Neuron. 2016; 92(2):333-335. PMID: 27764667
  2. Progress and challenges for treating Type 1 diabetes. Garyu JW, Meffre E, Cotsapas C, Herold KC. Journal of autoimmunity. 2016; 71:1-9.  PMID: 27210268 PMCID: PMC4903889
  3. Network Analysis of Genome-Wide Selective Constraint Reveals a Gene Network Active in Early Fetal Brain Intolerant of Mutation. Choi J, Shooshtari P, Samocha KE, Daly MJ, Cotsapas C. PLoS genetics. 2016; 12(6):e1006121. PMID: 27305007 PMCID: PMC4909280
  4. Survey of variation in human transcription factors reveals prevalent DNA binding changes. Barrera LA, Vedenko A, Kurland JV, Rogers JM, Gisselbrecht SS, Rossin EJ, Woodard J, Mariani L, Kock KH, Inukai S, Siggers T, Shokri L, Gordân R, Sahni N, Cotsapas C, Hao T, Yi S, Kellis M, Daly MJ, Vidal M, Hill DE, Bulyk ML. Science. 2016; 351(6280):1450-4. PMID: 27013732 PMCID: PMC4825693
  5. Regulatory polymorphisms modulate the expression of HLA class II molecules and promote autoimmunity. Raj P, Rai E, Song R, Khan S, Wakeland BE, Viswanathan K, Arana C, Liang C, Zhang B, Dozmorov I, Carr-Johnson F, Mitrovic M, Wiley GB, Kelly JA, Lauwerys BR, Olsen NJ, Cotsapas C, Garcia CK, Wise CA, Harley JB, Nath SK, James JA, Jacob CO, Tsao BP, Pasare C, Karp DR, Li QZ, Gaffney PM, Wakeland EK. eLife. 2016; 5. PMID: 26880555 PMCID: PMC4811771
  6. Changes in T-cell subsets identify responders to FcR-nonbinding anti-CD3 mAb (teplizumab) in patients with type 1 diabetes. Tooley JE, Vudattu N, Choi J, Cotsapas C, Devine L, Raddassi K, Ehlers MR, McNamara JG, Harris KM, Kanaparthi S, Phippard D, Herold KC. European journal of immunology. 2016; 46(1):230-41. PMID: 26518356 PMCID: PMC4882099

2015

  1. Class II HLA interactions modulate genetic risk for multiple sclerosis. Moutsianas L, et al, on behalf of the International MS Genetics Consortium. Nature genetics. 2015; 47(10):1107-13.  PMID: 26343388 PMCID: PMC4874245
  2. Genetic variants associated with autoimmunity drive NFκB signaling and responses to inflammatory stimuli. Housley WJ, Fernandez SD, Vera K, Murikinati SR, Grutzendler J, Cuerdon N, Glick L, De Jager PL, Mitrovic M, Cotsapas C, Hafler DA. Science translational medicine. 2015; 7(291):291ra93. PMID: 26062845 PMCID: PMC4574294
  3. Genetic analysis for a shared biological basis between migraine and coronary artery disease. Winsvold BS, Nelson CP, Malik R, Gormley P, Anttila V, Vander Heiden J, Elliott KS, Jacobsen LM, Palta P, Amin N, de Vries B, Hämäläinen E, Freilinger T, Ikram MA, Kessler T, Koiranen M, Ligthart L, McMahon G, Pedersen LM, Willenborg C, Won HH, Olesen J, Artto V, Assimes TL, Blankenberg S, Boomsma DI, Cherkas L, Davey Smith G, Epstein SE, Erdmann J, Ferrari MD, Göbel H, Hall AS, Jarvelin MR, Kallela M, Kaprio J, Kathiresan S, Lehtimäki T, McPherson R, März W, Nyholt DR, O'Donnell CJ, Quaye L, Rader DJ, Raitakari O, Roberts R, Schunkert H, Schürks M, Stewart AF, Terwindt GM, Thorsteinsdottir U, van den Maagdenberg AM, van Duijn C, Wessman M, Kurth T, Kubisch C, Dichgans M, Chasman DI, Cotsapas C, Zwart JA, Samani NJ, Palotie A. Neurology Genetics. 2015; 1(1):e10. PMID: 27066539 PMCID: PMC4821079
  4. Shared genetic basis for migraine and ischemic stroke: A genome-wide analysis of common variants. Malik R, Freilinger T, Winsvold BS, Anttila V, Vander Heiden J, Traylor M, de Vries B, Holliday EG, Terwindt GM, Sturm J, Bis JC, Hopewell JC, Ferrari MD, Rannikmae K, Wessman M, Kallela M, Kubisch C, Fornage M, Meschia JF, Lehtimäki T, Sudlow C, Clarke R, Chasman DI, Mitchell BD, Maguire J, Kaprio J, Farrall M, Raitakari OT, Kurth T, Ikram MA, Reiner AP, Longstreth WT Jr, Rothwell PM, Strachan DP, Sharma P, Seshadri S, Quaye L, Cherkas L, Schürks M, Rosand J, Ligthart L, Boncoraglio GB, Davey Smith G, van Duijn CM, Stefansson K, Worrall BB, Nyholt DR, Markus HS, van den Maagdenberg AM, Cotsapas C, Zwart JA, Palotie A, Dichgans M. Neurology. 2015; 84(21):2132-45. PMID: 25934857 PMCID: PMC4451048

2014

  1. MHC associations with clinical and autoantibody manifestations in European SLE. Morris DL, Fernando MM, Taylor KE, Chung SA, Nititham J, Alarcón-Riquelme ME, Barcellos LF, Behrens TW, Cotsapas C, Gaffney PM, Graham RR, Pons-Estel BA, Gregersen PK, Harley JB, Hauser SL, Hom G, Langefeld CD, Noble JA, Rioux JD, Seldin MF, Vyse TJ, Criswell LA. Genes and immunity. 2014; 15(4):210-7. PMID: 24598797 PMCID: PMC4102853
  2. A gene pathway analysis highlights the role of cellular adhesion molecules in multiple sclerosis susceptibility. Damotte V et al, on behalf of the International MS Genetics Consortium. Genes and immunity. 2014; 15(2):126-32. PMID: 24430173

2013

  1. Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis. Beecham AH et al, on behalf of the International MS Genetics Consortium. Nature genetics. 2013; 45(11):1353-60. PMID: 24076602 PMCID: PMC3832895
  2. Protein array-based profiling of CSF identifies RBPJ as an autoantigen in multiple sclerosis. Querol L, Clark PL, Bailey MA, Cotsapas C, Cross AH, Hafler DA, Kleinstein SH, Lee JY, Yaari G, Willis SN, O'Connor KC. Neurology. 2013; 81(11):956-63. PMID: 23921886 PMCID: PMC3888197
  3. Pleiotropy in complex traits: challenges and strategies. Solovieff N, Cotsapas C, Lee PH, Purcell SM, Smoller JW. Nature Reviews Genetics. 2013; 14(7):483-95. PMID: 23752797 PMCID: PMC4104202
  4. Network-based multiple sclerosis pathway analysis with GWAS data from 15,000 cases and 30,000 controls. Baranzini SE et al, on behalf of the International MS Genetics Consortium. American journal of human genetics. 2013; 92(6):854-65. PMID: 23731539 PMCID: PMC3958952
  5. Weight loss after gastric bypass is associated with a variant at 15q26.1. Hatoum IJ, Greenawalt DM, Cotsapas C, Daly MJ, Reitman ML, Kaplan LM. American journal of human genetics. 2013; 92(5):827-34. PMID: 23643386 PMCID: PMC3644642
  6. Immune-mediated disease genetics: the shared basis of pathogenesis. Cotsapas C, Hafler DA. Trends in immunology. 2013; 34(1):22-6. PMID: 23031829

2012

  1. Unraveling multiple MHC gene associations with systemic lupus erythematosus: model choice indicates a role for HLA alleles and non-HLA genes in Europeans. Morris DL, Taylor KE, Fernando MM, Nititham J, Alarcón-Riquelme ME, Barcellos LF, Behrens TW, Cotsapas C, Gaffney PM, Graham RR, Pons-Estel BA, Gregersen PK, Harley JB, Hauser SL, Hom G, Langefeld CD, Noble JA, Rioux JD, Seldin MF, Criswell LA, Vyse TJ. American journal of human genetics. 2012; 91(5):778-93. PMID: 23084292 PMCID: PMC3487133
  2. Human genetics offers an emerging picture of common pathways and mechanisms in autoimmunity. Voight BF, Cotsapas C. Current opinion in immunology. 2012; 24(5):552-7. PMID: 23041452
  3. Systematic localization of common disease-associated variation in regulatory DNA. Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R, Qu H, Brody J, Shafer A, Neri F, Lee K, Kutyavin T, Stehling-Sun S, Johnson AK, Canfield TK, Giste E, Diegel M, Bates D, Hansen RS, Neph S, Sabo PJ, Heimfeld S, Raubitschek A, Ziegler S, Cotsapas C, Sotoodehnia N, Glass I, Sunyaev SR, Kaul R, Stamatoyannopoulos JA. Science. 2012; 337(6099):1190-5. PMID: 22955828 PMCID: PMC3771521

2011

  1. Heritability of the weight loss response to gastric bypass surgery. Hatoum IJ, Greenawalt DM, Cotsapas C, Reitman ML, Daly MJ, Kaplan LM. The Journal of clinical endocrinology and metabolism. 2011; 96(10):E1630-3. PMID: 21832118 PMCID: PMC3200251
  2. Pervasive sharing of genetic effects in autoimmune disease. Cotsapas C, Voight BF, Rossin E, Lage K, Neale BM, Wallace C, Abecasis GR, Barrett JC, Behrens T, Cho J, De Jager PL, Elder JT, Graham RR, Gregersen P, Klareskog L, Siminovitch KA, van Heel DA, Wijmenga C, Worthington J, Todd JA, Hafler DA, Rich SS, Daly MJ. PLoS genetics. 2011; 7(8):e1002254. PMID: 21852963 PMCID: PMC3154137
  3. Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology. Rossin EJ, Lage K, Raychaudhuri S, Xavier RJ, Tatar D, Benita Y, Cotsapas C, Daly MJ. PLoS genetics. 2011; 7(1):e1001273. PMID: 21249183 PMCID: PMC3020935

2010

  1. Expression analysis of loci associated with type 2 diabetes in human tissues. Cotsapas C, Prokunina-Olsson L, Welch C, Saxena R, Weaver C, Usher N, Guiducci C, Bonakdar S, Turner N, LaCroix B, Hall JL. Diabetologia. 2010; 53(11):2334-9. PMID: 20703447
  2. Fine mapping in 94 inbred mouse strains using a high-density haplotype resource. Kirby A, Kang HM, Wade CM, Cotsapas C, Kostem E, Han B, Furlotte N, Kang EY, Rivas M, Bogue MA, Frazer KA, Johnson FM, Beilharz EJ, Cox DR, Eskin E, Daly MJ. Genetics. 2010; 185(3):1081-95. PMID: 20439770 PMCID: PMC2907194

2009

  1. Common body mass index-associated variants confer risk of extreme obesity. Cotsapas C, Speliotes EK, Hatoum IJ, Greenawalt DM, Dobrin R, Lum PY, Suver C, Chudin E, Kemp D, Reitman M, Voight BF, Neale BM, Schadt EE, Hirschhorn JN, Kaplan LM, Daly MJ. Human molecular genetics. 2009; 18(18):3502-7. PMID: 19553259 PMCID: PMC2729668
  2. Intra- and inter-individual genetic differences in gene expression. Cowley MJ, Cotsapas CJ, Williams RB, Chan EK, Pulvers JN, Liu MY, Luo OJ, Nott DJ, Little PF. Mammalian genome. 2009; 20(5):281-95. PMID: 19424753 PMCID: PMC2690833

2008

  1. Genetic analysis of human traits in vitro: drug response and gene expression in lymphoblastoid cell lines. Choy E, Yelensky R, Bonakdar S, Plenge RM, Saxena R, De Jager PL, Shaw SY, Wolfish CS, Slavik JM, Cotsapas C, Rivas M, Dermitzakis ET, Cahir-McFarland E, Kieff E, Hafler D, Daly MJ, Altshuler D. PLoS genetics. 2008; 4(11):e1000287. PMID: 19043577 PMCID: PMC2583954
  2. Identifying genetic components of drug response in mice. Cotsapas C. Pharmacogenomics. 2008; 9(9):1323-30. PMID: 18781858
  3. Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus. Graham RR, Cotsapas C, Davies L, Hackett R, Lessard CJ, Leon JM, Burtt NP, Guiducci C, Parkin M, Gates C, Plenge RM, Behrens TW, Wither JE, Rioux JD, Fortin PR, Graham DC, Wong AK, Vyse TJ, Daly MJ, Altshuler D, Moser KL, Gaffney PM. Nature genetics. 2008; 40(9):1059-61. PMID: 19165918 PMCID: PMC2772171

2007

  1. Two independent alleles at 6q23 associated with risk of rheumatoid arthritis. Plenge RM, Cotsapas C, Davies L, Price AL, de Bakker PI, Maller J, Pe'er I, Burtt NP, Blumenstiel B, DeFelice M, Parkin M, Barry R, Winslow W, Healy C, Graham RR, Neale BM, Izmailova E, Roubenoff R, Parker AN, Glass R, Karlson EW, Maher N, Hafler DA, Lee DM, Seldin MF, Remmers EF, Lee AT, Padyukov L, Alfredsson L, Coblyn J, Weinblatt ME, Gabriel SB, Purcell S, Klareskog L, Gregersen PK, Shadick NA, Daly MJ, Altshuler D. Nature genetics. 2007; 39(12):1477-82. PMID: 17982456 PMCID: PMC2652744
  2. Gene expression profiles in zebrafish (Danio rerio) liver cells exposed to a mixture of pharmaceuticals at environmentally relevant concentrations. Pomati F, Cotsapas CJ, Castiglioni S, Zuccato E, Calamari D. Chemosphere. 2007; 70(1):65-73. PMID: 17764721
  3. Genome-wide detection and characterization of positive selection in human populations. Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES, on behalf of the HapMap Consortium. Nature. 2007; 449(7164):913-8. PMID: 17943131 PMCID: PMC2687721

2006

  1. Normalization procedures and detection of linkage signal in genetical-genomics experiments. Williams RB, Cotsapas CJ, Cowley MJ, Chan E, Nott DJ, Little PF. Nature genetics. 2006; 38(8):855-6; author reply 856-9. PMID: 16874319
  2. Genetic dissection of gene regulation in multiple mouse tissues. Cotsapas CJ, Williams RB, Pulvers JN, Nott DJ, Chan EK, Cowley MJ, Little PF. Mammalian genome. 2006; 17(6):490-5. PMID: 16783630

2003

  1. Genetic variation and the control of transcription. Cotsapas C, Chan E, Kirk M, Tanaka M, Little P. Cold Spring Harbor symposia on quantitative biology. 2003; 68:109-14. PMID: 15338608