Highlighted Recent Papers

 

A method to decipher pleiotropy by detecting underlying heterogeneity driven by hidden subgroups applied to autoimmune and neuropsychiatric diseases.

Buhm Han, Jennie Pouget, Kamil Slowikowski, Eli Stahl Cue HyunKyu Lee et al. Nature Genetics. In Press, 2016.

 

Pervasive non-additive and interaction effects in the HLA modulate the risk of autoimmune diseases.

Tobias Lenz, Aaron Deutsch, Buhm Han, Xinli Hu, et al. Nature Genetics. 47, 1085–1090, 2015.

 

Additive and interaction effects at three amino acid positions in HLA-DQ and HLA-DR molecules drive type 1 diabetes risks.

Xinli Hu, Aaron J Deutsch, Tobias L Lenz, Suna Onengut-Gumuscu, Buhm Han, Wei-Min Chen, Joanna M M Howson, John A Todd, Paul I W de Bakker, Stephen S Rich & Soumya Raychaudhuri. Nature Genetics. 47: 898–905, 2015.

 

Regulation of gene expression in autoimmune disease loci and the genetic basis of proliferation in CD4+ effector memory T cells.

Xinli Hu, Hyun Kim, Towfique Raj, Patrick Brennan, Gosia Trynka, Nick Teslovich, Kamil Slowikowski, Wei-Min Chen , Suna Onengut, Claire Baecher-Allan, Phil de Jager, Stephen S Rich, Barbara E Stranger, Michael B Brenner , Soumya Raychaudhuri. PLoS Genetics. 10:e1004404. 2014.

 

Chromatin marks identify critical cell-types for fine-mapping complex trait variants.

Gosia Trynka, Cynthia Sandor, Buhm Han, Han Xu, Barbara E Stranger, X Shirley Liu, and Soumya Raychaudhuri. Nature Genetics. 45: 124-30, 2013.

Books

OUPBook

Computational Text Analysis for Functional Genomics and Bioinformatics.
by Soumya Raychaudhuri.Oxford University Press. Oxford, 300 pages. 2006.

Textbook that outlines basic bioinformatics applications of text mining to analyze large-scale data sets such as gene-expression data.

Amazon

 

For all publications click here.


Selected Recent Research Papers (from >100)

  • Han B, Pouget J, Slowikowski K, Stahl E, Lee CH, Diogo D, Hu X, Park YR, Kim E, Gregersen PK, Rantapää-Dahlqvist S, Worthington J, Martin J, Eyre S, Klareskog L, Huizinga T, Chen W-M, Onengut-Gumuscu S, Rich SS, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Wray NR, Raychaudhuri S. Deciphering pleiotropy among complex traits: using genotype data to detect underlying heterogeneity driven by a hidden subgroup. Nature Genetics 2016. In Press.
  • Han B, Duong D, Sul JH, de Bakker PIW, Eskin E, Raychaudhuri S. A general framework for meta-analyzing dependent studies with overlapping subjects in association mapping. Hum Mol Genet. 2016. In Press.
  • Lee SH, Byrne EM, Hultman CM, Kähler A, Vinkhuyzen AA, Ripke S, Andreassen OA, Frisell T, Gusev A, Hu X, Karlsson R, Mantzioris VX, McGrath JJ, Mehta D, Stahl EA, Zhao Q, Kendler KS, Sullivan PF, Price AL, O'Donovan M, Okada Y, Mowry BJ, Raychaudhuri S, Wray NR; Schizophrenia Working Group of the Psychiatric Genomics Consortium and Rheumatoid Arthritis Consortium International; New data and an old puzzle: the negative association between schizophrenia and rheumatoid arthritis. International Journal of Epidemiology. 2015. In Press.
  • Frisell T, Hellgren K, Alfredsson L, Raychaudhuri S, Klareskog L, Askling J.Familial Aggregation of Arthritis-Related Diseases in Seropositive and Seronegative Rheumatoid Arthritis – A Register-based Case-Control Study in Sweden. Ann Rhem Disease. 2016 Jan;75(1):183-9.
  • Finucane HK, Bulik-Sullivan B, Gusev A, Trynka G, Reshef Y, Loh PR, Anttila V, Xu H, Zang C, Farh K, Ripke S, Day FR; ReproGen Consortium; Schizophrenia Working Group of the Psychiatric Genomics Consortium; RACI Consortium, Purcell S, Stahl E, Lindstrom S, Perry JR, Okada Y, Raychaudhuri S, Daly MJ, Patterson N, Neale BM, Price AL. Partitioning heritability by functional annotation using genome-wide association summary statistics. Nature Genetics. 2015 Nov;47(11):1228-35.
  • Triebwasser MP, Roberson ED, Yu Y, Schramm EC, Wagner EK, Raychaudhuri S, Seddon JM, Atkinson JP. Rare Variants in the Functional Domains of Complement Factor H Are Associated with Age-Related Macular Degeneration. Invest Ophthalmol Vis Sci. 2015 Oct;56(11):6873-8.
  • Lenz TL, Deutsch AJ, Han B, Hu X, Okada Y, Eyre S, Knapp M, Zhernakova A, Tom W.J. Huizinga TWJ, Abecasis G, Becker J, Boeckxstaens GE, Chen W-M, Franke A, Gladman DG, Gockel I, Gutierrez-Achury J, Martin J, Nair RP, Nöthen MM, Onengut-Gumuscu S, Rahman P, Rantapää-Dahlqvist S, Stuart PE, Tsoi LC, van Heel DA, Worthington J, Wouters MM, Klareskog L, Elder JT, Gregersen PK, Schumacher J, Rich SS, Wijmenga C, Sunyaev SR, de Bakker PIW, Raychaudhuri S. Widespread non-additive and interaction effects within the HLA modulate the risk of autoimmune diseases. Nature Genetics. 2015 Sep;47(9):1085-90.
  • Hu X, Deutsch AJ, Lenz TL, Onengut-Gumuscu S, Han B, Chen W-M, Howson JMM, Todd JA, de Bakker PIW, Rich SS, Raychaudhuri S. Additive and interaction effects at three key amino acid positions in HLA-DQ and HLA-DR molecules drive type 1 diabetes genetic risk. Nat Genet. 2015 Aug;47(8):898-905.
  • Scott IC, Rijsdijk F, Walker J, Quist J, Spain SL, Tan R, Steer S, Okada Y, Raychaudhuri S, Cope AP, Lewis CM. Do Genetic Susceptibility Variants Associate with Disease Severity in Early Active Rheumatoid Arthritis? J Rheumatol. 2015 Jul;42(7):1131-40.
  • Kavanagh D, Yu Y, Schramm EC, Triebwasser M, Wagner EK, Raychaudhuri S, Daly MJ, Atkinson JP, Seddon JM. Rare genetic variants in the CFI gene are associated with advanced age-related macular degeneration and commonly result in reduced serum factor I levels. Hum. Mol. Genet. 2015 Jul 1;24(13):3861–70.
  • Trynka G, Westra H-J, Slowikowski K, Hu X, Xu H, Stranger B, Klein R, Han B, Raychaudhuri S. Disentangling effects of colocalizing genomic annotations to functionally prioritize non-coding variants within complex trait loci. Am J Hum Genet. 2015 Jul 2; 97:139–152
  • Sul JH, Raj T, de Jong S, de Bakker PIW, Raychaudhuri S, Ophoff RA, Stranger BE, Eskin E, Han B. Accurate and fast multiple testing correction in eQTL studies. Am J Hum Genet. 2015 Jun 4;96(6):857-68.
  • Viatte S, Plant D, Han B, Morgan C, Hyrich KL, Morgan AW, Wilson AG, Isaacs JD, Biologics in Rheumatoid Arthritis Genetics and Genomics Study Syndicate BRAGGSS, Raychaudhuri S, Barton A. Association of HLA-DRB1 haplotypes with rheumatoid arthritis severity, mortality and treatment response. Journal of the American Medical Association. 2015 Apr 28;313(16):1645-56
  • Pers TH, Karjalainen JM, Chan Y, Westra HJ, Wood AR, Yang J, Lui JC, Vedantam S, Gustafsson S, Esko T, Frayling T, Speliotes EK; Genetic Investigation of ANthropometric Traits (GIANT) Consortium, Boehnke M, Raychaudhuri S, Fehrmann RS, Hirschhorn JN, Franke L. Biological interpretation of genome-wide association studies using predicted gene functions. Nature Communications. 2015 Jan 19;6:5890.
  • Gusev A, Lee SH, Trynka G, Finucane H, Vilhjálmsson BJ, Xu H, Zang C, Ripke S, Bulik-Sullivan B, Stahl E; Schizophrenia Working Group of the Psychiatric Genomics Consortium; SWE-SCZ Consortium, Kähler AK, Hultman CM, Purcell SM, McCarroll SA, Daly M, Pasaniuc B, Sullivan PF, Neale BM, Wray NR, Raychaudhuri S, Price AL; Schizophrenia Working Group of the Psychiatric Genomics Consortium; SWE-SCZ Consortium. Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases. Am J Hum Genet. 2014 Nov 6;95(5):535-52.
  • Slowikowski K, Hu X, Raychaudhuri S. SNPsea: an algorithm to identify cell types, tissues, and pathways affected by risk loci. Bioinformatics. 2014 Sep 1;30(17):2496-7.
  • Okada Y, Han B, Tsoi LC, Stuart PE, Ellinghaus E, Tejasvi T, Chandran V, Pellett F, Pollock R, Bowcock AM, Krueger GG, Weichenthal M, Voorhees JJ, Rahman P, Gregersen PK, Franke A, Nair RP, Abecasis GR, Gladman DD, Elder JT, de Bakker PIW, Raychaudhuri S. Fine-mapping major histocompatibility complex associations in psoriasis and its clinical subtypes. Am J Hum Genet. 2014 Aug 7;95(2):162-72.
  • Hu X, Kim H, Raj T, Brennan PJ, Trynka G, Teslovich N, Slowikowski K, Chen W-M, Onengut S, Baecher-Allan C, de Jager, P, Rich SS, Stranger BE, Brenner MB, Raychaudhuri S. Regulation of gene expression in autoimmune disease loci and the genetic basis of proliferation in CD4+ effector memory T cells. PLoS Genetics. 2014. Jun 26;10(6):e1004404.
  • Raj T, Rothamel K, Mostafavi S, Ye C, Lee M, Replogle JM, Feng T, Lee M, Asinovski N, Frohlich I, Imboya S, Von Korff A, Okada Y, Patsopoulos NA, Davis S, McCabe C, Paik H, Srivastava GP, Raychaudhuri S, Hafler DA, Koller D, Regev A, Hacohen N, Mathis D, Benoist C, Stranger BE, De Jager PL. Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes. Science. 2014 May 2;344(6183):519–23.
  • Han B, Diogo D, Eyre, S, Kallberg H, Zhernakova A, Bowes J, Padyukov L, Okada Y, González-Gay MA, Rantapää-Dahlqvist S, Martin J, Huizinga TWJ, Plenge RM, Worthington J, Gregersen P, Klareskog L, de Bakker PIW, Raychaudhuri S. Fine-mapping seronegative and seropositive rheumatoid arthritis to shared and distinct HLA alleles by adjusting for the effects of heterogeneity. Am J Hum Genet. 2014 Apr 3;94(4):522-32.
  • Lee MN, Ye C, Villani A-C, Raj T, Li W, Eisenhaure TM, Imboywa SH, Chipendo PI, Ran FA, Slowikowski K, Ward LD, Raddassi K, McCabe C, Lee MH, Frohlich IY, Hafler DA, Kellis M, Raychaudhuri S, Zhang F, Stranger BE, Benoist CO, De Jager PL, Regev A, Hacohen N. Common genetic variants modulate pathogen-sensing responses in human dendritic cells. Science. 2014 Mar 7;343(6175):1246980.
  • Okada Y, Wu D, Trynka G, Raj T, Terao C, Ikari K, Kochi Y, Ohmura K,et al Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature. 506:376-81. 2014.
  • Hu X, Kim H, Brennan P, Han B, Baecher-Allan C, de Jager PL, Brenner M, Raychaudhuri S. User-guided cytometric data analysis for large-scale immunoprofiling studies: application to invariant natural killer T cells. Proc Natl Acad Sci. 110:19030–19035, 2013.
  • Seddon JM, Yu Y, Miller EC, Reynolds R, Tan PL, Gowrisankar S, Goldstein JI, Triebwasser M, Anderson HE, Zerbib J, Kavanagh D, Souied E, Katsanis N, Daly MJ, Atkinson JP, Raychaudhuri S. Rare variants in CFI, C3 and C9 are associated with high risk of advanced age-related macular degeneration. Nature Genetics. 45:1366-1370. 2013
  • Jia X, Han B, Onengut-Gumuscu S, Chen W-M, Concannon PJ, Rich S, Raychaudhuri S ,and de Bakker PIW. Imputing amino acid polymorphisms in human leukocyte antigens. PLoS One. 8:e64683. 2013
  • Trynka G, Sandor C, Han B, Xu H, Stranger BE, Liu X, Raychaudhuri S. Chromatin marks identify critical cell-types for fine-mapping complex trait variants. Nature Genetics. 45: 124-30. 2013.
  • Eyre S, Bowes J, Diogo D, Lee A, Barton A, Martin P, et al. High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis. Nature Genetics. 44: 1336-40. 2012.
  • Stahl EA, Wegmann D, Trynka G, Guitierrez-Achury J, Do R, Voight BF, Kraft P, Chen R, Kallberg HJ, Kurreeman FAS, DIAGRAM, MIGEN, Kathiresan S, Wijmenga C, Gregersen PK, Alfredsson L, Siminovitch KA, Worthington J, de Bakker PIW, Raychaudhuri S, and Plenge RM. Bayesian inference reveals the hidden polygenic architecture of rheumatoid arthritis. Nature Genetics. 44:483–489. 2012.
  • Raychaudhuri S, Cynthia Sandor, Eli Stahl, Jan Freudenberg et al. Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis. Nature Genetics. 44:291–6, 2012.
  • Raychaudhuri S, Iartchouk O, Chin K, Tan PL, Tai AK, Ripke S, Gowrisankar S, Vemuri S, Montgomery K, Yu Y, Reynolds R, Zack DJ, Campochiaro B, Campochiaro P, Katsanis N, Daly MJ, Seddon JM. A rare penetrant mutation in CFH confers high risk of age-related macular degeneration. Nat Genet. 2011 Dec; 43(12):1232-6.
  • Hu X, Kim H, Stahl E, Plenge R, Daly M, Raychaudhuri S. Integrating autoimmune risk loci with gene-expression data identifies specific pathogenic immune cell subsets. Am J Hum Genet. 2011 Oct 7; 89(4):496-506.