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Soumya Raychaudhuri, M.D., Ph.D.

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Other Positions
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Overview
overview
Soumya Raychaudhuri is interested in using human genetics to understand key pathogenic pathways that cause human disease, with a particular focus on rheumatoid arthritis and other autoimmune diseases.

Mentoring
completed student projects
Non-additive effects of HLA genes in three common autoimmune diseases
Summer, 06/01/14 - 08/31/14

Research
research activities and funding
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
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  1. U01HG009379 (PRICE, ALKES L) Feb 1, 2017 - Jan 31, 2021
    NIH/NHGRI
    Functionally specialized components of disease heritability in ENCODE data
    Role: Co-Principal Investigator
  2. U19AI111224 (MOODY, DAVID BRANCH) Feb 1, 2015 - Jan 31, 2022
    NIH/NIAID
    Metabolic factors that control the spectrum of human tuberculosis
    Role: Co-Principal Investigator
  3. UH2AR067677 (RAYCHAUDHURI, SOUMYA) Sep 24, 2014 - May 31, 2019
    NIH/NIAMS
    RA-SLE Molecular Deconstruction Leadership Center
    Role: Co-Principal Investigator
  4. R01AR063759 (RAYCHAUDHURI, SOUMYA) Aug 2, 2013 - Apr 30, 2019
    NIH/NIAMS
    Discovery and Functional Impact of Common and Rare Variants in RA
    Role: Principal Investigator
  5. U01GM092691 (RAYCHAUDHURI, SOUMYA) Jul 1, 2010 - Jun 30, 2015
    NIH/NIGMS
    Genetic predictors of response to anti-TNF therapy in rheumatoid arthritis
    Role: Co-Principal Investigator

Featured Content

Bibliographic
selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Westra HJ, Martínez-Bonet M, Onengut-Gumuscu S, Lee A, Luo Y, Teslovich N, Worthington J, Martin J, Huizinga T, Klareskog L, Rantapaa-Dahlqvist S, Chen WM, Quinlan A, Todd JA, Eyre S, Nigrovic PA, Gregersen PK, Rich SS, Raychaudhuri S. Fine-mapping and functional studies highlight potential causal variants for rheumatoid arthritis and type 1 diabetes. Nat Genet. 2018 Oct; 50(10):1366-1374. PMID: 30224649.
    View in: PubMed
  2. Haghighi A, Krier JB, Toth-Petroczy A, Cassa CA, Frank NY, Carmichael N, Fieg E, Bjonnes A, Mohanty A, Briere LC, Lincoln S, Lucia S, Gupta VA, Söylemez O, Sutti S, Kooshesh K, Qiu H, Fay CJ, Perroni V, Valerius J, Hanna M, Frank A, Ouahed J, Snapper SB, Pantazi A, Chopra SS, Leshchiner I, Stitziel NO, Feldweg A, Mannstadt M, Loscalzo J, Sweetser DA, Liao E, Stoler JM, Nowak CB, Sanchez-Lara PA, Klein OD, Perry H, Patsopoulos NA, Raychaudhuri S, Goessling W, Green RC, Seidman CE, MacRae CA, Sunyaev SR, Maas RL, Vuzman D. An integrated clinical program and crowdsourcing strategy for genomic sequencing and Mendelian disease gene discovery. NPJ Genom Med. 2018; 3:21. PMID: 30131872.
    View in: PubMed
  3. Li G, Martínez-Bonet M, Wu D, Yang Y, Cui J, Nguyen HN, Cunin P, Levescot A, Bai M, Westra HJ, Okada Y, Brenner MB, Raychaudhuri S, Hendrickson EA, Maas RL, Nigrovic PA. High-throughput identification of noncoding functional SNPs via type IIS enzyme restriction. Nat Genet. 2018 Aug; 50(8):1180-1188. PMID: 30013183.
    View in: PubMed
  4. Cortes A, Gladman D, Raychaudhuri S, Cui J, Wheeler L, Brown MA. Imputation-based analysis of MICA alleles in the susceptibility to ankylosing spondylitis. Ann Rheum Dis. 2018 Apr 28. PMID: 29705741.
    View in: PubMed
  5. Finucane HK, Reshef YA, Anttila V, Slowikowski K, Gusev A, Byrnes A, Gazal S, Loh PR, Lareau C, Shoresh N, Genovese G, Saunders A, Macosko E, Pollack S, Perry JRB, Buenrostro JD, Bernstein BE, Raychaudhuri S, McCarroll S, Neale BM, Price AL. Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types. Nat Genet. 2018 Apr; 50(4):621-629. PMID: 29632380.
    View in: PubMed
  6. Mizoguchi F, Slowikowski K, Wei K, Marshall JL, Rao DA, Chang SK, Nguyen HN, Noss EH, Turner JD, Earp BE, Blazar PE, Wright J, Simmons BP, Donlin LT, Kalliolias GD, Goodman SM, Bykerk VP, Ivashkiv LB, Lederer JA, Hacohen N, Nigrovic PA, Filer A, Buckley CD, Raychaudhuri S, Brenner MB. Functionally distinct disease-associated fibroblast subsets in rheumatoid arthritis. Nat Commun. 2018 02 23; 9(1):789. PMID: 29476097.
    View in: PubMed
  7. Slowikowski K, Wei K, Brenner MB, Raychaudhuri S. Functional genomics of stromal cells in chronic inflammatory diseases. Curr Opin Rheumatol. 2018 Jan; 30(1):65-71. PMID: 28984647.
    View in: PubMed
  8. Nigrovic PA, Raychaudhuri S, Thompson SD. Review: Genetics and the Classification of Arthritis in Adults and Children. Arthritis Rheumatol. 2018 Jan; 70(1):7-17. PMID: 29024575.
    View in: PubMed
  9. Terao C, Okada Y, Ikari K, Kochi Y, Suzuki A, Ohmura K, Matsuo K, Taniguchi A, Kubo M, Raychaudhuri S, Yamamoto K, Yamanaka H, Kamatani Y, Mimori T, Matsuda F. Genetic landscape of interactive effects of HLA-DRB1 alleles on susceptibility to ACPA(+) rheumatoid arthritis and ACPA levels in Japanese population. J Med Genet. 2017 Dec; 54(12):853-858. PMID: 29025870.
    View in: PubMed
  10. Fonseka CY, Rao DA, Raychaudhuri S. Leveraging blood and tissue CD4+ T cell heterogeneity at the single cell level to identify mechanisms of disease in rheumatoid arthritis. Curr Opin Immunol. 2017 Dec; 49:27-36. PMID: 28888129.
    View in: PubMed
  11. Scally SW, Law SC, Ting YT, Heemst JV, Sokolove J, Deutsch AJ, Bridie Clemens E, Moustakas AK, Papadopoulos GK, van der Woude D, Smolik I, Hitchon CA, Robinson DB, Ferucci ED, Bernstein CN, Meng X, Anaparti V, Huizinga T, Kedzierska K, Reid HH, Raychaudhuri S, Toes RE, Rossjohn J, El-Gabalawy H, Thomas R. Molecular basis for increased susceptibility of Indigenous North Americans to seropositive rheumatoid arthritis. Ann Rheum Dis. 2017 11; 76(11):1915-1923. PMID: 28801345.
    View in: PubMed
  12. Aung T, Ozaki M, Lee MC, Schlötzer-Schrehardt U, Thorleifsson G, Mizoguchi T, Igo RP, Haripriya A, Williams SE, Astakhov YS, Orr AC, Burdon KP, Nakano S, Mori K, Abu-Amero K, Hauser M, Li Z, Prakadeeswari G, Bailey JNC, Cherecheanu AP, Kang JH, Nelson S, Hayashi K, Manabe SI, Kazama S, Zarnowski T, Inoue K, Irkec M, Coca-Prados M, Sugiyama K, Järvelä I, Schlottmann P, Lerner SF, Lamari H, Nilgün Y, Bikbov M, Park KH, Cha SC, Yamashiro K, Zenteno JC, Jonas JB, Kumar RS, Perera SA, Chan ASY, Kobakhidze N, George R, Vijaya L, Do T, Edward DP, de Juan Marcos L, Pakravan M, Moghimi S, Ideta R, Bach-Holm D, Kappelgaard P, Wirostko B, Thomas S, Gaston D, Bedard K, Greer WL, Yang Z, Chen X, Huang L, Sang J, Jia H, Jia L, Qiao C, Zhang H, Liu X, Zhao B, Wang YX, Xu L, Leruez S, Reynier P, Chichua G, Tabagari S, Uebe S, Zenkel M, Berner D, Mossböck G, Weisschuh N, Hoja U, Welge-Luessen UC, Mardin C, Founti P, Chatzikyriakidou A, Pappas T, Anastasopoulos E, Lambropoulos A, Ghosh A, Shetty R, Porporato N, Saravanan V, Venkatesh R, Shivkumar C, Kalpana N, Sarangapani S, Kanavi MR, Beni AN, Yazdani S, Lashay A, Naderifar H, Khatibi N, Fea A, Lavia C, Dallorto L, Rolle T, Frezzotti P, Paoli D, Salvi E, Manunta P, Mori Y, Miyata K, Higashide T, Chihara E, Ishiko S, Yoshida A, Yanagi M, Kiuchi Y, Ohashi T, Sakurai T, Sugimoto T, Chuman H, Aihara M, Inatani M, Miyake M, Gotoh N, Matsuda F, Yoshimura N, Ikeda Y, Ueno M, Sotozono C, Jeoung JW, Sagong M, Park KH, Ahn J, Cruz-Aguilar M, Ezzouhairi SM, Rafei A, Chong YF, Ng XY, Goh SR, Chen Y, Yong VHK, Khan MI, Olawoye OO, Ashaye AO, Ugbede I, Onakoya A, Kizor-Akaraiwe N, Teekhasaenee C, Suwan Y, Supakontanasan W, Okeke S, Uche NJ, Asimadu I, Ayub H, Akhtar F, Kosior-Jarecka E, Lukasik U, Lischinsky I, Castro V, Grossmann RP, Sunaric Megevand G, Roy S, Dervan E, Silke E, Rao A, Sahay P, Fornero P, Cuello O, Sivori D, Zompa T, Mills RA, Souzeau E, Mitchell P, Wang JJ, Hewitt AW, Coote M, Crowston JG, Astakhov SY, Akopov EL, Emelyanov A, Vysochinskaya V, Kazakbaeva G, Fayzrakhmanov R, Al-Obeidan SA, Owaidhah O, Aljasim LA, Chowbay B, Foo JN, Soh RQ, Sim KS, Xie Z, Cheong AWO, Mok SQ, Soo HM, Chen XY, Peh SQ, Heng KK, Husain R, Ho SL, Hillmer AM, Cheng CY, Escudero-Domínguez FA, González-Sarmiento R, Martinon-Torres F, Salas A, Pathanapitoon K, Hansapinyo L, Wanichwecharugruang B, Kitnarong N, Sakuntabhai A, Nguyn HX, Nguyn GTT, Nguyn TV, Zenz W, Binder A, Klobassa DS, Hibberd ML, Davila S, Herms S, Nöthen MM, Moebus S, Rautenbach RM, Ziskind A, Carmichael TR, Ramsay M, Álvarez L, García M, González-Iglesias H, Rodríguez-Calvo PP, Fernández-Vega Cueto L, Oguz Ç, Tamcelik N, Atalay E, Batu B, Aktas D, Kasim B, Wilson MR, Coleman AL, Liu Y, Challa P, Herndon L, Kuchtey RW, Kuchtey J, Curtin K, Chaya CJ, Crandall A, Zangwill LM, Wong TY, Nakano M, Kinoshita S, den Hollander AI, Vesti E, Fingert JH, Lee RK, Sit AJ, Shingleton BJ, Wang N, Cusi D, Qamar R, Kraft P, Pericak-Vance MA, Raychaudhuri S, Heegaard S, Kivelä T, Reis A, Kruse FE, Weinreb RN, Pasquale LR, Haines JL, Thorsteinsdottir U, Jonasson F, Allingham RR, Milea D, Ritch R, Kubota T, Tashiro K, Vithana EN, Micheal S, Topouzis F, Craig JE, Dubina M, Sundaresan P, Stefansson K, Wiggs JL, Pasutto F, Khor CC. Genetic association study of exfoliation syndrome identifies a protective rare variant at LOXL1 and five new susceptibility loci. Nat Genet. 2017 07; 49(7):993-1004. PMID: 28553957.
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  13. Budu-Aggrey A, Bowes J, Stuart PE, Zawistowski M, Tsoi LC, Nair R, Jadon DR, McHugh N, Korendowych E, Elder JT, Barton A, Raychaudhuri S. A rare coding allele in IFIH1 is protective for psoriatic arthritis. Ann Rheum Dis. 2017 Jul; 76(7):1321-1324. PMID: 28501801.
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  14. Karnes JH, Bastarache L, Shaffer CM, Gaudieri S, Xu Y, Glazer AM, Mosley JD, Zhao S, Raychaudhuri S, Mallal S, Ye Z, Mayer JG, Brilliant MH, Hebbring SJ, Roden DM, Phillips EJ, Denny JC. Phenome-wide scanning identifies multiple diseases and disease severity phenotypes associated with HLA variants. Sci Transl Med. 2017 05 10; 9(389). PMID: 28490672.
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  15. Cui J, Diogo D, Stahl EA, Canhao H, Mariette X, Greenberg JD, Okada Y, Pappas DA, Fulton RS, Tak PP, Nurmohamed MT, Lee A, Larson DE, Kurreeman F, Deluca TL, O'Laughlin M, Fronick CC, Fulton LL, Mardis ER, van der Horst-Bruinsma IE, Wolbink GJ, Gregersen PK, Kremer JM, Crusius JB, de Vries N, Huizinga TW, Fonseca JE, Miceli-Richard C, Karlson EW, Coenen MJ, Barton A, Plenge RM, Raychaudhuri S. Brief Report: The Role of Rare Protein-Coding Variants in Anti-Tumor Necrosis Factor Treatment Response in Rheumatoid Arthritis. Arthritis Rheumatol. 2017 04; 69(4):735-741. PMID: 27788309.
    View in: PubMed
  16. Terao C, Kawaguchi T, Dieude P, Varga J, Kuwana M, Hudson M, Kawaguchi Y, Matucci-Cerinic M, Ohmura K, Riemekasten G, Kawasaki A, Airo P, Horita T, Oka A, Hachulla E, Yoshifuji H, Caramaschi P, Hunzelmann N, Baron M, Atsumi T, Hassoun P, Torii T, Takahashi M, Tabara Y, Shimizu M, Tochimoto A, Ayuzawa N, Yanagida H, Furukawa H, Tohma S, Hasegawa M, Fujimoto M, Ishikawa O, Yamamoto T, Goto D, Asano Y, Jinnin M, Endo H, Takahashi H, Takehara K, Sato S, Ihn H, Raychaudhuri S, Liao K, Gregersen P, Tsuchiya N, Riccieri V, Melchers I, Valentini G, Cauvet A, Martinez M, Mimori T, Matsuda F, Allanore Y. Transethnic meta-analysis identifies GSDMA and PRDM1 as susceptibility genes to systemic sclerosis. Ann Rheum Dis. 2017 Jun; 76(6):1150-1158. PMID: 28314753.
    View in: PubMed
  17. Mitra A, Kundu-Raychaudhuri S, Abria C, Rona A, Chaudhari AJ, Raychaudhuri SP. In-vivo quantitative assessment of the therapeutic response in a mouse model of collagen-induced arthritis using 18 F-fluorodeoxyglucose positron emission tomography. Clin Exp Immunol. 2017 05; 188(2):293-298. PMID: 28090641.
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  18. Sparks JA, Barbhaiya M, Karlson EW, Ritter SY, Raychaudhuri S, Corrigan CC, Lu F, Selhub J, Chasman DI, Paynter NP, Ridker PM, Solomon DH. Investigating methotrexate toxicity within a randomized double-blinded, placebo-controlled trial: Rationale and design of the Cardiovascular Inflammation Reduction Trial-Adverse Events (CIRT-AE) Study. Semin Arthritis Rheum. 2017 08; 47(1):133-142. PMID: 28284844.
    View in: PubMed
  19. Rao DA, Gurish MF, Marshall JL, Slowikowski K, Fonseka CY, Liu Y, Donlin LT, Henderson LA, Wei K, Mizoguchi F, Teslovich NC, Weinblatt ME, Massarotti EM, Coblyn JS, Helfgott SM, Lee YC, Todd DJ, Bykerk VP, Goodman SM, Pernis AB, Ivashkiv LB, Karlson EW, Nigrovic PA, Filer A, Buckley CD, Lederer JA, Raychaudhuri S, Brenner MB. Pathologically expanded peripheral T helper cell subset drives B cells in rheumatoid arthritis. Nature. 2017 02 01; 542(7639):110-114. PMID: 28150777.
    View in: PubMed
  20. Yu Y, Wagner EK, Souied EH, Seitsonen S, Immonen IJ, Häppölä P, Raychaudhuri S, Daly MJ, Seddon JM. Protective coding variants in CFH and PELI3 and a variant near CTRB1 are associated with age-related macular degeneration†. Hum Mol Genet. 2016 12 01; 25(23):5276-5285. PMID: 28011711.
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  21. van der Harst P, van Setten J, Verweij N, Vogler G, Franke L, Maurano MT, Wang X, Mateo Leach I, Eijgelsheim M, Sotoodehnia N, Hayward C, Sorice R, Meirelles O, Lyytikäinen LP, Polašek O, Tanaka T, Arking DE, Ulivi S, Trompet S, Müller-Nurasyid M, Smith AV, Dörr M, Kerr KF, Magnani JW, Del Greco M F, Zhang W, Nolte IM, Silva CT, Padmanabhan S, Tragante V, Esko T, Abecasis GR, Adriaens ME, Andersen K, Barnett P, Bis JC, Bodmer R, Buckley BM, Campbell H, Cannon MV, Chakravarti A, Chen LY, Delitala A, Devereux RB, Doevendans PA, Dominiczak AF, Ferrucci L, Ford I, Gieger C, Harris TB, Haugen E, Heinig M, Hernandez DG, Hillege HL, Hirschhorn JN, Hofman A, Hubner N, Hwang SJ, Iorio A, Kähönen M, Kellis M, Kolcic I, Kooner IK, Kooner JS, Kors JA, Lakatta EG, Lage K, Launer LJ, Levy D, Lundby A, Macfarlane PW, May D, Meitinger T, Metspalu A, Nappo S, Naitza S, Neph S, Nord AS, Nutile T, Okin PM, Olsen JV, Oostra BA, Penninger JM, Pennacchio LA, Pers TH, Perz S, Peters A, Pinto YM, Pfeufer A, Pilia MG, Pramstaller PP, Prins BP, Raitakari OT, Raychaudhuri S, Rice KM, Rossin EJ, Rotter JI, Schafer S, Schlessinger D, Schmidt CO, Sehmi J, Silljé HHW, Sinagra G, Sinner MF, Slowikowski K, Soliman EZ, Spector TD, Spiering W, Stamatoyannopoulos JA, Stolk RP, Strauch K, Tan ST, Tarasov KV, Trinh B, Uitterlinden AG, van den Boogaard M, van Duijn CM, van Gilst WH, Viikari JS, Visscher PM, Vitart V, Völker U, Waldenberger M, Weichenberger CX, Westra HJ, Wijmenga C, Wolffenbuttel BH, Yang J, Bezzina CR, Munroe PB, Snieder H, Wright AF, Rudan I, Boyer LA, Asselbergs FW, van Veldhuisen DJ, Stricker BH, Psaty BM, Ciullo M, Sanna S, Lehtimäki T, Wilson JF, Bandinelli S, Alonso A, Gasparini P, Jukema JW, Kääb S, Gudnason V, Felix SB, Heckbert SR, de Boer RA, Newton-Cheh C, Hicks AA, Chambers JC, Jamshidi Y, Visel A, Christoffels VM, Isaacs A, Samani NJ, de Bakker PIW. 52 Genetic Loci Influencing Myocardial Mass. J Am Coll Cardiol. 2016 09 27; 68(13):1435-1448. PMID: 27659466.
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  22. Wagner EK, Raychaudhuri S, Villalonga MB, Java A, Triebwasser MP, Daly MJ, Atkinson JP, Seddon JM. Mapping rare, deleterious mutations in Factor H: Association with early onset, drusen burden, and lower antigenic levels in familial AMD. Sci Rep. 2016 08 30; 6:31531. PMID: 27572114.
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  23. Okada Y, Suzuki A, Ikari K, Terao C, Kochi Y, Ohmura K, Higasa K, Akiyama M, Ashikawa K, Kanai M, Hirata J, Suita N, Teo YY, Xu H, Bae SC, Takahashi A, Momozawa Y, Matsuda K, Momohara S, Taniguchi A, Yamada R, Mimori T, Kubo M, Brown MA, Raychaudhuri S, Matsuda F, Yamanaka H, Kamatani Y, Yamamoto K. Contribution of a Non-classical HLA Gene, HLA-DOA, to the Risk of Rheumatoid Arthritis. Am J Hum Genet. 2016 Aug 04; 99(2):366-74. PMID: 27486778; PMCID: PMC4974094 [Available on 02/04/17].
    View in: PubMed, PubMed Central
  24. Li Z, Xia Y, Feng LN, Chen JR, Li HM, Cui J, Cai QQ, Sim KS, Nairismägi ML, Laurensia Y, Meah WY, Liu WS, Guo YM, Chen LZ, Feng QS, Pang CP, Chen LJ, Chew SH, Ebstein RP, Foo JN, Liu J, Ha J, Khoo LP, Chin ST, Zeng YX, Aung T, Chowbay B, Diong CP, Zhang F, Liu YH, Tang T, Tao M, Quek R, Mohamad F, Tan SY, Teh BT, Ng SB, Chng WJ, Ong CK, Okada Y, Raychaudhuri S, Lim ST, Tan W, Peng RJ, Khor CC, Bei JX. Genetic risk of extranodal natural killer T-cell lymphoma: a genome-wide association study. Lancet Oncol. 2016 Sep; 17(9):1240-7. PMID: 27470079.
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  25. Prins BP, Abbasi A, Wong A, Vaez A, Nolte I, Franceschini N, Stuart PE, Guterriez Achury J, Mistry V, Bradfield JP, Valdes AM, Bras J, Shatunov A, Lu C, Han B, Raychaudhuri S, Bevan S, Mayes MD, Tsoi LC, Evangelou E, Nair RP, Grant SF, Polychronakos C, Radstake TR, van Heel DA, Dunstan ML, Wood NW, Al-Chalabi A, Dehghan A, Hakonarson H, Markus HS, Elder JT, Knight J, Arking DE, Spector TD, Koeleman BP, van Duijn CM, Martin J, Morris AP, Weersma RK, Wijmenga C, Munroe PB, Perry JR, Pouget JG, Jamshidi Y, Snieder H, Alizadeh BZ. Investigating the Causal Relationship of C-Reactive Protein with 32 Complex Somatic and Psychiatric Outcomes: A Large-Scale Cross-Consortium Mendelian Randomization Study. PLoS Med. 2016 06; 13(6):e1001976. PMID: 27327646.
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  26. Pouget JG, Gonçalves VF, Spain SL, Finucane HK, Raychaudhuri S, Kennedy JL, Knight J. Genome-Wide Association Studies Suggest Limited Immune Gene Enrichment in Schizophrenia Compared to 5 Autoimmune Diseases. Schizophr Bull. 2016 09; 42(5):1176-84. PMID: 27242348.
    View in: PubMed
  27. Terao C, Raychaudhuri S, Gregersen PK. Recent Advances in Defining the Genetic Basis of Rheumatoid Arthritis. Annu Rev Genomics Hum Genet. 2016 08 31; 17:273-301. PMID: 27216775.
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  28. Han B, Pouget JG, Slowikowski K, Stahl E, Lee CH, Diogo D, Hu X, Park YR, Kim E, Gregersen PK, Dahlqvist SR, Worthington J, Martin J, Eyre S, Klareskog L, Huizinga T, Chen WM, Onengut-Gumuscu S, Rich SS, Wray NR, Raychaudhuri S. A method to decipher pleiotropy by detecting underlying heterogeneity driven by hidden subgroups applied to autoimmune and neuropsychiatric diseases. Nat Genet. 2016 07; 48(7):803-10. PMID: 27182969; PMCID: PMC4925284 [Available on 11/16/16].
    View in: PubMed, PubMed Central
  29. Gusev A, Shi H, Kichaev G, Pomerantz M, Li F, Long HW, Ingles SA, Kittles RA, Strom SS, Rybicki BA, Nemesure B, Isaacs WB, Zheng W, Pettaway CA, Yeboah ED, Tettey Y, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Chokkalingam AP, John EM, Murphy AB, Signorello LB, Carpten J, Leske MC, Wu SY, Hennis AJ, Neslund-Dudas C, Hsing AW, Chu L, Goodman PJ, Klein EA, Witte JS, Casey G, Kaggwa S, Cook MB, Stram DO, Blot WJ, Eeles RA, Easton D, Kote-Jarai Z, Al Olama AA, Benlloch S, Muir K, Giles GG, Southey MC, Fitzgerald LM, Gronberg H, Wiklund F, Aly M, Henderson BE, Schleutker J, Wahlfors T, Tammela TL, Nordestgaard BG, Key TJ, Travis RC, Neal DE, Donovan JL, Hamdy FC, Pharoah P, Pashayan N, Khaw KT, Stanford JL, Thibodeau SN, McDonnell SK, Schaid DJ, Maier C, Vogel W, Luedeke M, Herkommer K, Kibel AS, Cybulski C, Wokolorczyk D, Kluzniak W, Cannon-Albright L, Teerlink C, Brenner H, Dieffenbach AK, Arndt V, Park JY, Sellers TA, Lin HY, Slavov C, Kaneva R, Mitev V, Batra J, Spurdle A, Clements JA, Teixeira MR, Pandha H, Michael A, Paulo P, Maia S, Kierzek A, Conti DV, Albanes D, Berg C, Berndt SI, Campa D, Crawford ED, Diver WR, Gapstur SM, Gaziano JM, Giovannucci E, Hoover R, Hunter DJ, Johansson M, Kraft P, Le Marchand L, Lindström S, Navarro C, Overvad K, Riboli E, Siddiq A, Stevens VL, Trichopoulos D, Vineis P, Yeager M, Trynka G, Raychaudhuri S, Schumacher FR, Price AL, Freedman ML, Haiman CA, Pasaniuc B. Atlas of prostate cancer heritability in European and African-American men pinpoints tissue-specific regulation. Nat Commun. 2016 Apr 07; 7:10979. PMID: 27052111.
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  30. Ellinghaus D, Jostins L, Spain SL, Cortes A, Bethune J, Han B, Park YR, Raychaudhuri S, Pouget JG, Hübenthal M, Folseraas T, Wang Y, Esko T, Metspalu A, Westra HJ, Franke L, Pers TH, Weersma RK, Collij V, D'Amato M, Halfvarson J, Jensen AB, Lieb W, Degenhardt F, Forstner AJ, Hofmann A, Schreiber S, Mrowietz U, Juran BD, Lazaridis KN, Brunak S, Dale AM, Trembath RC, Weidinger S, Weichenthal M, Ellinghaus E, Elder JT, Barker JN, Andreassen OA, McGovern DP, Karlsen TH, Barrett JC, Parkes M, Brown MA, Franke A. Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci. Nat Genet. 2016 05; 48(5):510-8. PMID: 26974007.
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  31. Han B, Duong D, Sul JH, de Bakker PI, Eskin E, Raychaudhuri S. A general framework for meta-analyzing dependent studies with overlapping subjects in association mapping. Hum Mol Genet. 2016 05 01; 25(9):1857-66. PMID: 26908615; PMCID: PMC4986332 [Available on 05/01/17].
    View in: PubMed, PubMed Central
  32. Gutierrez-Arcelus M, Rich SS, Raychaudhuri S. Autoimmune diseases - connecting risk alleles with molecular traits of the immune system. Nat Rev Genet. 2016 Mar; 17(3):160-74. PMID: 26907721; PMCID: PMC4896831.
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  33. Terao C, Yamakawa N, Yano K, Markusse IM, Ikari K, Yoshida S, Furu M, Hashimoto M, Ito H, Fujii T, Ohmura K, Murakami K, Takahashi M, Hamaguchi M, Tabara Y, Taniguchi A, Momohara S, Raychaudhuri S, Allaart CF, Yamanaka H, Mimori T, Matsuda F. Rheumatoid Factor Is Associated With the Distribution of Hand Joint Destruction in Rheumatoid Arthritis. Arthritis Rheumatol. 2015 Dec; 67(12):3113-23. PMID: 26245322.
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  136. Voight BF, Scott LJ, Steinthorsdottir V, Morris AP, Dina C, Welch RP, Zeggini E, Huth C, Aulchenko YS, Thorleifsson G, McCulloch LJ, Ferreira T, Grallert H, Amin N, Wu G, Willer CJ, Raychaudhuri S, McCarroll SA, Langenberg C, Hofmann OM, Dupuis J, Qi L, Segrè AV, van Hoek M, Navarro P, Ardlie K, Balkau B, Benediktsson R, Bennett AJ, Blagieva R, Boerwinkle E, Bonnycastle LL, Bengtsson Boström K, Bravenboer B, Bumpstead S, Burtt NP, Charpentier G, Chines PS, Cornelis M, Couper DJ, Crawford G, Doney AS, Elliott KS, Elliott AL, Erdos MR, Fox CS, Franklin CS, Ganser M, Gieger C, Grarup N, Green T, Griffin S, Groves CJ, Guiducci C, Hadjadj S, Hassanali N, Herder C, Isomaa B, Jackson AU, Johnson PR, Jørgensen T, Kao WH, Klopp N, Kong A, Kraft P, Kuusisto J, Lauritzen T, Li M, Lieverse A, Lindgren CM, Lyssenko V, Marre M, Meitinger T, Midthjell K, Morken MA, Narisu N, Nilsson P, Owen KR, Payne F, Perry JR, Petersen AK, Platou C, Proença C, Prokopenko I, Rathmann W, Rayner NW, Robertson NR, Rocheleau G, Roden M, Sampson MJ, Saxena R, Shields BM, Shrader P, Sigurdsson G, Sparsø T, Strassburger K, Stringham HM, Sun Q, Swift AJ, Thorand B, Tichet J, Tuomi T, van Dam RM, van Haeften TW, van Herpt T, van Vliet-Ostaptchouk JV, Walters GB, Weedon MN, Wijmenga C, Witteman J, Bergman RN, Cauchi S, Collins FS, Gloyn AL, Gyllensten U, Hansen T, Hide WA, Hitman GA, Hofman A, Hunter DJ, Hveem K, Laakso M, Mohlke KL, Morris AD, Palmer CN, Pramstaller PP, Rudan I, Sijbrands E, Stein LD, Tuomilehto J, Uitterlinden A, Walker M, Wareham NJ, Watanabe RM, Abecasis GR, Boehm BO, Campbell H, Daly MJ, Hattersley AT, Hu FB, Meigs JB, Pankow JS, Pedersen O, Wichmann HE, Barroso I, Florez JC, Frayling TM, Groop L, Sladek R, Thorsteinsdottir U, Wilson JF, Illig T, Froguel P, van Duijn CM, Stefansson K, Altshuler D, Boehnke M, McCarthy MI. Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet. 2010 Jul; 42(7):579-89. PMID: 20581827.
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  137. Stahl EA, Raychaudhuri S, Remmers EF, Xie G, Eyre S, Thomson BP, Li Y, Kurreeman FA, Zhernakova A, Hinks A, Guiducci C, Chen R, Alfredsson L, Amos CI, Ardlie KG, Barton A, Bowes J, Brouwer E, Burtt NP, Catanese JJ, Coblyn J, Coenen MJ, Costenbader KH, Criswell LA, Crusius JB, Cui J, de Bakker PI, De Jager PL, Ding B, Emery P, Flynn E, Harrison P, Hocking LJ, Huizinga TW, Kastner DL, Ke X, Lee AT, Liu X, Martin P, Morgan AW, Padyukov L, Posthumus MD, Radstake TR, Reid DM, Seielstad M, Seldin MF, Shadick NA, Steer S, Tak PP, Thomson W, van der Helm-van Mil AH, van der Horst-Bruinsma IE, van der Schoot CE, van Riel PL, Weinblatt ME, Wilson AG, Wolbink GJ, Wordsworth BP, Wijmenga C, Karlson EW, Toes RE, de Vries N, Begovich AB, Worthington J, Siminovitch KA, Gregersen PK, Klareskog L, Plenge RM. Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci. Nat Genet. 2010 Jun; 42(6):508-14. PMID: 20453842; PMCID: PMC4243840.
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  138. Plenge RM, Raychaudhuri S. Leveraging human genetics to develop future therapeutic strategies in rheumatoid arthritis. Rheum Dis Clin North Am. 2010 May; 36(2):259-70. PMID: 20510233; PMCID: PMC2879392.
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  139. Neale BM, Fagerness J, Reynolds R, Sobrin L, Parker M, Raychaudhuri S, Tan PL, Oh EC, Merriam JE, Souied E, Bernstein PS, Li B, Frederick JM, Zhang K, Brantley MA, Lee AY, Zack DJ, Campochiaro B, Campochiaro P, Ripke S, Smith RT, Barile GR, Katsanis N, Allikmets R, Daly MJ, Seddon JM. Genome-wide association study of advanced age-related macular degeneration identifies a role of the hepatic lipase gene (LIPC). Proc Natl Acad Sci U S A. 2010 Apr 20; 107(16):7395-400. PMID: 20385826; PMCID: PMC2867697.
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  140. Karlson EW, Chibnik LB, Kraft P, Cui J, Keenan BT, Ding B, Raychaudhuri S, Klareskog L, Alfredsson L, Plenge RM. Cumulative association of 22 genetic variants with seropositive rheumatoid arthritis risk. Ann Rheum Dis. 2010 Jun; 69(6):1077-85. PMID: 20233754; PMCID: PMC2933175.
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  141. Raychaudhuri S. Recent advances in the genetics of rheumatoid arthritis. Curr Opin Rheumatol. 2010 Mar; 22(2):109-18. PMID: 20075733; PMCID: PMC3121048.
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  142. Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, Donovan J, Barretina J, Boehm JS, Dobson J, Urashima M, Mc Henry KT, Pinchback RM, Ligon AH, Cho YJ, Haery L, Greulich H, Reich M, Winckler W, Lawrence MS, Weir BA, Tanaka KE, Chiang DY, Bass AJ, Loo A, Hoffman C, Prensner J, Liefeld T, Gao Q, Yecies D, Signoretti S, Maher E, Kaye FJ, Sasaki H, Tepper JE, Fletcher JA, Tabernero J, Baselga J, Tsao MS, Demichelis F, Rubin MA, Janne PA, Daly MJ, Nucera C, Levine RL, Ebert BL, Gabriel S, Rustgi AK, Antonescu CR, Ladanyi M, Letai A, Garraway LA, Loda M, Beer DG, True LD, Okamoto A, Pomeroy SL, Singer S, Golub TR, Lander ES, Getz G, Sellers WR, Meyerson M. The landscape of somatic copy-number alteration across human cancers. Nature. 2010 Feb 18; 463(7283):899-905. PMID: 20164920; PMCID: PMC2826709.
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  143. Raychaudhuri S, Thomson BP, Remmers EF, Eyre S, Hinks A, Guiducci C, Catanese JJ, Xie G, Stahl EA, Chen R, Alfredsson L, Amos CI, Ardlie KG, Barton A, Bowes J, Burtt NP, Chang M, Coblyn J, Costenbader KH, Criswell LA, Crusius JB, Cui J, De Jager PL, Ding B, Emery P, Flynn E, Harrison P, Hocking LJ, Huizinga TW, Kastner DL, Ke X, Kurreeman FA, Lee AT, Liu X, Li Y, Martin P, Morgan AW, Padyukov L, Reid DM, Seielstad M, Seldin MF, Shadick NA, Steer S, Tak PP, Thomson W, van der Helm-van Mil AH, van der Horst-Bruinsma IE, Weinblatt ME, Wilson AG, Wolbink GJ, Wordsworth P, Altshuler D, Karlson EW, Toes RE, de Vries N, Begovich AB, Siminovitch KA, Worthington J, Klareskog L, Gregersen PK, Daly MJ, Plenge RM. Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk. Nat Genet. 2009 Dec; 41(12):1313-8. PMID: 19898481; PMCID: PMC3142887.
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  144. van der Linden MP, Feitsma AL, le Cessie S, Kern M, Olsson LM, Raychaudhuri S, Begovich AB, Chang M, Catanese JJ, Kurreeman FA, van Nies J, van der Heijde DM, Gregersen PK, Huizinga TW, Toes RE, van der Helm-Van Mil AH. Association of a single-nucleotide polymorphism in CD40 with the rate of joint destruction in rheumatoid arthritis. Arthritis Rheum. 2009 Aug; 60(8):2242-7. PMID: 19644859; PMCID: PMC3121053.
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  145. Kraft P, Raychaudhuri S. Complex diseases, complex genes: keeping pathways on the right track. Epidemiology. 2009 Jul; 20(4):508-11. PMID: 19525687; PMCID: PMC2704602.
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  146. Raychaudhuri S, Plenge RM, Rossin EJ, Ng AC, Purcell SM, Sklar P, Scolnick EM, Xavier RJ, Altshuler D, Daly MJ. Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions. PLoS Genet. 2009 Jun; 5(6):e1000534. PMID: 19557189; PMCID: PMC2694358.
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  147. De Jager PL, Jia X, Wang J, de Bakker PI, Ottoboni L, Aggarwal NT, Piccio L, Raychaudhuri S, Tran D, Aubin C, Briskin R, Romano S, Baranzini SE, McCauley JL, Pericak-Vance MA, Haines JL, Gibson RA, Naeglin Y, Uitdehaag B, Matthews PM, Kappos L, Polman C, McArdle WL, Strachan DP, Evans D, Cross AH, Daly MJ, Compston A, Sawcer SJ, Weiner HL, Hauser SL, Hafler DA, Oksenberg JR. Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci. Nat Genet. 2009 Jul; 41(7):776-82. PMID: 19525953; PMCID: PMC2757648.
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  148. Lee YC, Raychaudhuri S, Cui J, De Vivo I, Ding B, Alfredsson L, Padyukov L, Costenbader KH, Seielstad M, Graham RR, Klareskog L, Gregersen PK, Plenge RM, Karlson EW. The PRL -1149 G/T polymorphism and rheumatoid arthritis susceptibility. Arthritis Rheum. 2009 May; 60(5):1250-4. PMID: 19404952; PMCID: PMC2956274.
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  149. Raychaudhuri SP, Raychaudhuri SK. The regulatory role of nerve growth factor and its receptor system in fibroblast-like synovial cells. Scand J Rheumatol. 2009 May-Jun; 38(3):207-15. PMID: 19177265.
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  150. de Bakker PI, Ferreira MA, Jia X, Neale BM, Raychaudhuri S, Voight BF. Practical aspects of imputation-driven meta-analysis of genome-wide association studies. Hum Mol Genet. 2008 Oct 15; 17(R2):R122-8. PMID: 18852200; PMCID: PMC2782358.
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  151. Raychaudhuri S, Remmers EF, Lee AT, Hackett R, Guiducci C, Burtt NP, Gianniny L, Korman BD, Padyukov L, Kurreeman FA, Chang M, Catanese JJ, Ding B, Wong S, van der Helm-van Mil AH, Neale BM, Coblyn J, Cui J, Tak PP, Wolbink GJ, Crusius JB, van der Horst-Bruinsma IE, Criswell LA, Amos CI, Seldin MF, Kastner DL, Ardlie KG, Alfredsson L, Costenbader KH, Altshuler D, Huizinga TW, Shadick NA, Weinblatt ME, de Vries N, Worthington J, Seielstad M, Toes RE, Karlson EW, Begovich AB, Klareskog L, Gregersen PK, Daly MJ, Plenge RM. Common variants at CD40 and other loci confer risk of rheumatoid arthritis. Nat Genet. 2008 Oct; 40(10):1216-23. PMID: 18794853.
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  152. Raychaudhuri S, Shmerling R, Ermann J, Helfgott S. Development of active tuberculosis following initiation of infliximab despite appropriate prophylaxis. Rheumatology (Oxford). 2007 May; 46(5):887-8. PMID: 17363399; PMCID: PMC2666304.
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  153. Soumya Raychaudhuri. Computational text analysis for functional genomics and bioinformatics. 2006; 288.
  154. Denko NC, Fontana LA, Hudson KM, Sutphin PD, Raychaudhuri S, Altman R, Giaccia AJ. Investigating hypoxic tumor physiology through gene expression patterns. Oncogene. 2003 Sep 01; 22(37):5907-14. PMID: 12947397.
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  155. Raychaudhuri S, Chang JT, Imam F, Altman RB. The computational analysis of scientific literature to define and recognize gene expression clusters. Nucleic Acids Res. 2003 Aug 01; 31(15):4553-60. PMID: 12888516; PMCID: PMC169898.
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  156. Raychaudhuri S, Altman RB. A literature-based method for assessing the functional coherence of a gene group. Bioinformatics. 2003 Feb 12; 19(3):396-401. PMID: 12584126; PMCID: PMC2669934.
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  157. Raychaudhuri, S Schutze, H Altman, RB. Inclusion of textual documentation in the analysis of multidimensional data sets: application to gene expression data. Machine Learning. 2003; 52:119-145.
  158. Le QT, Sutphin PD, Raychaudhuri S, Yu SC, Terris DJ, Lin HS, Lum B, Pinto HA, Koong AC, Giaccia AJ. Identification of osteopontin as a prognostic plasma marker for head and neck squamous cell carcinomas. Clin Cancer Res. 2003 Jan; 9(1):59-67. PMID: 12538452.
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  159. Raychaudhuri S, Schütze H, Altman RB. Using text analysis to identify functionally coherent gene groups. Genome Res. 2002 Oct; 12(10):1582-90. PMID: 12368251; PMCID: PMC187532.
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  160. Soumya Raychaudhuri. Using text to enhance the interpretation of large multi-dimension data sets. 2002.
  161. Kivi M, Liu X, Raychaudhuri S, Altman RB, Small PM. Determining the genomic locations of repetitive DNA sequences with a whole-genome microarray: IS6110 in Mycobacterium tuberculosis. J Clin Microbiol. 2002 Jun; 40(6):2192-8. PMID: 12037086; PMCID: PMC130717.
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  162. Raychaudhuri S, Chang JT, Sutphin PD, Altman RB. Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature. Genome Res. 2002 Jan; 12(1):203-14. PMID: 11779846; PMCID: PMC155261.
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  163. Altman RB, Raychaudhuri S. Whole-genome expression analysis: challenges beyond clustering. Curr Opin Struct Biol. 2001 Jun; 11(3):340-7. PMID: 11406385.
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  164. Raychaudhuri S, Sutphin PD, Chang JT, Altman RB. Basic microarray analysis: grouping and feature reduction. Trends Biotechnol. 2001 May; 19(5):189-93. PMID: 11301132.
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  165. Chang JT, Raychaudhuri S, Altman RB. Including biological literature improves homology search. Pac Symp Biocomput. 2001; 374-83. PMID: 11262956; PMCID: PMC2671075.
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  166. Raychaudhuri S, Stuart JM, Liu X, Small PM, Altman RB. Pattern recognition of genomic features with microarrays: site typing of Mycobacterium tuberculosis strains. Proc Int Conf Intell Syst Mol Biol. 2000; 8:286-95. PMID: 10977090; PMCID: PMC2865887.
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  167. Raychaudhuri S, Stuart JM, Altman RB. Principal components analysis to summarize microarray experiments: application to sporulation time series. Pac Symp Biocomput. 2000; 455-66. PMID: 10902193; PMCID: PMC2669932.
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  168. Raychaudhuri S, Younas F, Karplus PA, Faerman CH, Ripoll DR. Backbone makes a significant contribution to the electrostatics of alpha/beta-barrel proteins. Protein Sci. 1997 Sep; 6(9):1849-57. PMID: 9300484; PMCID: PMC2143784.
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  169. Van Liew HD, Raychaudhuri S. Stabilized bubbles in the body: pressure-radius relationships and the limits to stabilization. J Appl Physiol (1985). 1997 Jun; 82(6):2045-53. PMID: 9173975.
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  170. Loader CA, Garland JL, Raychaudhuri S, Wheeler RM. A simple mass balance model of nitrogen flow in a bioregenerative life support system. Life Support Biosph Sci. 1997; 4(1-2):31-41. PMID: 11540450.
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  171. Li Z, Raychaudhuri S, Wand AJ. Insights into the local residual entropy of proteins provided by NMR relaxation. Protein Sci. 1996 Dec; 5(12):2647-50. PMID: 8976574; PMCID: PMC2143310.
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  172. DAS GUPTA NN, DE ML, RAYCHAUDHURI SP. Structure of sannhemp (Crotalaria juncea Linn.) mosaic virus with the electron microscope. Nature. 1951 Jul 21; 168(4264):114. PMID: 14852976.
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