My Bibliography

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Xu Z, Tao S, Feng S, Ye X, Wang T, Hu H, Heidrich-O'Hare E, Chen W, Duerr RH. Dissecting PGE(2)-driven inhibition of T cell activation using single-cell multi-omic and inflammatory bowel disease genetic association analysis. Nat Commun. 2026 Apr 7;. doi: 10.1038/s41467-026-71383-2. [Epub ahead of print] PubMed PMID: 41942471.

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Tan T, Vincent M, Jain U, Deepak P, SPARC I. B. D. Investigators. Metabolomic Profiling of Fecal Samples Reveals Distinct Signatures Associated with Disease Phenotypes and Locations in Crohn's Disease. Dig Dis Sci. 2026 Mar 9;. doi: 10.1007/s10620-026-09779-9. [Epub ahead of print] PubMed PMID: 41801634.

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Gettler K, Nagpal S, Washburn S, Tastad C, Zhang J, Sabic K, Lazarev M, Bitton A, Cohen R, Schwartz MB, Barrie A, Gu P, Fleshner P, Bao M, Hernández-Rocha C, McCauley J, Abreu M, Kugathasan S, McGovern DP, Brant SR, Duerr RH, Silverberg MS, Rioux JD, Gibson G, Cho JH. Postoperative Ileum Transcriptomics Implicate Sex-Biased Mechanisms in Crohn's Disease Recurrence. Gastroenterology. 2026 Mar;170(3):511-522. doi: 10.1053/j.gastro.2025.08.038. Epub 2025 Nov 18. PubMed PMID: 41251630; PubMed Central PMCID: PMC12812310.

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Gudmundsson S, Singer-Berk M, Stenton SL, Goodrich JK, Wilson MW, Einson J, Watts NA, Genome Aggregation Database Consortium, Lappalainen T, Rehm HL, MacArthur DG, O'Donnell-Luria A. Exploring penetrance of clinically relevant variants in over 800,000 humans from the Genome Aggregation Database. Nat Commun. 2025 Oct 31;16(1):9623. doi: 10.1038/s41467-025-61698-x. PubMed PMID: 41173899; PubMed Central PMCID: PMC12579199.

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Bak MTJ, Boland K, Nayeri S, Borowksi K, Olivera PA, Hernandez-Rocha C, Turpin W, Stempak JM, Brant SR, Cho JH, Duerr RH, Haritunians T, Lazarev MG, Mengesha E, McGovern DPB, Rioux JD, Schumm LP, Lee SH, Silverberg MS, NIDDK Inflammatory Bowel Disease Genetics Consortium. Micronutrients are associated with endoscopic postoperative recurrence in Crohn's disease: a multicenter prospective cohort study in North america. J Crohns Colitis. 2025 Aug 20;. doi: 10.1093/ecco-jcc/jjaf148. [Epub ahead of print] PubMed PMID: 40833017.

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Cao S, Nguyen KM, Ma K, Tan T, Yao X, Liu TC, Ayoub M, Devi J, Samaan S, Liu Y, Smith R, Silviera ML, Hunt SR, Wise PE, Mutch MG, Glasgow SC, Chapman WC Jr, Cowan ML, Ciorba MA, Colonna M, Deepak P, SPARC IBD Investigators. Revealing hyperactivated IFN-γ pathways in perianal fistulizing Crohn's disease using single-cell and spatial multi-omics. J Clin Invest. 2025 Sep 2;135(17). doi: 10.1172/JCI193413. eCollection 2025 Sep 2. PubMed PMID: 40608410; PubMed Central PMCID: PMC12404762.

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Alizadeh M, Motwani K, Siaton BC, Abutaleb A, Ravel J, Cross RK, SPARC-IBD Investigators. Factors Associated With Extraintestinal Manifestations of Inflammatory Bowel Disease in SPARC-IBD. Inflamm Bowel Dis. 2024 Nov 4;30(11):2027-2036. doi: 10.1093/ibd/izad280. PubMed PMID: 38102817; PubMed Central PMCID: PMC11532592.

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Correia Marques M, Rubin D, Shuldiner EG, Datta M, Schmitz E, Gutierrez Cruz G, Patt A, Bennett E, Grom A, Foell D, Gattorno M, Bohnsack J, Yeung RSM, Prahalad S, Mellins E, Anton J, Len CA, Oliveira S, Woo P, Ozen S, Deng Z, Ombrello MJ, INCHARGE Consortium. Enrichment of Rare Variants of Hemophagocytic Lymphohistiocytosis Genes in Systemic Juvenile Idiopathic Arthritis. Arthritis Rheumatol. 2024 Oct;76(10):1566-1572. doi: 10.1002/art.42938. Epub 2024 Aug 9. PubMed PMID: 38937141; PubMed Central PMCID: PMC12341541.

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Hernández-Rocha C, Turpin W, Borowski K, Stempak JM, Sabic K, Gettler K, Tastad C, Chasteau C, Korie U, Hanna M, Khan A, Mengesha E, Bitton A, Schwartz MB, Barrie A, Datta LW, Lazarev M, Brant SR, Rioux JD, McGovern DPB, Duerr RH, Schumm LP, Cho JH, Silverberg MS. After Surgically Induced Remission, Ileal and Colonic Mucosa-Associated Microbiota Predicts Crohn's Disease Recurrence. Clin Gastroenterol Hepatol. 2025 Mar;23(4):612-620.e10. doi: 10.1016/j.cgh.2024.06.022. Epub 2024 Jul 4. PubMed PMID: 38969076; PubMed Central PMCID: PMC11979954.

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Hu H, Wang X, Feng S, Xu Z, Liu J, Heidrich-O'Hare E, Chen Y, Yue M, Zeng L, Rong Z, Chen T, Billiar T, Ding Y, Huang H, Duerr RH, Chen W. A unified model-based framework for doublet or multiplet detection in single-cell multiomics data. Nat Commun. 2024 Jul 2;15(1):5562. doi: 10.1038/s41467-024-49448-x. PubMed PMID: 38956023; PubMed Central PMCID: PMC11220103.

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Lewis JD, Daniel SG, Li H, Hao F, Patterson AD, Hecht AL, Brensinger CM, Wu GD, Bittinger K, DINE-CD, SPARC IBD Investigators. Surgery for Crohn's Disease Is Associated With a Dysbiotic Microbiome and Metabolome: Results From Two Prospective Cohorts. Cell Mol Gastroenterol Hepatol. 2024;18(3):101357. doi: 10.1016/j.jcmgh.2024.05.005. Epub 2024 May 14. PubMed PMID: 38750900; PubMed Central PMCID: PMC11278594.

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Hernández-Rocha C, Walshe M, Birch S, Sabic K, Korie U, Chasteau C, Miladinova VM, Sabol WB, Mengesha E, Hanna M, Pozdnyakova V, Datta L, Kohen R, Milgrom R, Stempak JM, Bitton A, Brant SR, Rioux JD, McGovern DPB, Duerr RH, Cho JH, Schumm PL, Silverberg MS, Lazarev M. Clinical Predictors of Early and Late Endoscopic Recurrence Following Ileocolonic Resection in Crohn's Disease. J Crohns Colitis. 2024 Apr 23;18(4):615-627. doi: 10.1093/ecco-jcc/jjad186. PubMed PMID: 37976264; PubMed Central PMCID: PMC11037109.

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Motwani KK, Alizadeh M, Abutaleb A, Grossman J, Wellington J, Cross RK, SPARC-IBD investigators. Correlation Between Serum and Fecal Biomarkers and Patient-Reported Outcomes in Patients with Crohn's Disease and Ulcerative Colitis. Dig Dis Sci. 2024 Jun;69(6):2154-2163. doi: 10.1007/s10620-024-08421-w. Epub 2024 Apr 5. PubMed PMID: 38580888.

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Khrom M, Long M, Dube S, Robbins L, Botwin GJ, Yang S, Mengesha E, Li D, Naito T, Bonthala NN, Ha C, Melmed G, Rabizadeh S, Syal G, Vasiliauskas E, Ziring D, Brant SR, Cho J, Duerr RH, Rioux J, Schumm P, Silverberg M, Ananthakrishnan AN, Faubion WA, Jabri B, Lira SA, Newberry RD, Sandler RS, Xavier RJ, Kugathasan S, Hercules D, Targan SR, Sartor RB, Haritunians T, McGovern DPB. Comprehensive Association Analyses of Extraintestinal Manifestations in Inflammatory Bowel Disease. Gastroenterology. 2024 Jul;167(2):315-332. doi: 10.1053/j.gastro.2024.02.026. Epub 2024 Mar 13. PubMed PMID: 38490347; PubMed Central PMCID: PMC11193636.

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Baumdick ME, Niehrs A, Degenhardt F, Schwerk M, Hinrichs O, Jordan-Paiz A, Padoan B, Wegner LHM, Schloer S, Zecher BF, Malsy J, Joshi VR, Illig C, Schröder-Schwarz J, Möller KJ, Hamburg Intestinal Tissue Study Group, Martin MP, Yuki Y, Ozawa M, Sauter J, Schmidt AH, Perez D, Giannou AD, Carrington M, Davis RS, Schumacher U, Sauter G, Huber S, Puelles VG, Melling N, Franke A, International Inflammatory Bowel Disease Genetics Consortium, Altfeld M, Bunders MJ. HLA-DP on Epithelial Cells Enables Tissue Damage by NKp44(+) Natural Killer Cells in Ulcerative Colitis. Gastroenterology. 2023 Oct;165(4):946-962.e13. doi: 10.1053/j.gastro.2023.06.034. Epub 2023 Jul 15. PubMed PMID: 37454979; PubMed Central PMCID: PMC10529779.

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Ferru-Clément R, Boucher G, Forest A, Bouchard B, Bitton A, Lesage S, Schumm P, Lazarev M, Brant S, Duerr RH, McGovern DPB, Silverberg M, Cho JH, NIDDK IBD Genetics Consortium, iGenoMed Consortium, Ananthakrishnan A, Xavier RJ, Rioux JD, Des Rosiers C. Serum Lipidomic Screen Identifies Key Metabolites, Pathways, and Disease Classifiers in Crohn's Disease. Inflamm Bowel Dis. 2023 Jul 5;29(7):1024-1037. doi: 10.1093/ibd/izac281. PubMed PMID: 36662167; PubMed Central PMCID: PMC10320374.

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Lapp SL, Bewtra M, Lewis JD, SPARC IBD Investigators. Yield of Serial Testing for Tuberculosis Exposure in Patients With Inflammatory Bowel Diseases: One Test is Not Enough. Clin Gastroenterol Hepatol. 2024 Feb;22(2):420-422.e2. doi: 10.1016/j.cgh.2023.06.003. Epub 2023 Jun 17. PubMed PMID: 37331412; PubMed Central PMCID: PMC10725512.

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Liu Z, Liu R, Gao H, Jung S, Gao X, Sun R, Liu X, Kim Y, Lee HS, Kawai Y, Nagasaki M, Umeno J, Tokunaga K, Kinouchi Y, Masamune A, Shi W, Shen C, Guo Z, Yuan K, FinnGen, International Inflammatory Bowel Disease Genetics Consortium, Chinese Inflammatory Bowel Disease Genetics Consortium, Zhu S, Li D, Liu J, Ge T, Cho J, Daly MJ, McGovern DPB, Ye BD, Song K, Kakuta Y, Li M, Huang H. Genetic architecture of the inflammatory bowel diseases across East Asian and European ancestries. Nat Genet. 2023 May;55(5):796-806. doi: 10.1038/s41588-023-01384-0. Epub 2023 May 8. PubMed PMID: 37156999; PubMed Central PMCID: PMC10290755.

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Wu Y, Gettler K, Kars ME, Giri M, Li D, Bayrak CS, Zhang P, Jain A, Maffucci P, Sabic K, Van Vleck T, Nadkarni G, Denson LA, Ostrer H, Levine AP, Schiff ER, Segal AW, Kugathasan S, Stenson PD, Cooper DN, Philip Schumm L, Snapper S, Daly MJ, Haritunians T, Duerr RH, Silverberg MS, Rioux JD, Brant SR, McGovern DPB, Cho JH, Itan Y. Identifying high-impact variants and genes in exomes of Ashkenazi Jewish inflammatory bowel disease patients. Nat Commun. 2023 Apr 20;14(1):2256. doi: 10.1038/s41467-023-37849-3. PubMed PMID: 37080976; PubMed Central PMCID: PMC10119186.

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Akhlaghpour M, Haritunians T, More SK, Thomas LS, Stamps DT, Dube S, Li D, Yang S, Landers CJ, Mengesha E, Hamade H, Murali R, Potdar AA, Wolf AJ, Botwin GJ, Khrom M, International IBD Genetics Consortium, Ananthakrishnan AN, Faubion WA, Jabri B, Lira SA, Newberry RD, Sandler RS, Sartor RB, Xavier RJ, Brant SR, Cho JH, Duerr RH, Lazarev MG, Rioux JD, Schumm LP, Silverberg MS, Zaghiyan K, Fleshner P, Melmed GY, Vasiliauskas EA, Ha C, Rabizadeh S, Syal G, Bonthala NN, Ziring DA, Targan SR, Long MD, McGovern DPB, Michelsen KS. Genetic coding variant in complement factor B (CFB) is associated with increased risk for perianal Crohn's disease and leads to impaired CFB cleavage and phagocytosis. Gut. 2023 Nov;72(11):2068-2080. doi: 10.1136/gutjnl-2023-329689. Epub 2023 Apr 20. PubMed PMID: 37080587; PubMed Central PMCID: PMC11036449.

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Yang JY, Lund JL, Funk MJ, Hudgens MG, Lewis JD, Kappelman MD, SPARC IBD Investigators. Utilization of Treat-to-Target Monitoring Colonoscopy After Treatment Initiation in the US-Based Study of a Prospective Adult Research Cohort With Inflammatory Bowel Disease. Am J Gastroenterol. 2023 Sep 1;118(9):1638-1647. doi: 10.14309/ajg.0000000000002294. Epub 2023 Apr 13. PubMed PMID: 37053548.

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Sazonovs A, Stevens CR, Venkataraman GR, Yuan K, Avila B, Abreu MT, Ahmad T, Allez M, Ananthakrishnan AN, Atzmon G, Baras A, Barrett JC, Barzilai N, Beaugerie L, Beecham A, Bernstein CN, Bitton A, Bokemeyer B, Chan A, Chung D, Cleynen I, Cosnes J, Cutler DJ, Daly A, Damas OM, Datta LW, Dawany N, Devoto M, Dodge S, Ellinghaus E, Fachal L, Farkkila M, Faubion W, Ferreira M, Franchimont D, Gabriel SB, Ge T, Georges M, Gettler K, Giri M, Glaser B, Goerg S, Goyette P, Graham D, Hämäläinen E, Haritunians T, Heap GA, Hiltunen M, Hoeppner M, Horowitz JE, Irving P, Iyer V, Jalas C, Kelsen J, Khalili H, Kirschner BS, Kontula K, Koskela JT, Kugathasan S, Kupcinskas J, Lamb CA, Laudes M, Lévesque C, Levine AP, Lewis JD, Liefferinckx C, Loescher BS, Louis E, Mansfield J, May S, McCauley JL, Mengesha E, Mni M, Moayyedi P, Moran CJ, Newberry RD, O'Charoen S, Okou DT, Oldenburg B, Ostrer H, Palotie A, Paquette J, Pekow J, Peter I, Pierik MJ, Ponsioen CY, Pontikos N, Prescott N, Pulver AE, Rahmouni S, Rice DL, Saavalainen P, Sands B, Sartor RB, Schiff ER, Schreiber S, Schumm LP, Segal AW, Seksik P, Shawky R, Sheikh SZ, Silverberg MS, Simmons A, Skeiceviciene J, Sokol H, Solomonson M, Somineni H, Sun D, Targan S, Turner D, Uhlig HH, van der Meulen AE, Vermeire S, Verstockt S, Voskuil MD, Winter HS, Young J, Belgium IBD Consortium, Cedars-Sinai IBD, International IBD Genetics Consortium, NIDDK IBD Genetics Consortium, NIHR IBD BioResource, Regeneron Genetics Center, SHARE Consortium, SPARC IBD Network, UK IBD Genetics Consortium, Duerr RH, Franke A, Brant SR, Cho J, Weersma RK, Parkes M, Xavier RJ, Rivas MA, Rioux JD, McGovern DPB, Huang H, Anderson CA, Daly MJ. Large-scale sequencing identifies multiple genes and rare variants associated with Crohn's disease susceptibility. Nat Genet. 2022 Sep;54(9):1275-1283. doi: 10.1038/s41588-022-01156-2. Epub 2022 Aug 29. PubMed PMID: 36038634; PubMed Central PMCID: PMC9700438.

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Wang X, Xu Z, Hu H, Zhou X, Zhang Y, Lafyatis R, Chen K, Huang H, Ding Y, Duerr RH, Chen W. SECANT: a biology-guided semi-supervised method for clustering, classification, and annotation of single-cell multi-omics. PNAS Nexus. 2022 Sep;1(4):pgac165. doi: 10.1093/pnasnexus/pgac165. eCollection 2022 Sep. PubMed PMID: 36157595; PubMed Central PMCID: PMC9491696.

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Walshe M, Nayeri S, Ji J, Hernandez-Rocha C, Sabic K, Hu L, Giri M, Nayar S, Brant S, McGovern DPB, Rioux JD, Duerr RH, Cho JH, Schumm PL, Lazarev M, Silverberg MS. A Role for CXCR3 Ligands as Biomarkers of Post-Operative Crohn's Disease Recurrence. J Crohns Colitis. 2022 Jul 14;16(6):900-910. doi: 10.1093/ecco-jcc/jjab186. PubMed PMID: 34698823; PubMed Central PMCID: PMC9282882.

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Xu Z, Heidrich-O'Hare E, Chen W, Duerr RH. Comprehensive benchmarking of CITE-seq versus DOGMA-seq single cell multimodal omics. Genome Biol. 2022 Jun 23;23(1):135. doi: 10.1186/s13059-022-02698-8. PubMed PMID: 35739535; PubMed Central PMCID: PMC9219143.

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Raffals LE, Saha S, Bewtra M, Norris C, Dobes A, Heller C, O'Charoen S, Fehlmann T, Sweeney S, Weaver A, Bishu S, Cross R, Dassopoulos T, Fischer M, Yarur A, Hudesman D, Parakkal D, Duerr R, Caldera F, Korzenik J, Pekow J, Wells K, Bohm M, Perera L, Kaur M, Ciorba M, Snapper S, Scoville EA, Dalal S, Wong U, Lewis JD. The Development and Initial Findings of A Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease (SPARC IBD). Inflamm Bowel Dis. 2022 Feb 1;28(2):192-199. doi: 10.1093/ibd/izab071. PubMed PMID: 34436563; PubMed Central PMCID: PMC9013198.

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Boucher G, Paradis A, Chabot-Roy G, Coderre L, Hillhouse EE, Bitton A, Des Rosiers C, Levings MK, Schumm LP, Lazarev M, Brant SR, Duerr R, McGovern D, Silverberg MS, Cho J, Lesage S, Rioux JD, iGenoMed Consortium, NIDDK IBD Genetics Consortium. Serum Analyte Profiles Associated With Crohn's Disease and Disease Location. Inflamm Bowel Dis. 2022 Jan 5;28(1):9-20. doi: 10.1093/ibd/izab123. PubMed PMID: 34106269; PubMed Central PMCID: PMC8730700.

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Somineni HK, Nagpal S, Venkateswaran S, Cutler DJ, Okou DT, Haritunians T, Simpson CL, Begum F, Datta LW, Quiros AJ, Seminerio J, Mengesha E, Alexander JS, Baldassano RN, Dudley-Brown S, Cross RK, Dassopoulos T, Denson LA, Dhere TA, Iskandar H, Dryden GW, Hou JK, Hussain SZ, Hyams JS, Isaacs KL, Kader H, Kappelman MD, Katz J, Kellermayer R, Kuemmerle JF, Lazarev M, Li E, Mannon P, Moulton DE, Newberry RD, Patel AS, Pekow J, Saeed SA, Valentine JF, Wang MH, McCauley JL, Abreu MT, Jester T, Molle-Rios Z, Palle S, Scherl EJ, Kwon J, Rioux JD, Duerr RH, Silverberg MS, Zwick ME, Stevens C, Daly MJ, Cho JH, Gibson G, McGovern DPB, Brant SR, Kugathasan S. Whole-genome sequencing of African Americans implicates differential genetic architecture in inflammatory bowel disease. Am J Hum Genet. 2021 Mar 4;108(3):431-445. doi: 10.1016/j.ajhg.2021.02.001. Epub 2021 Feb 17. PubMed PMID: 33600772; PubMed Central PMCID: PMC8008495.

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Chen E, Chuang LS, Giri M, Villaverde N, Hsu NY, Sabic K, Joshowitz S, Gettler K, Nayar S, Chai Z, Alter IL, Chasteau CC, Korie UM, Dzedzik S, Thin TH, Jain A, Moscati A, Bongers G, Duerr RH, Silverberg MS, Brant SR, Rioux JD, Peter I, Schumm LP, Haritunians T, McGovern DP, Itan Y, Cho JH. Inflamed Ulcerative Colitis Regions Associated With MRGPRX2-Mediated Mast Cell Degranulation and Cell Activation Modules, Defining a New Therapeutic Target. Gastroenterology. 2021 Apr;160(5):1709-1724. doi: 10.1053/j.gastro.2020.12.076. Epub 2021 Jan 6. PubMed PMID: 33421512; PubMed Central PMCID: PMC8494017.

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Gettler K, Levantovsky R, Moscati A, Giri M, Wu Y, Hsu NY, Chuang LS, Sazonovs A, Venkateswaran S, Korie U, Chasteau C, UK IBD Genetics Consortium , Duerr RH, Silverberg MS, Snapper SB, Daly MJ, McGovern DP, Brant SR, Rioux JD, Kugathasan S, Anderson CA, Itan Y, Cho JH. Common and Rare Variant Prediction and Penetrance of IBD in a Large, Multi-ethnic, Health System-based Biobank Cohort. Gastroenterology. 2021 Apr;160(5):1546-1557. doi: 10.1053/j.gastro.2020.12.034. Epub 2020 Dec 24. PubMed PMID: 33359885; PubMed Central PMCID: PMC8237248.

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Naito T, Botwin GJ, Haritunians T, Li D, Yang S, Khrom M, Braun J, NIDDK IBD Genetics Consortium, Abbou L, Mengesha E, Stevens C, Masamune A, Daly M, McGovern DPB. Prevalence and Effect of Genetic Risk of Thromboembolic Disease in Inflammatory Bowel Disease. Gastroenterology. 2021 Feb;160(3):771-780.e4. doi: 10.1053/j.gastro.2020.10.019. Epub 2020 Oct 21. PubMed PMID: 33098885; PubMed Central PMCID: PMC11057914.

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Xin H, Lian Q, Jiang Y, Luo J, Wang X, Erb C, Xu Z, Zhang X, Heidrich-O'Hare E, Yan Q, Duerr RH, Chen K, Chen W. GMM-Demux: sample demultiplexing, multiplet detection, experiment planning, and novel cell-type verification in single cell sequencing. Genome Biol. 2020 Jul 30;21(1):188. doi: 10.1186/s13059-020-02084-2. PubMed PMID: 32731885; PubMed Central PMCID: PMC7393741.

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Wang X, Sun Z, Zhang Y, Xu Z, Xin H, Huang H, Duerr RH, Chen K, Ding Y, Chen W. BREM-SC: a bayesian random effects mixture model for joint clustering single cell multi-omics data. Nucleic Acids Res. 2020 Jun 19;48(11):5814-5824. doi: 10.1093/nar/gkaa314. PubMed PMID: 32379315; PubMed Central PMCID: PMC7293045.

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Serra EG, Schwerd T, Moutsianas L, Cavounidis A, Fachal L, Pandey S, Kammermeier J, Croft NM, Posovszky C, Rodrigues A, Russell RK, Barakat F, Auth MKH, Heuschkel R, Zilbauer M, Fyderek K, Braegger C, Travis SP, Satsangi J, Parkes M, Thapar N, Ferry H, Matte JC, Gilmour KC, Wedrychowicz A, Sullivan P, Moore C, Sambrook J, Ouwehand W, Roberts D, Danesh J, Baeumler TA, Fulga TA, Carrami EM, Ahmed A, Wilson R, Barrett JC, Elkadri A, Griffiths AM, COLORS in IBD group investigators, Oxford IBD cohort study investigators, INTERVAL Study, Swiss IBD cohort investigators, UK IBD Genetics Consortium, NIDDK IBD Genetics Consortium, Snapper SB, Shah N, Muise AM, Wilson DC, Uhlig HH, Anderson CA. Somatic mosaicism and common genetic variation contribute to the risk of very-early-onset inflammatory bowel disease. Nat Commun. 2020 Feb 21;11(1):995. doi: 10.1038/s41467-019-14275-y. PubMed PMID: 32081864; PubMed Central PMCID: PMC7035382.

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Romagnoni A, Jégou S, Van Steen K, Wainrib G, Hugot JP, International Inflammatory Bowel Disease Genetics Consortium (IIBDGC). Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data. Sci Rep. 2019 Jul 17;9(1):10351. doi: 10.1038/s41598-019-46649-z. PubMed PMID: 31316157; PubMed Central PMCID: PMC6637191.

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Denson LA, Curran M, McGovern DPB, Koltun WA, Duerr RH, Kim SC, Sartor RB, Sylvester FA, Abraham C, de Zoeten EF, Siegel CA, Burns RM, Dobes AM, Shtraizent N, Honig G, Heller CA, Hurtado-Lorenzo A, Cho JH. Challenges in IBD Research: Precision Medicine. Inflamm Bowel Dis. 2019 May 16;25(Suppl 2):S31-S39. doi: 10.1093/ibd/izz078. Review. PubMed PMID: 31095701.

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Rivas MA, Avila BE, Koskela J, Huang H, Stevens C, Pirinen M, Haritunians T, Neale BM, Kurki M, Ganna A, Graham D, Glaser B, Peter I, Atzmon G, Barzilai N, Levine AP, Schiff E, Pontikos N, Weisburd B, Lek M, Karczewski KJ, Bloom J, Minikel EV, Petersen BS, Beaugerie L, Seksik P, Cosnes J, Schreiber S, Bokemeyer B, Bethge J, International IBD Genetics Consortium, NIDDK IBD Genetics Consortium, T2D-GENES Consortium, Heap G, Ahmad T, Plagnol V, Segal AW, Targan S, Turner D, Saavalainen P, Farkkila M, Kontula K, Palotie A, Brant SR, Duerr RH, Silverberg MS, Rioux JD, Weersma RK, Franke A, Jostins L, Anderson CA, Barrett JC, MacArthur DG, Jalas C, Sokol H, Xavier RJ, Pulver A, Cho JH, McGovern DPB, Daly MJ. Correction: Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population. PLoS Genet. 2019 May;15(5):e1008190. doi: 10.1371/journal.pgen.1008190. eCollection 2019 May. PubMed PMID: 31145742; PubMed Central PMCID: PMC6542503.

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Márquez A, Kerick M, Zhernakova A, Gutierrez-Achury J, Chen WM, Onengut-Gumuscu S, González-Álvaro I, Rodriguez-Rodriguez L, Rios-Fernández R, González-Gay MA, Coeliac Disease Immunochip Consortium, Rheumatoid Arthritis Consortium International for Immunochip (RACI), International Scleroderma Group, Type 1 Diabetes Genetics Consortium, Mayes MD, Raychaudhuri S, Rich SS, Wijmenga C, Martín J. Meta-analysis of Immunochip data of four autoimmune diseases reveals novel single-disease and cross-phenotype associations. Genome Med. 2018 Dec 20;10(1):97. doi: 10.1186/s13073-018-0604-8. PubMed PMID: 30572963; PubMed Central PMCID: PMC6302306.

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Arthur VL, Shuldiner E, Remmers EF, Hinks A, Grom AA, Foell D, Martini A, Gattorno M, Özen S, Prahalad S, Zeft AS, Bohnsack JF, Ilowite NT, Mellins ED, Russo R, Len C, Oliveira S, Yeung RSM, Rosenberg AM, Wedderburn LR, Anton J, Haas JP, Rösen-Wolff A, Minden K, Szymanski AM, INCHARGE Consortium, Thomson W, Kastner DL, Woo P, Ombrello MJ. IL1RN Variation Influences Both Disease Susceptibility and Response to Recombinant Human Interleukin-1 Receptor Antagonist Therapy in Systemic Juvenile Idiopathic Arthritis. Arthritis Rheumatol. 2018 Aug;70(8):1319-1330. doi: 10.1002/art.40498. Epub 2018 Jun 28. PubMed PMID: 29609200; PubMed Central PMCID: PMC6105455.

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Momozawa Y, Dmitrieva J, Théâtre E, Deffontaine V, Rahmouni S, Charloteaux B, Crins F, Docampo E, Elansary M, Gori AS, Lecut C, Mariman R, Mni M, Oury C, Altukhov I, Alexeev D, Aulchenko Y, Amininejad L, Bouma G, Hoentjen F, Löwenberg M, Oldenburg B, Pierik MJ, Vander Meulen-de Jong AE, Janneke van der Woude C, Visschedijk MC, International IBD Genetics Consortium, Lathrop M, Hugot JP, Weersma RK, De Vos M, Franchimont D, Vermeire S, Kubo M, Louis E, Georges M. IBD risk loci are enriched in multigenic regulatory modules encompassing putative causative genes. Nat Commun. 2018 Jun 21;9(1):2427. doi: 10.1038/s41467-018-04365-8. PubMed PMID: 29930244; PubMed Central PMCID: PMC6013502.

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Rivas MA, Avila BE, Koskela J, Huang H, Stevens C, Pirinen M, Haritunians T, Neale BM, Kurki M, Ganna A, Graham D, Glaser B, Peter I, Atzmon G, Barzilai N, Levine AP, Schiff E, Pontikos N, Weisburd B, Lek M, Karczewski KJ, Bloom J, Minikel EV, Petersen BS, Beaugerie L, Seksik P, Cosnes J, Schreiber S, Bokemeyer B, Bethge J, International IBD Genetics Consortium, NIDDK IBD Genetics Consortium, T2D-GENES Consortium, Heap G, Ahmad T, Plagnol V, Segal AW, Targan S, Turner D, Saavalainen P, Farkkila M, Kontula K, Palotie A, Brant SR, Duerr RH, Silverberg MS, Rioux JD, Weersma RK, Franke A, Jostins L, Anderson CA, Barrett JC, MacArthur DG, Jalas C, Sokol H, Xavier RJ, Pulver A, Cho JH, McGovern DPB, Daly MJ. Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population. PLoS Genet. 2018 May;14(5):e1007329. doi: 10.1371/journal.pgen.1007329. eCollection 2018 May. PubMed PMID: 29795570; PubMed Central PMCID: PMC5967709.

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Hinks A, Marion MC, Cobb J, Comeau ME, Sudman M, Ainsworth HC, Bowes J, Juvenile Idiopathic Arthritis Consortium for Immunochip, Becker ML, Bohnsack JF, Haas JP, Lovell DJ, Mellins ED, Nelson JL, Nordal E, Punaro M, Reed AM, Rose CD, Rosenberg AM, Rygg M, Smith SL, Stevens AM, Videm V, Wallace CA, Wedderburn LR, Yarwood A, Yeung RSM, Langefeld CD, Thompson SD, Thomson W, Prahalad S. Brief Report: The Genetic Profile of Rheumatoid Factor-Positive Polyarticular Juvenile Idiopathic Arthritis Resembles That of Adult Rheumatoid Arthritis. Arthritis Rheumatol. 2018 Jun;70(6):957-962. doi: 10.1002/art.40443. Epub 2018 Apr 21. PubMed PMID: 29426059; PubMed Central PMCID: PMC5984672.

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Hui KY, Fernandez-Hernandez H, Hu J, Schaffner A, Pankratz N, Hsu NY, Chuang LS, Carmi S, Villaverde N, Li X, Rivas M, Levine AP, Bao X, Labrias PR, Haritunians T, Ruane D, Gettler K, Chen E, Li D, Schiff ER, Pontikos N, Barzilai N, Brant SR, Bressman S, Cheifetz AS, Clark LN, Daly MJ, Desnick RJ, Duerr RH, Katz S, Lencz T, Myers RH, Ostrer H, Ozelius L, Payami H, Peter Y, Rioux JD, Segal AW, Scott WK, Silverberg MS, Vance JM, Ubarretxena-Belandia I, Foroud T, Atzmon G, Pe'er I, Ioannou Y, McGovern DPB, Yue Z, Schadt EE, Cho JH, Peter I. Functional variants in the LRRK2 gene confer shared effects on risk for Crohn's disease and Parkinson's disease. Sci Transl Med. 2018 Jan 10;10(423). doi: 10.1126/scitranslmed.aai7795. PubMed PMID: 29321258; PubMed Central PMCID: PMC6028002.

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Schwerd T, Bryant RV, Pandey S, Capitani M, Meran L, Cazier JB, Jung J, Mondal K, Parkes M, Mathew CG, Fiedler K, McCarthy DJ, WGS500 Consortium, Oxford IBD cohort study investigators, COLORS in IBD group investigators, UK IBD Genetics Consortium, Sullivan PB, Rodrigues A, Travis SPL, Moore C, Sambrook J, Ouwehand WH, Roberts DJ, Danesh J, INTERVAL Study, Russell RK, Wilson DC, Kelsen JR, Cornall R, Denson LA, Kugathasan S, Knaus UG, Serra EG, Anderson CA, Duerr RH, McGovern DP, Cho J, Powrie F, Li VS, Muise AM, Uhlig HH. NOX1 loss-of-function genetic variants in patients with inflammatory bowel disease. Mucosal Immunol. 2018 Mar;11(2):562-574. doi: 10.1038/mi.2017.74. Epub 2017 Nov 1. PubMed PMID: 29091079; PubMed Central PMCID: PMC5924597.

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Huang H, Fang M, Jostins L, Umićević Mirkov M, Boucher G, Anderson CA, Andersen V, Cleynen I, Cortes A, Crins F, D'Amato M, Deffontaine V, Dmitrieva J, Docampo E, Elansary M, Farh KK, Franke A, Gori AS, Goyette P, Halfvarson J, Haritunians T, Knight J, Lawrance IC, Lees CW, Louis E, Mariman R, Meuwissen T, Mni M, Momozawa Y, Parkes M, Spain SL, Théâtre E, Trynka G, Satsangi J, van Sommeren S, Vermeire S, Xavier RJ, International Inflammatory Bowel Disease Genetics Consortium, Weersma RK, Duerr RH, Mathew CG, Rioux JD, McGovern DPB, Cho JH, Georges M, Daly MJ, Barrett JC. Fine-mapping inflammatory bowel disease loci to single-variant resolution. Nature. 2017 Jul 13;547(7662):173-178. doi: 10.1038/nature22969. Epub 2017 Jun 28. PubMed PMID: 28658209; PubMed Central PMCID: PMC5511510.

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Ombrello MJ, Arthur VL, Remmers EF, Hinks A, Tachmazidou I, Grom AA, Foell D, Martini A, Gattorno M, Özen S, Prahalad S, Zeft AS, Bohnsack JF, Ilowite NT, Mellins ED, Russo R, Len C, Hilario MO, Oliveira S, Yeung RS, Rosenberg AM, Wedderburn LR, Anton J, Haas JP, Rosen-Wolff A, Minden K, Tenbrock K, Demirkaya E, Cobb J, Baskin E, Signa S, Shuldiner E, Duerr RH, Achkar JP, Kamboh MI, Kaufman KM, Kottyan LC, Pinto D, Scherer SW, Alarcón-Riquelme ME, Docampo E, Estivill X, Gül A, British Society of Pediatric and Adolescent Rheumatology (BSPAR) Study Group, Inception Cohort of Newly Diagnosed Patients with Juvenile Idiopathic Arthritis (ICON-JIA) Study Group, Childhood Arthritis Prospective Study (CAPS) Group, Randomized Placebo Phase Study of Rilonacept in sJIA (RAPPORT) Investigators, Sparks-Childhood Arthritis Response to Medication Study (CHARMS) Group, Biologically Based Outcome Predictors in JIA (BBOP) Group, Langefeld CD, Thompson S, Zeggini E, Kastner DL, Woo P, Thomson W. Genetic architecture distinguishes systemic juvenile idiopathic arthritis from other forms of juvenile idiopathic arthritis: clinical and therapeutic implications. Ann Rheum Dis. 2017 May;76(5):906-913. doi: 10.1136/annrheumdis-2016-210324. Epub 2016 Dec 7. PubMed PMID: 27927641; PubMed Central PMCID: PMC5530341.

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Kopylov U, Boucher G, Waterman M, Rivers CR, Patel M, Cho JH, Colombel JF, Duerr RH, Binion D, McGovern DP, Schumm PP, Brant SR, Silverberg MS, Rioux JD, Bitton A. Genetic Predictors of Benign Course of Ulcerative Colitis-A North American Inflammatory Bowel Disease Genetics Consortium Study. Inflamm Bowel Dis. 2016 Oct;22(10):2311-6. doi: 10.1097/MIB.0000000000000913. PubMed PMID: 27575496; PubMed Central PMCID: PMC5098421.

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Brant SR, Okou DT, Simpson CL, Cutler DJ, Haritunians T, Bradfield JP, Chopra P, Prince J, Begum F, Kumar A, Huang C, Venkateswaran S, Datta LW, Wei Z, Thomas K, Herrinton LJ, Klapproth JA, Quiros AJ, Seminerio J, Liu Z, Alexander JS, Baldassano RN, Dudley-Brown S, Cross RK, Dassopoulos T, Denson LA, Dhere TA, Dryden GW, Hanson JS, Hou JK, Hussain SZ, Hyams JS, Isaacs KL, Kader H, Kappelman MD, Katz J, Kellermayer R, Kirschner BS, Kuemmerle JF, Kwon JH, Lazarev M, Li E, Mack D, Mannon P, Moulton DE, Newberry RD, Osuntokun BO, Patel AS, Saeed SA, Targan SR, Valentine JF, Wang MH, Zonca M, Rioux JD, Duerr RH, Silverberg MS, Cho JH, Hakonarson H, Zwick ME, McGovern DP, Kugathasan S. Genome-Wide Association Study Identifies African-Specific Susceptibility Loci in African Americans With Inflammatory Bowel Disease. Gastroenterology. 2017 Jan;152(1):206-217.e2. doi: 10.1053/j.gastro.2016.09.032. Epub 2016 Sep 28. PubMed PMID: 27693347; PubMed Central PMCID: PMC5164948.

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Rivas MA, Graham D, Sulem P, Stevens C, Desch AN, Goyette P, Gudbjartsson D, Jonsdottir I, Thorsteinsdottir U, Degenhardt F, Mucha S, Kurki MI, Li D, D'Amato M, Annese V, Vermeire S, Weersma RK, Halfvarson J, Paavola-Sakki P, Lappalainen M, Lek M, Cummings B, Tukiainen T, Haritunians T, Halme L, Koskinen LL, Ananthakrishnan AN, Luo Y, Heap GA, Visschedijk MC, UK IBD Genetics Consortium, NIDDK IBD Genetics Consortium, MacArthur DG, Neale BM, Ahmad T, Anderson CA, Brant SR, Duerr RH, Silverberg MS, Cho JH, Palotie A, Saavalainen P, Kontula K, Färkkilä M, McGovern DP, Franke A, Stefansson K, Rioux JD, Xavier RJ, Daly MJ. Erratum: A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis. Nat Commun. 2016 Sep 13;7:12869. doi: 10.1038/ncomms12869. PubMed PMID: 27619887; PubMed Central PMCID: PMC5027274.

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Rivas MA, Graham D, Sulem P, Stevens C, Desch AN, Goyette P, Gudbjartsson D, Jonsdottir I, Thorsteinsdottir U, Degenhardt F, Mucha S, Kurki MI, Li D, D'Amato M, Annese V, Vermeire S, Weersma RK, Halfvarson J, Paavola-Sakki P, Lappalainen M, Lek M, Cummings B, Tukiainen T, Haritunians T, Halme L, Koskinen LL, Ananthakrishnan AN, Luo Y, Heap GA, Visschedijk MC, UK IBD Genetics Consortium, NIDDK IBD Genetics Consortium, MacArthur DG, Neale BM, Ahmad T, Anderson CA, Brant SR, Duerr RH, Silverberg MS, Cho JH, Palotie A, Saavalainen P, Kontula K, Färkkilä M, McGovern DP, Franke A, Stefansson K, Rioux JD, Xavier RJ, Daly MJ, Barrett J, de Lane K, Edwards C, Hart A, Hawkey C, Jostins L, Kennedy N, Lamb C, Lee J, Lees C, Mansfield J, Mathew C, Mowatt C, Newman B, Nimmo E, Parkes M, Pollard M, Prescott N, Randall J, Rice D, Satsangi J, Simmons A, Tremelling M, Uhlig H, Wilson D, Abraham C, Achkar JP, Bitton A, Boucher G, Croitoru K, Fleshner P, Glas J, Kugathasan S, Limbergen JV, Milgrom R, Proctor D, Regueiro M, Schumm PL, Sharma Y, Stempak JM, Targan SR, Wang MH. A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis. Nat Commun. 2016 Aug 9;7:12342. doi: 10.1038/ncomms12342. PubMed PMID: 27503255; PubMed Central PMCID: PMC4980482.