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1 | PhenoGeneRanker: Gene and Phenotype Prioritization Using Multiplex Heterogeneous Networks. (Dursun C, Kwitek AE, Bozdag S) IEEE/ACM Trans Comput Biol Bioinform 2022;19(5):2950-2962 1 Citation |
1 | E2A-regulated epigenetic landscape promotes memory CD8 T cell differentiation. (Schauder DM, Shen J, Chen Y, Kasmani MY, Kudek MR, Burns R, Cui W) Proc Natl Acad Sci U S A 2021 Apr 20;118(16) 15 Citations |
2 | A GATA6-centred gene regulatory network involving HNFs and ΔNp63 controls plasticity and immune escape in pancreatic cancer. (Kloesch B, Ionasz V, Paliwal S, Hruschka N, Martinez de Villarreal J, Öllinger R, Mueller S, Dienes HP, Schindl M, Gruber ES, Stift J, Herndler-Brandstetter D, Lomberk GA, Seidler B, Saur D, Rad R, Urrutia RA, Real FX, Martinelli P) Gut 2022 Apr;71(4):766-777 36 Citations |
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1 | PGC1/PPAR drive cardiomyocyte maturation at single cell level via YAP1 and SF3B2. (Murphy SA, Miyamoto M, Kervadec A, Kannan S, Tampakakis E, Kambhampati S, Lin BL, Paek S, Andersen P, Lee DI, Zhu R, An SS, Kass DA, Uosaki H, Colas AR, Kwon C) Nat Commun 2021 Mar 12;12(1):1648 39 Citations |
1 | Identification and analysis of circulating long non-coding RNAs with high significance in diabetic cardiomyopathy. (Pant T, Dhanasekaran A, Zhao M, Thorp EB, Forbess JM, Bosnjak ZJ, Benjamin IJ, Ge ZD) Sci Rep 2021 Jan 28;11(1):2571 10 Citations |
1 | The Polygenic and Monogenic Basis of Blood Traits and Diseases. (Vuckovic D, Bao EL, Akbari P, Lareau CA, Mousas A, Jiang T, Chen MH, Raffield LM, Tardaguila M, Huffman JE, Ritchie SC, Megy K, Ponstingl H, Penkett CJ, Albers PK, Wigdor EM, Sakaue S, Moscati A, Manansala R, Lo KS, Qian H, Akiyama M, Bartz TM, Ben-Shlomo Y, Beswick A, Bork-Jensen J, Bottinger EP, Brody JA, van Rooij FJA, Chitrala KN, Wilson PWF, Choquet H, Danesh J, Di Angelantonio E, Dimou N, Ding J, Elliott P, Esko T, Evans MK, Felix SB, Floyd JS, Broer L, Grarup N, Guo MH, Guo Q, Greinacher A, Haessler J, Hansen T, Howson JMM, Huang W, Jorgenson E, Kacprowski T, Kähönen M, Kamatani Y, Kanai M, Karthikeyan S, Koskeridis F, Lange LA, Lehtimäki T, Linneberg A, Liu Y, Lyytikäinen LP, Manichaikul A, Matsuda K, Mohlke KL, Mononen N, Murakami Y, Nadkarni GN, Nikus K, Pankratz N, Pedersen O, Preuss M, Psaty BM, Raitakari OT, Rich SS, Rodriguez BAT, Rosen JD, Rotter JI, Schubert P, Spracklen CN, Surendran P, Tang H, Tardif JC, Ghanbari M, Völker U, Völzke H, Watkins NA, Weiss S, VA Million Veteran Program, Cai N, Kundu K, Watt SB, Walter K, Zonderman AB, Cho K, Li Y, Loos RJF, Knight JC, Georges M, Stegle O, Evangelou E, Okada Y, Roberts DJ, Inouye M, Johnson AD, Auer PL, Astle WJ, Reiner AP, Butterworth AS, Ouwehand WH, Lettre G, Sankaran VG, Soranzo N) Cell 2020 Sep 03;182(5):1214-1231.e11 262 Citations |
1 | Discovering How Heme Controls Genome Function Through Heme-omics. (Liao R, Zheng Y, Liu X, Zhang Y, Seim G, Tanimura N, Wilson GM, Hematti P, Coon JJ, Fan J, Xu J, Keles S, Bresnick EH) Cell Rep 2020 Jun 30;31(13):107832 16 Citations |
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1 | Genome-wide differential expression profiling of lncRNAs and mRNAs associated with early diabetic cardiomyopathy. (Pant T, Dhanasekaran A, Bai X, Zhao M, Thorp EB, Forbess JM, Bosnjak ZJ, Ge ZD) Sci Rep 2019 Oct 25;9(1):15345 24 Citations |
1 | Prioritizing Crohn's disease genes by integrating association signals with gene expression implicates monocyte subsets. (Gettler K, Giri M, Kenigsberg E, Martin J, Chuang LS, Hsu NY, Denson LA, Hyams JS, Griffiths A, Noe JD, Crandall WV, Mack DR, Kellermayer R, Abraham C, Hoffman G, Kugathasan S, Cho JH) Genes Immun 2019 Sep;20(7):577-588 12 Citations |
1 | Three-dimensional analysis reveals altered chromatin interaction by enhancer inhibitors harbors TCF7L2-regulated cancer gene signature. (Gerrard DL, Wang Y, Gaddis M, Zhou Y, Wang J, Witt H, Lin S, Farnham PJ, Jin VX, Frietze SE) J Cell Biochem 2019 Mar;120(3):3056-3070 7 Citations |
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3 | Mechanisms Underlying the Regulation of HP1γ by the NGF-PKA Signaling Pathway. (Seo S, Mathison A, Grzenda A, Podratz J, Calvo E, Brimijoin S, Windebank A, Iovanna J, Lomberk G, Urrutia R) Sci Rep 2018 Oct 10;8(1):15077 4 Citations |
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2 | A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. (Berger AC, Korkut A, Kanchi RS, Hegde AM, Lenoir W, Liu W, Liu Y, Fan H, Shen H, Ravikumar V, Rao A, Schultz A, Li X, Sumazin P, Williams C, Mestdagh P, Gunaratne PH, Yau C, Bowlby R, Robertson AG, Tiezzi DG, Wang C, Cherniack AD, Godwin AK, Kuderer NM, Rader JS, Zuna RE, Sood AK, Lazar AJ, Ojesina AI, Adebamowo C, Adebamowo SN, Baggerly KA, Chen TW, Chiu HS, Lefever S, Liu L, MacKenzie K, Orsulic S, Roszik J, Shelley CS, Song Q, Vellano CP, Wentzensen N, Cancer Genome Atlas Research Network, Weinstein JN, Mills GB, Levine DA, Akbani R) Cancer Cell 2018 Apr 09;33(4):690-705.e9 369 Citations |
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1 | Conceptual and Experimental Tools to Understand Spatial Effects and Transport Phenomena in Nonlinear Biochemical Networks Illustrated with Patchy Switching. (Pompano RR, Chiang AH, Kastrup CJ, Ismagilov RF) Annu Rev Biochem 2017 Jun 20;86:333-356 8 Citations |
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1 | HAND2 Target Gene Regulatory Networks Control Atrioventricular Canal and Cardiac Valve Development. (Laurent F, Girdziusaite A, Gamart J, Barozzi I, Osterwalder M, Akiyama JA, Lincoln J, Lopez-Rios J, Visel A, Zuniga A, Zeller R) Cell Rep 2017 May 23;19(8):1602-1613 39 Citations |
1 | Discovery of Stromal Regulatory Networks that Suppress Ras-Sensitized Epithelial Cell Proliferation. (Liu H, Dowdle JA, Khurshid S, Sullivan NJ, Bertos N, Rambani K, Mair M, Daniel P, Wheeler E, Tang X, Toth K, Lause M, Harrigan ME, Eiring K, Sullivan C, Sullivan MJ, Chang SW, Srivastava S, Conway JS, Kladney R, McElroy J, Bae S, Lu Y, Tofigh A, Saleh SMI, Fernandez SA, Parvin JD, Coppola V, Macrae ER, Majumder S, Shapiro CL, Yee LD, Ramaswamy B, Hallett M, Ostrowski MC, Park M, Chamberlin HM, Leone G) Dev Cell 2017 May 22;41(4):392-407.e6 23 Citations |
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2 | The Role of the Histone Methyltransferase Enhancer of Zeste Homolog 2 (EZH2) in the Pathobiological Mechanisms Underlying Inflammatory Bowel Disease (IBD). (Sarmento OF, Svingen PA, Xiong Y, Sun Z, Bamidele AO, Mathison AJ, Smyrk TC, Nair AA, Gonzalez MM, Sagstetter MR, Baheti S, McGovern DP, Friton JJ, Papadakis KA, Gautam G, Xavier RJ, Urrutia RA, Faubion WA) J Biol Chem 2017 Jan 13;292(2):706-722 53 Citations |
1 | Whole Transcriptome Profiling Identifies CD93 and Other Plasma Cell Survival Factor Genes Associated with Measles-Specific Antibody Response after Vaccination. (Haralambieva IH, Zimmermann MT, Ovsyannikova IG, Grill DE, Oberg AL, Kennedy RB, Poland GA) PLoS One 2016;11(8):e0160970 18 Citations |
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1 | A miR-192-EGR1-HOXB9 regulatory network controls the angiogenic switch in cancer. (Wu SY, Rupaimoole R, Shen F, Pradeep S, Pecot CV, Ivan C, Nagaraja AS, Gharpure KM, Pham E, Hatakeyama H, McGuire MH, Haemmerle M, Vidal-Anaya V, Olsen C, Rodriguez-Aguayo C, Filant J, Ehsanipour EA, Herbrich SM, Maiti SN, Huang L, Kim JH, Zhang X, Han HD, Armaiz-Pena GN, Seviour EG, Tucker S, Zhang M, Yang D, Cooper LJ, Ali-Fehmi R, Bar-Eli M, Lee JS, Ram PT, Baggerly KA, Lopez-Berestein G, Hung MC, Sood AK) Nat Commun 2016 Apr 04;7:11169 107 Citations |
1 | Roles of Distal and Genic Methylation in the Development of Prostate Tumorigenesis Revealed by Genome-wide DNA Methylation Analysis. (Wang Y, Jadhav RR, Liu J, Wilson D, Chen Y, Thompson IM, Troyer DA, Hernandez J, Shi H, Leach RJ, Huang TH, Jin VX) Sci Rep 2016 Feb 29;6:22051 17 Citations |
1 | Variants in TRIM22 That Affect NOD2 Signaling Are Associated With Very-Early-Onset Inflammatory Bowel Disease. (Li Q, Lee CH, Peters LA, Mastropaolo LA, Thoeni C, Elkadri A, Schwerd T, Zhu J, Zhang B, Zhao Y, Hao K, Dinarzo A, Hoffman G, Kidd BA, Murchie R, Al Adham Z, Guo C, Kotlarz D, Cutz E, Walters TD, Shouval DS, Curran M, Dobrin R, Brodmerkel C, Snapper SB, Klein C, Brumell JH, Hu M, Nanan R, Snanter-Nanan B, Wong M, Le Deist F, Haddad E, Roifman CM, Deslandres C, Griffiths AM, Gaskin KJ, Uhlig HH, Schadt EE, Muise AM) Gastroenterology 2016 May;150(5):1196-1207 86 Citations |
1 | FOXM1 is a therapeutic target for high-risk multiple myeloma. (Gu C, Yang Y, Sompallae R, Xu H, Tompkins VS, Holman C, Hose D, Goldschmidt H, Tricot G, Zhan F, Janz S) Leukemia 2016 Apr;30(4):873-82 39 Citations |
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