Medical College of Wisconsin
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Publications indexed to the term Gene Regulatory Networks

FacultyTitle
2Molecular inflammatory expression profiles associated with the frequency of pain in individuals with sickle cell disease. (Mucalo Katunaric L, Jia S, Singh A, Roethle MF, Panepinto JA, Brousseau DC, Hessner MJ, Brandow AM) Blood Adv 2025 Aug 12;9(15):3790-3800       1 Citation
1Protocol for assessing distances in pathway space for classifier feature sets from machine learning methods. (Tercan B, Apolonio VH, Chagas VS, Wong CK, Lee JA, Yau C, Benz CC, Stuart JM, Karlberg BJ, Ellrott K, Grewal JK, Jones SJM, Cancer Genome Atlas Analysis Network, Zenklusen JC, Robertson AG, Laird PW, Cherniack AD, Castro MAA) STAR Protoc 2025 Jun 20;6(2):103681    
1Network-based meta-analysis and confirmation of genes ATP1A2, FXYD1, and ADCY3 associated with cAMP signaling in breast tumors compared to corresponding normal marginal tissues. (Torki Z, Ghavi D, Foruzandeh Z, Zeinali Sehrig F, Hashemi S, Alivand MR, Pornour M) Cell Mol Biol (Noisy-le-grand) 2024 Nov 27;70(11):16-30       2 Citations
2Estrogen-related receptor alpha promotes thyroid tumor cell survival via a tumor subtype-specific regulation of target gene networks. (Chen W, Song YS, Lee HS, Lin CW, Lee J, Kang YE, Kim SK, Kim SY, Park YJ, Park JI) Oncogene 2024 Jul;43(31):2431-2446       6 Citations
1Systems biology dissection of PTSD and MDD across brain regions, cell types, and blood. (Daskalakis NP, Iatrou A, Chatzinakos C, Jajoo A, Snijders C, Wylie D, DiPietro CP, Tsatsani I, Chen CY, Pernia CD, Soliva-Estruch M, Arasappan D, Bharadwaj RA, Collado-Torres L, Wuchty S, Alvarez VE, Dammer EB, Deep-Soboslay A, Duong DM, Eagles N, Huber BR, Huuki L, Holstein VL, Logue MW, Lugenbühl JF, Maihofer AX, Miller MW, Nievergelt CM, Pertea G, Ross D, Sendi MSE, Sun BB, Tao R, Tooke J, Wolf EJ, Zeier Z, PTSD Working Group of Psychiatric Genomics Consortium**, Berretta S, Champagne FA, Hyde T, Seyfried NT, Shin JH, Weinberger DR, Nemeroff CB, Kleinman JE, Ressler KJ, PTSD Working Group of Psychiatric Genomics Consortium) Science 2024 May 24;384(6698):eadh3707       50 Citations
1Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms. (Pividori M, Lu S, Li B, Su C, Johnson ME, Wei WQ, Feng Q, Namjou B, Kiryluk K, Kullo IJ, Luo Y, Sullivan BD, Voight BF, Skarke C, Ritchie MD, Grant SFA, eMERGE Consortium, Greene CS) Nat Commun 2023 Sep 09;14(1):5562       13 Citations
1Dual-Stream Subspace Clustering Network for revealing gene targets in Alzheimer's disease. (Chen M, Jia S, Xue M, Huang H, Xu Z, Yang D, Zhu W, Song Q) Comput Biol Med 2022 Dec;151(Pt A):106305       11 Citations
1CASP5 and CR1 as potential biomarkers for Kawasaki disease: an Integrated Bioinformatics-Experimental Study. (Rahmati Y, Mollanoori H, Najafi S, Esmaeili S, Alivand MR) BMC Pediatr 2021 Dec 11;21(1):566       5 Citations
1Biological features between miRNAs and their targets are unveiled from deep learning models. (Gu T, Xie M, Barbazuk WB, Lee JH) Sci Rep 2021 Dec 10;11(1):23825       8 Citations
1Integrative analysis of DNA methylation and gene expression profiles to identify biomarkers of glioblastoma. (Alivand MR, Najafi S, Esmaeili S, Rahmanpour D, Zhaleh H, Rahmati Y) Cancer Genet 2021 Nov;258-259:135-150       17 Citations
1PhenoGeneRanker: 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       4 Citations
1E2A-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)       29 Citations
2A 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       68 Citations
5RNA Sequencing and Pathways Analyses of Middle Ear Epithelia From Patients With Otitis Media. (Stabenau KA, Zimmermann MT, Mathison A, Zeighami A, Samuels TL, Chun RH, Papsin BC, McCormick ME, Johnston N, Kerschner JE) Laryngoscope 2021 Nov;131(11):2590-2597       9 Citations
1PGC1/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       70 Citations
3Identification 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       17 Citations
1The 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       482 Citations
1Discovering 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       24 Citations
1Complete genome sequence of Paracoccus sp. strain AK26: Insights into multipartite genome architecture and methylotropy. (Puri A, Bajaj A, Verma H, Kumar R, Singh Y, Lal R) Genomics 2020 May;112(3):2572-2582       12 Citations
2Integrative pathway enrichment analysis of multivariate omics data. (Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC, PCAWG Drivers and Functional Interpretation Working Group, Reimand J, PCAWG Consortium) Nat Commun 2020 Feb 05;11(1):735       172 Citations
1A network analysis to identify mediators of germline-driven differences in breast cancer prognosis. (Escala-Garcia M, Abraham J, Andrulis IL, Anton-Culver H, Arndt V, Ashworth A, Auer PL, Auvinen P, Beckmann MW, Beesley J, Behrens S, Benitez J, Bermisheva M, Blomqvist C, Blot W, Bogdanova NV, Bojesen SE, Bolla MK, Børresen-Dale AL, Brauch H, Brenner H, Brucker SY, Burwinkel B, Caldas C, Canzian F, Chang-Claude J, Chanock SJ, Chin SF, Clarke CL, Couch FJ, Cox A, Cross SS, Czene K, Daly MB, Dennis J, Devilee P, Dunn JA, Dunning AM, Dwek M, Earl HM, Eccles DM, Eliassen AH, Ellberg C, Evans DG, Fasching PA, Figueroa J, Flyger H, Gago-Dominguez M, Gapstur SM, García-Closas M, García-Sáenz JA, Gaudet MM, George A, Giles GG, Goldgar DE, González-Neira A, Grip M, Guénel P, Guo Q, Haiman CA, Håkansson N, Hamann U, Harrington PA, Hiller L, Hooning MJ, Hopper JL, Howell A, Huang CS, Huang G, Hunter DJ, Jakubowska A, John EM, Kaaks R, Kapoor PM, Keeman R, Kitahara CM, Koppert LB, Kraft P, Kristensen VN, Lambrechts D, Le Marchand L, Lejbkowicz F, Lindblom A, Lubiński J, Mannermaa A, Manoochehri M, Manoukian S, Margolin S, Martinez ME, Maurer T, Mavroudis D, Meindl A, Milne RL, Mulligan AM, Neuhausen SL, Nevanlinna H, Newman WG, Olshan AF, Olson JE, Olsson H, Orr N, Peterlongo P, Petridis C, Prentice RL, Presneau N, Punie K, Ramachandran D, Rennert G, Romero A, Sachchithananthan M, Saloustros E, Sawyer EJ, Schmutzler RK, Schwentner L, Scott C, Simard J, Sohn C, Southey MC, Swerdlow AJ, Tamimi RM, Tapper WJ, Teixeira MR, Terry MB, Thorne H, Tollenaar RAEM, Tomlinson I, Troester MA, Truong T, Turnbull C, Vachon CM, van der Kolk LE, Wang Q, Winqvist R, Wolk A, Yang XR, Ziogas A, Pharoah PDP, Hall P, Wessels LFA, Chenevix-Trench G, Bader GD, Dörk T, Easton DF, Canisius S, Schmidt MK) Nat Commun 2020 Jan 16;11(1):312       31 Citations
6miRNA551b-3p Activates an Oncostatin Signaling Module for the Progression of Triple-Negative Breast Cancer. (Parashar D, Geethadevi A, Aure MR, Mishra J, George J, Chen C, Mishra MK, Tahiri A, Zhao W, Nair B, Lu Y, Mangala LS, Rodriguez-Aguayo C, Lopez-Berestein G, Camara AKS, Liang M, Rader JS, Ramchandran R, You M, Sood AK, Kristensen VN, Mills GB, Pradeep S, Chaluvally-Raghavan P) Cell Rep 2019 Dec 24;29(13):4389-4406.e10       66 Citations
2Genome-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       28 Citations
1Expression of long non-coding RNAs (lncRNAs) has been dysregulated in non-small cell lung cancer tissues. (Esfandi F, Taheri M, Omrani MD, Shadmehr MB, Arsang-Jang S, Shams R, Ghafouri-Fard S) BMC Cancer 2019 Mar 12;19(1):222       51 Citations
1Prioritizing 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       13 Citations
1Three-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       9 Citations
2Microarray analysis of long non-coding RNA and mRNA expression profiles in diabetic cardiomyopathy using human induced pluripotent stem cell-derived cardiomyocytes. (Pant T, Mishra MK, Bai X, Ge ZD, Bosnjak ZJ, Dhanasekaran A) Diab Vasc Dis Res 2019 Jan;16(1):57-68       16 Citations
3Mechanisms 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       6 Citations
1Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas. (Liu Y, Sethi NS, Hinoue T, Schneider BG, Cherniack AD, Sanchez-Vega F, Seoane JA, Farshidfar F, Bowlby R, Islam M, Kim J, Chatila W, Akbani R, Kanchi RS, Rabkin CS, Willis JE, Wang KK, McCall SJ, Mishra L, Ojesina AI, Bullman S, Pedamallu CS, Lazar AJ, Sakai R, Cancer Genome Atlas Research Network, Thorsson V, Bass AJ, Laird PW) Cancer Cell 2018 Apr 09;33(4):721-735.e8       453 Citations
2A 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       490 Citations
1Long ncRNA Landscape in the Ileum of Treatment-Naive Early-Onset Crohn Disease. (Haberman Y, BenShoshan M, Di Segni A, Dexheimer PJ, Braun T, Weiss B, Walters TD, Baldassano RN, Noe JD, Markowitz J, Rosh J, Heyman MB, Griffiths AM, Crandall WV, Mack DR, Baker SS, Kellermayer R, Patel A, Otley A, Steiner SJ, Gulati AS, Guthery SL, LeLeiko N, Moulton D, Kirschner BS, Snapper S, Avivi C, Barshack I, Oliva-Hemker M, Cohen SA, Keljo DJ, Ziring D, Anikster Y, Aronow B, Hyams JS, Kugathasan S, Denson LA) Inflamm Bowel Dis 2018 Jan 18;24(2):346-360       60 Citations
1Interferon-Stimulated Genes Are Transcriptionally Repressed by PR in Breast Cancer. (Walter KR, Goodman ML, Singhal H, Hall JA, Li T, Holloran SM, Trinca GM, Gibson KA, Jin VX, Greene GL, Hagan CR) Mol Cancer Res 2017 Oct;15(10):1331-1340       32 Citations
1Conceptual 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       10 Citations
7Host genetic modifiers of nonproductive angiogenesis inhibit breast cancer. (Flister MJ, Tsaih SW, Stoddard A, Plasterer C, Jagtap J, Parchur AK, Sharma G, Prisco AR, Lemke A, Murphy D, Al-Gizawiy M, Straza M, Ran S, Geurts AM, Dwinell MR, Greene AS, Bergom C, LaViolette PS, Joshi A) Breast Cancer Res Treat 2017 Aug;165(1):53-64       15 Citations
1HAND2 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       49 Citations
1Discovery 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       25 Citations
1Our Genome's "Dark Matter" Is the Next Frontier in Molecular Diagnostics. (Nerenz RD, Lefferts J) Clin Chem 2017 Mar;63(3):792-793       3 Citations
1Investigation of coordination and order in transcription regulation of innate and adaptive immunity genes in type 1 diabetes. (Gao S, Wolanyk N, Chen Y, Jia S, Hessner MJ, Wang X) BMC Med Genomics 2017 Jan 31;10(1):7       8 Citations
2The 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       58 Citations
1Whole 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       23 Citations
1Predisposition to treatment response in major depressive episode: A peripheral blood gene coexpression network analysis. (Belzeaux R, Lin CW, Ding Y, Bergon A, Ibrahim EC, Turecki G, Tseng G, Sibille E) J Psychiatr Res 2016 Oct;81:119-26       28 Citations
1A 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       118 Citations
1Roles 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       18 Citations
1Variants 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       102 Citations
1FOXM1 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       48 Citations
1Cyclin alterations in diverse cancers: Outcome and co-amplification network. (Schwaederlé M, Daniels GA, Piccioni DE, Fanta PT, Schwab RB, Shimabukuro KA, Parker BA, Kurzrock R) Oncotarget 2015 Feb 20;6(5):3033-42       36 Citations
1A full bayesian approach for boolean genetic network inference. (Han S, Wong RK, Lee TC, Shen L, Li SY, Fan X) PLoS One 2014;9(12):e115806       16 Citations
1Transcriptional reversion of cardiac myocyte fate during mammalian cardiac regeneration. (O'Meara CC, Wamstad JA, Gladstone RA, Fomovsky GM, Butty VL, Shrikumar A, Gannon JB, Boyer LA, Lee RT) Circ Res 2015 Feb 27;116(5):804-15       135 Citations
3Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease. (Petri V, Hayman GT, Tutaj M, Smith JR, Laulederkind SJ, Wang SJ, Nigam R, De Pons J, Shimoyama M, Dwinell MR, Worthey EA, Jacob HJ) Hum Genomics 2014 Sep 30;8(1):17       7 Citations
1Sequence co-evolution gives 3D contacts and structures of protein complexes. (Hopf TA, Schärfe CP, Rodrigues JP, Green AG, Kohlbacher O, Sander C, Bonvin AM, Marks DS) Elife 2014 Sep 25;3       396 Citations
1Study familial hypertrophic cardiomyopathy using patient-specific induced pluripotent stem cells. (Han L, Li Y, Tchao J, Kaplan AD, Lin B, Li Y, Mich-Basso J, Lis A, Hassan N, London B, Bett GC, Tobita K, Rasmusson RL, Yang L) Cardiovasc Res 2014 Nov 01;104(2):258-69       166 Citations
1The inferred cardiogenic gene regulatory network in the mammalian heart. (Bazil JN, Stamm KD, Li X, Thiagarajan R, Nelson TJ, Tomita-Mitchell A, Beard DA) PLoS One 2014;9(6):e100842       11 Citations
3Single and combinatorial chromatin coupling events underlies the function of transcript factor Krüppel-like factor 11 in the regulation of gene networks. (Calvo E, Grzenda A, Lomberk G, Mathison A, Iovanna J, Urrutia R) BMC Mol Biol 2014 May 25;15:10       6 Citations
1A conserved BDNF, glutamate- and GABA-enriched gene module related to human depression identified by coexpression meta-analysis and DNA variant genome-wide association studies. (Chang LC, Jamain S, Lin CW, Rujescu D, Tseng GC, Sibille E) PLoS One 2014;9(3):e90980       89 Citations
1Identification of candidate B-lymphoma genes by cross-species gene expression profiling. (Tompkins VS, Han SS, Olivier A, Syrbu S, Bair T, Button A, Jacobus L, Wang Z, Lifton S, Raychaudhuri P, Morse HC 3rd, Weiner G, Link B, Smith BJ, Janz S) PLoS One 2013;8(10):e76889       11 Citations
3Krüppel-like factor 11 regulates the expression of metabolic genes via an evolutionarily conserved protein interaction domain functionally disrupted in maturity onset diabetes of the young. (Lomberk G, Grzenda A, Mathison A, Escande C, Zhang JS, Calvo E, Miller LJ, Iovanna J, Chini EN, Fernandez-Zapico ME, Urrutia R) J Biol Chem 2013 Jun 14;288(24):17745-58       30 Citations
1The updated RGD Pathway Portal utilizes increased curation efficiency and provides expanded pathway information. (Hayman GT, Jayaraman P, Petri V, Tutaj M, Liu W, De Pons J, Dwinell MR, Shimoyama M) Hum Genomics 2013 Feb 05;7(1):4       7 Citations
1Cancer omics: from regulatory networks to clinical outcomes. (Tang B, Hsu PY, Huang TH, Jin VX) Cancer Lett 2013 Nov 01;340(2):277-83       9 Citations
1Integrative analysis of the zinc finger transcription factor Lame duck in the Drosophila myogenic gene regulatory network. (Busser BW, Huang D, Rogacki KR, Lane EA, Shokri L, Ni T, Gamble CE, Gisselbrecht SS, Zhu J, Bulyk ML, Ovcharenko I, Michelson AM) Proc Natl Acad Sci U S A 2012 Dec 11;109(50):20768-73       20 Citations
1Hierarchical modularity in ERα transcriptional network is associated with distinct functions and implicates clinical outcomes. (Tang B, Hsu HK, Hsu PY, Bonneville R, Chen SS, Huang TH, Jin VX) Sci Rep 2012;2:875       25 Citations
1Predicting disease-related subnetworks for type 1 diabetes using a new network activity score. (Gao S, Jia S, Hessner MJ, Wang X) OMICS 2012 Oct;16(10):566-78       10 Citations
3Role of genetic modifiers in an orthologous rat model of ARPKD. (O'Meara CC, Hoffman M, Sweeney WE Jr, Tsaih SW, Xiao B, Jacob HJ, Avner ED, Moreno C) Physiol Genomics 2012 Aug 01;44(15):741-53       23 Citations
1ChIP-seq defined genome-wide map of TGFβ/SMAD4 targets: implications with clinical outcome of ovarian cancer. (Kennedy BA, Deatherage DE, Gu F, Tang B, Chan MW, Nephew KP, Huang TH, Jin VX) PLoS One 2011;6(7):e22606       30 Citations
1Integrative identification of core genetic regulatory modules via a structural model-based clustering method. (Tang B, Chen SS, Jin VX) Int J Comput Biol Drug Des 2011;4(2):127-46       2 Citations
1The Rat Genome Database pathway portal. (Petri V, Shimoyama M, Hayman GT, Smith JR, Tutaj M, de Pons J, Dwinell MR, Munzenmaier DH, Twigger SN, Jacob HJ, RGD Team) Database (Oxford) 2011;2011:bar010       19 Citations
1Aberrant DNA methylation of matrix remodeling and cell adhesion related genes in pterygium. (Riau AK, Wong TT, Lan W, Finger SN, Chaurasia SS, Hou AH, Chen S, Yu SJ, Tong L) PLoS One 2011 Feb 16;6(2):e14687       55 Citations
1Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data. (Gu F, Hsu HK, Hsu PY, Wu J, Ma Y, Parvin J, Huang TH, Jin VX) BMC Syst Biol 2010 Dec 17;4:170       43 Citations
1Global analysis of phase locking in gene expression during cell cycle: the potential in network modeling. (Gao S, Hartman JL 4th, Carter JL, Hessner MJ, Wang X) BMC Syst Biol 2010 Dec 03;4:167       9 Citations
1Loss of individual microRNAs causes mutant phenotypes in sensitized genetic backgrounds in C. elegans. (Brenner JL, Jasiewicz KL, Fahley AF, Kemp BJ, Abbott AL) Curr Biol 2010 Jul 27;20(14):1321-5       110 Citations
1Two supporting factors greatly improve the efficiency of human iPSC generation. (Zhao Y, Yin X, Qin H, Zhu F, Liu H, Yang W, Zhang Q, Xiang C, Hou P, Song Z, Liu Y, Yong J, Zhang P, Cai J, Liu M, Li H, Li Y, Qu X, Cui K, Zhang W, Xiang T, Wu Y, Zhao Y, Liu C, Yu C, Yuan K, Lou J, Ding M, Deng H) Cell Stem Cell 2008 Nov 06;3(5):475-9       419 Citations
2Molecular networks in Dahl salt-sensitive hypertension based on transcriptome analysis of a panel of consomic rats. (Liang M, Lee NH, Wang H, Greene AS, Kwitek AE, Kaldunski ML, Luu TV, Frank BC, Bugenhagen S, Jacob HJ, Cowley AW Jr) Physiol Genomics 2008 Jun 12;34(1):54-64       43 Citations
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