Medical College of Wisconsin
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Victor X. Jin PhD

Victor X. Jin PhD profile photo picture

Professor

Institution: Medical College of Wisconsin
Department: Institute for Health and Equity
Division: Biostatistics
Program: Research

Member of the Cancer Center
Member of the Institute for Health & Equity

Research Areas of Interest

  • 3) Adapting/applying genome-wide omics-seq techniques in patient tissues to identify epigenetic-driven therapeutic targets and biomarkers.
  • 2) Functionally and mechanistically characterizing the roles of epigenetic marks in cancer development and progression using novel techniques such as 3C/ChIP/RT-qPCR, 3D-FISH and CRISPR/Cas9.
  • 1) Developing genomics and computational approaches for the identification of three-dimensional (3D) chromatin interactions from the various omics-seq data.

    • Research Experience

  • Dr. Jin has extensive experience in developing computational and genomics approaches for analyzing various omics-seq data, and runs a systems biology lab with a balanced dry and wet components.

    • Leadership Positions

  • Director, Bioinformatics Shared Resources
  • Associate Director of Bioinformatics and Systems Biology, Mellowes Center for Genomic Sciences and Precision Medicine

    • Publications (121)

  • Reprogramming of 3D chromatin domains by antagonizing the β-catenin/CBP interaction attenuates insulin signaling in pancreatic cancer. (Zhou Y, Li T, He Z, Choppavarapu L, Hu X, Cao R, Leone GW, Kahn M, Jin VX) bioRxiv 2023 Nov 14 PMID: 38013997 PMCID: PMC10680786 11/28/2023    
  • Integration of scHi-C and scRNA-seq data defines distinct 3D-regulated and biological-context dependent cell subpopulations. (Zhou Y, Li T, Choppavarapu L, Jin VX) bioRxiv 2023 Oct 02 PMID: 37873257 PMCID: PMC10592853 10/24/2023    
  • An essential signaling function of cytoplasmic NELFB is independent of RNA polymerase II pausing. (Pan H, Cheng X, Rodríguez PFG, Zhang X, Chung I, Jin VX, Li W, Hu Y, Li R) J Biol Chem 2023 Nov;299(11):105259 PMID: 37717699 PMCID: PMC10591015 SCOPUS ID: 2-s2.0-85173908191 09/18/2023    
  • A Deeply Quiescent Subset of CML LSC depend on FAO yet Avoid Deleterious ROS by Suppressing Mitochondrial Complex I. (Chimge NO, Chen MH, Nguyen C, Zhao Y, Wu X, Gonzalez PG, Ogana H, Hurwitz S, Teo JL, Chen X, Du J, Jin V, Kim YM, Ono M, Argüello RJ, Kahn M) Curr Mol Pharmacol 2024;17(1):e060923220758 PMID: 37691195 SCOPUS ID: 2-s2.0-85180197208 09/11/2023       2 Citations
  • The splanchnic mesenchyme is the tissue of origin for pancreatic fibroblasts during homeostasis and tumorigenesis. (Han L, Wu Y, Fang K, Sweeney S, Roesner UK, Parrish M, Patel K, Walter T, Piermattei J, Trimboli A, Lefler J, Timmers CD, Yu XZ, Jin VX, Zimmermann MT, Mathison AJ, Urrutia R, Ostrowski MC, Leone G) Nat Commun 2023 Jan 03;14(1):1 PMID: 36596776 PMCID: PMC9810714 SCOPUS ID: 2-s2.0-85145429848 01/04/2023       16 Citations
  • Association of adenosine signaling gene signature with estrogen receptor-positive breast and prostate cancer bone metastasis. (Shropshire DB, Acosta FM, Fang K, Benavides J, Sun LZ, Jin VX, Jiang JX) Front Med (Lausanne) 2022;9:965429 PMID: 36186774 PMCID: PMC9520286 SCOPUS ID: 2-s2.0-85139267426 10/04/2022       2 Citations
  • Mapping nucleosome and chromatin architectures: A survey of computational methods. (Fang K, Wang J, Liu L, Jin VX) Comput Struct Biotechnol J 2022;20:3955-3962 PMID: 35950186 PMCID: PMC9340519 SCOPUS ID: 2-s2.0-85134894760 08/12/2022       1 Citation
  • Cas13d knockdown of lung protease Ctsl prevents and treats SARS-CoV-2 infection. (Cui Z, Zeng C, Huang F, Yuan F, Yan J, Zhao Y, Zhou Y, Hankey W, Jin VX, Huang J, Staats HF, Everitt JI, Sempowski GD, Wang H, Dong Y, Liu SL, Wang Q) Nat Chem Biol 2022 Oct;18(10):1056-1064 PMID: 35879545 PMCID: PMC10082993 SCOPUS ID: 2-s2.0-85134648919 07/26/2022       24 Citations
  • HiCImpute: A Bayesian hierarchical model for identifying structural zeros and enhancing single cell Hi-C data. (Xie Q, Han C, Jin V, Lin S) PLoS Comput Biol 2022 Jun;18(6):e1010129 PMID: 35696429 PMCID: PMC9232133 SCOPUS ID: 2-s2.0-85133102474 06/14/2022       3 Citations
  • Haploinsufficiency of a Circadian Clock Gene Bmal1 (Arntl or Mop3) Causes Brain-Wide mTOR Hyperactivation and Autism-like Behavioral Phenotypes in Mice. (Singla R, Mishra A, Lin H, Lorsung E, Le N, Tin S, Jin VX, Cao R) Int J Mol Sci 2022 Jun 05;23(11) PMID: 35682995 PMCID: PMC9181331 SCOPUS ID: 2-s2.0-85131235233 06/11/2022       9 Citations
  • Dynamic nucleosome landscape elicits a noncanonical GATA2 pioneer model. (Li T, Liu Q, Chen Z, Fang K, Huang F, Fu X, Wang Q, Jin VX) Nat Commun 2022 Jun 07;13(1):3145 PMID: 35672415 PMCID: PMC9174260 SCOPUS ID: 2-s2.0-85131472527 06/08/2022       2 Citations
  • Phosphorylated MED1 links transcription recycling and cancer growth. (Chen Z, Ye Z, Soccio RE, Nakadai T, Hankey W, Zhao Y, Huang F, Yuan F, Wang H, Cui Z, Sunkel B, Wu D, Dzeng RK, Thomas-Ahner JM, Huang THM, Clinton SK, Huang J, Lazar MA, Jin VX, Roeder RG, Wang Q) Nucleic Acids Res 2022 May 06;50(8):4450-4463 PMID: 35394046 PMCID: PMC9071494 SCOPUS ID: 2-s2.0-85129998167 04/09/2022       3 Citations
  • Autistic-like behavior and cerebellar dysfunction in Bmal1 mutant mice ameliorated by mTORC1 inhibition. (Liu D, Nanclares C, Simbriger K, Fang K, Lorsung E, Le N, Amorim IS, Chalkiadaki K, Pathak SS, Li J, Gewirtz JC, Jin VX, Kofuji P, Araque A, Orr HT, Gkogkas CG, Cao R) Mol Psychiatry 2023 Sep;28(9):3727-3738 PMID: 35301425 PMCID: PMC9481983 SCOPUS ID: 2-s2.0-85126344103 03/19/2022       13 Citations
  • abc4pwm: affinity based clustering for position weight matrices in applications of DNA sequence analysis. (Ali O, Farooq A, Yang M, Jin VX, Bjørås M, Wang J) BMC Bioinformatics 2022 Mar 03;23(1):83 PMID: 35240993 PMCID: PMC8896320 SCOPUS ID: 2-s2.0-85125689002 03/05/2022       1 Citation
  • Disruption of Circadian Rhythms by Ambient Light during Neurodevelopment Leads to Autistic-like Molecular and Behavioral Alterations in Adult Mice. (Fang K, Liu D, Pathak SS, Yang B, Li J, Karthikeyan R, Chao OY, Yang YM, Jin VX, Cao R) Cells 2021 Nov 26;10(12) PMID: 34943821 PMCID: PMC8699695 SCOPUS ID: 2-s2.0-85119915513 12/25/2021       9 Citations
  • Tumour DDR1 promotes collagen fibre alignment to instigate immune exclusion. (Sun X, Wu B, Chiang HC, Deng H, Zhang X, Xiong W, Liu J, Rozeboom AM, Harris BT, Blommaert E, Gomez A, Garcia RE, Zhou Y, Mitra P, Prevost M, Zhang D, Banik D, Isaacs C, Berry D, Lai C, Chaldekas K, Latham PS, Brantner CA, Popratiloff A, Jin VX, Zhang N, Hu Y, Pujana MA, Curiel TJ, An Z, Li R) Nature 2021 Nov;599(7886):673-678 PMID: 34732895 PMCID: PMC8839149 SCOPUS ID: 2-s2.0-85118481803 11/05/2021       132 Citations
  • Hi-C profiling of cancer spheroids identifies 3D-growth-specific chromatin interactions in breast cancer endocrine resistance. (Li J, Fang K, Choppavarapu L, Yang K, Yang Y, Wang J, Cao R, Jatoi I, Jin VX) Clin Epigenetics 2021 Sep 17;13(1):175 PMID: 34535185 PMCID: PMC8447690 SCOPUS ID: 2-s2.0-85115159581 09/19/2021       8 Citations
  • NucHMM: a method for quantitative modeling of nucleosome organization identifying functional nucleosome states distinctly associated with splicing potentiality. (Fang K, Li T, Huang Y, Jin VX) Genome Biol 2021 Aug 26;22(1):250 PMID: 34446075 PMCID: PMC8390234 SCOPUS ID: 2-s2.0-85113471118 08/28/2021       3 Citations
  • Estrogen receptor beta signaling in CD8+ T cells boosts T cell receptor activation and antitumor immunity through a phosphotyrosine switch. (Yuan B, Clark CA, Wu B, Yang J, Drerup JM, Li T, Jin VX, Hu Y, Curiel TJ, Li R) J Immunother Cancer 2021 Jan;9(1) PMID: 33462142 PMCID: PMC7816924 SCOPUS ID: 2-s2.0-85100094986 01/20/2021       16 Citations
  • The 3D genomic landscape of differential response to EGFR/HER2 inhibition in endocrine-resistant breast cancer cells. (Yang Y, Choppavarapu L, Fang K, Naeini AS, Nosirov B, Li J, Yang K, He Z, Zhou Y, Schiff R, Li R, Hu Y, Wang J, Jin VX) Biochim Biophys Acta Gene Regul Mech 2020 Nov;1863(11):194631 PMID: 32956836 PMCID: PMC7686120 SCOPUS ID: 2-s2.0-85091761490 09/22/2020       7 Citations
  • Modeling and analysis of Hi-C data by HiSIF identifies characteristic promoter-distal loops. (Zhou Y, Cheng X, Yang Y, Li T, Li J, Huang TH, Wang J, Lin S, Jin VX) Genome Med 2020 Aug 12;12(1):69 PMID: 32787954 PMCID: PMC7425017 SCOPUS ID: 2-s2.0-85089609836 08/14/2020       6 Citations
  • Epigenomics-based identification of oestrogen-regulated long noncoding RNAs in ER+ breast cancer. (Zhang Z, Yu W, Tang D, Zhou Y, Bi M, Wang H, Zheng Y, Chen M, Li L, Xu X, Zhang W, Tao H, Jin VX, Liu Z, Chen L) RNA Biol 2020 Nov;17(11):1590-1602 PMID: 32506995 PMCID: PMC7567493 SCOPUS ID: 2-s2.0-85087143219 06/09/2020       10 Citations
  • Enhancer reprogramming driven by high-order assemblies of transcription factors promotes phenotypic plasticity and breast cancer endocrine resistance. (Bi M, Zhang Z, Jiang YZ, Xue P, Wang H, Lai Z, Fu X, De Angelis C, Gong Y, Gao Z, Ruan J, Jin VX, Marangoni E, Montaudon E, Glass CK, Li W, Huang TH, Shao ZM, Schiff R, Chen L, Liu Z) Nat Cell Biol 2020 Jun;22(6):701-715 PMID: 32424275 PMCID: PMC7737911 SCOPUS ID: 2-s2.0-85085001723 05/20/2020       69 Citations
  • Reciprocal fine-tuning of progesterone and prolactin-regulated gene expression in breast cancer cells. (Holloran SM, Nosirov B, Walter KR, Trinca GM, Lai Z, Jin VX, Hagan CR) Mol Cell Endocrinol 2020 Jul 01;511:110859 PMID: 32407979 PMCID: PMC8941988 SCOPUS ID: 2-s2.0-85085168333 05/15/2020       3 Citations
  • Author Correction: Temporal dynamic reorganization of 3D chromatin architecture in hormone-induced breast cancer and endocrine resistance. (Zhou Y, Gerrard DL, Wang J, Li T, Yang Y, Fritz AJ, Rajendran M, Fu X, Stein G, Schiff R, Lin S, Frietze S, Jin VX) Nat Commun 2020 Apr 20;11(1):1967 PMID: 32313124 PMCID: PMC7170926 SCOPUS ID: 2-s2.0-85083755866 04/22/2020       1 Citation
  • Disruption of Broad Epigenetic Domains in PDAC Cells by HAT Inhibitors. (Gerrard DL, Boyd JR, Stein GS, Jin VX, Frietze S) Epigenomes 2019 Jun;3(2) PMID: 31815011 PMCID: PMC6897394 SCOPUS ID: 2-s2.0-85075188438 12/10/2019       10 Citations
  • The eIF2α Kinase GCN2 Modulates Period and Rhythmicity of the Circadian Clock by Translational Control of Atf4. (Pathak SS, Liu D, Li T, de Zavalia N, Zhu L, Li J, Karthikeyan R, Alain T, Liu AC, Storch KF, Kaufman RJ, Jin VX, Amir S, Sonenberg N, Cao R) Neuron 2019 Nov 20;104(4):724-735.e6 PMID: 31522764 PMCID: PMC6872934 SCOPUS ID: 2-s2.0-85074910349 09/17/2019       40 Citations
  • BRCA1 mutations attenuate super-enhancer function and chromatin looping in haploinsufficient human breast epithelial cells. (Zhang X, Wang Y, Chiang HC, Hsieh YP, Lu C, Park BH, Jatoi I, Jin VX, Hu Y, Li R) Breast Cancer Res 2019 Apr 17;21(1):51 PMID: 30995943 PMCID: PMC6472090 SCOPUS ID: 2-s2.0-85064390742 04/19/2019       15 Citations
  • Temporal dynamic reorganization of 3D chromatin architecture in hormone-induced breast cancer and endocrine resistance. (Zhou Y, Gerrard DL, Wang J, Li T, Yang Y, Fritz AJ, Rajendran M, Fu X, Stein G, Schiff R, Lin S, Frietze S, Jin VX) Nat Commun 2019 Apr 03;10(1):1522 PMID: 30944316 PMCID: PMC6447566 SCOPUS ID: 2-s2.0-85063964396 04/05/2019       45 Citations
  • Progesterone Receptor Attenuates STAT1-Mediated IFN Signaling in Breast Cancer. (Goodman ML, Trinca GM, Walter KR, Papachristou EK, D'Santos CS, Li T, Liu Q, Lai Z, Chalise P, Madan R, Fan F, Markiewicz MA, Jin VX, Carroll JS, Hagan CR) J Immunol 2019 May 15;202(10):3076-3086 PMID: 30936295 PMCID: PMC6504603 SCOPUS ID: 2-s2.0-85065678009 04/03/2019       26 Citations
  • 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 PMID: 30548288 PMCID: PMC6476548 SCOPUS ID: 2-s2.0-85058244236 12/15/2018       7 Citations
  • Adipokines Deregulate Cellular Communication via Epigenetic Repression of Gap Junction Loci in Obese Endometrial Cancer. (Polusani SR, Huang YW, Huang G, Chen CW, Wang CM, Lin LL, Osmulski P, Lucio ND, Liu L, Hsu YT, Zhou Y, Lin CL, Aguilera-Barrantes I, Valente PT, Kost ER, Chen CL, Shim EY, Lee SE, Ruan J, Gaczynska ME, Yan P, Goodfellow PJ, Mutch DG, Jin VX, Nicholson BJ, Huang TH, Kirma NB) Cancer Res 2019 Jan 01;79(1):196-208 PMID: 30389702 PMCID: PMC6705596 SCOPUS ID: 2-s2.0-85059446400 11/06/2018       15 Citations
  • Chromatin-associated APC regulates gene expression in collaboration with canonical WNT signaling and AP-1. (Hankey W, Chen Z, Bergman MJ, Fernandez MO, Hancioglu B, Lan X, Jegga AG, Zhang J, Jin VX, Aronow BJ, Wang Q, Groden J) Oncotarget 2018 Jul 27;9(58):31214-31230 PMID: 30131849 PMCID: PMC6101278 SCOPUS ID: 2-s2.0-85050699142 08/23/2018       6 Citations
  • Diverse AR-V7 cistromes in castration-resistant prostate cancer are governed by HoxB13. (Chen Z, Wu D, Thomas-Ahner JM, Lu C, Zhao P, Zhang Q, Geraghty C, Yan PS, Hankey W, Sunkel B, Cheng X, Antonarakis ES, Wang QE, Liu Z, Huang TH, Jin VX, Clinton SK, Luo J, Huang J, Wang Q) Proc Natl Acad Sci U S A 2018 Jun 26;115(26):6810-6815 PMID: 29844167 PMCID: PMC6042123 SCOPUS ID: 2-s2.0-85049003766 05/31/2018       105 Citations
  • Integrative analysis reveals functional and regulatory roles of H3K79me2 in mediating alternative splicing. (Li T, Liu Q, Garza N, Kornblau S, Jin VX) Genome Med 2018 Apr 17;10(1):30 PMID: 29665865 PMCID: PMC5902843 SCOPUS ID: 2-s2.0-85045508396 04/19/2018       25 Citations
  • Author Correction: Attenuation of RNA polymerase II pausing mitigates BRCA1-associated R-loop accumulation and tumorigenesis. (Zhang X, Chiang HC, Wang Y, Zhang C, Smith S, Zhao X, Nair SJ, Michalek J, Jatoi I, Lautner M, Oliver B, Wang H, Petit A, Soler T, Brunet J, Mateo F, Angel Pujana M, Poggi E, Chaldekas K, Isaacs C, Peshkin BN, Ochoa O, Chedin F, Theoharis C, Sun LZ, Curiel TJ, Elledge R, Jin VX, Hu Y, Li R) Nat Commun 2018 Mar 30;9:16211 PMID: 29600804 PMCID: PMC5882462 SCOPUS ID: 2-s2.0-85058610641 03/31/2018    
  • Phosphorylation of EZH2 by AMPK Suppresses PRC2 Methyltransferase Activity and Oncogenic Function. (Wan L, Xu K, Wei Y, Zhang J, Han T, Fry C, Zhang Z, Wang YV, Huang L, Yuan M, Xia W, Chang WC, Huang WC, Liu CL, Chang YC, Liu J, Wu Y, Jin VX, Dai X, Guo J, Liu J, Jiang S, Li J, Asara JM, Brown M, Hung MC, Wei W) Mol Cell 2018 Jan 18;69(2):279-291.e5 PMID: 29351847 PMCID: PMC5777296 SCOPUS ID: 2-s2.0-85041319667 01/21/2018       128 Citations
  • An Introduction to Integrative Genomics and Systems Medicine in Cancer. (Cheng X, Jin VX) Genes (Basel) 2018 Jan 12;9(1) PMID: 29329216 PMCID: PMC5793188 SCOPUS ID: 2-s2.0-85040914044 01/13/2018       2 Citations
  • Single-Cell RNA-seq Reveals a Subpopulation of Prostate Cancer Cells with Enhanced Cell-Cycle-Related Transcription and Attenuated Androgen Response. (Horning AM, Wang Y, Lin CK, Louie AD, Jadhav RR, Hung CN, Wang CM, Lin CL, Kirma NB, Liss MA, Kumar AP, Sun L, Liu Z, Chao WT, Wang Q, Jin VX, Chen CL, Huang TH) Cancer Res 2018 Feb 15;78(4):853-864 PMID: 29233929 PMCID: PMC5983359 SCOPUS ID: 2-s2.0-85042183241 12/14/2017       75 Citations
  • Advances in Genomic Profiling and Analysis of 3D Chromatin Structure and Interaction. (Tang B, Cheng X, Xi Y, Chen Z, Zhou Y, Jin VX) Genes (Basel) 2017 Sep 08;8(9) PMID: 28885554 PMCID: PMC5615356 SCOPUS ID: 2-s2.0-85029697541 09/09/2017       5 Citations
  • Interferon-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 PMID: 28684637 PMCID: PMC5626608 SCOPUS ID: 2-s2.0-85030481734 07/08/2017       27 Citations
  • Attenuation of RNA polymerase II pausing mitigates BRCA1-associated R-loop accumulation and tumorigenesis. (Zhang X, Chiang HC, Wang Y, Zhang C, Smith S, Zhao X, Nair SJ, Michalek J, Jatoi I, Lautner M, Oliver B, Wang H, Petit A, Soler T, Brunet J, Mateo F, Angel Pujana M, Poggi E, Chaldekas K, Isaacs C, Peshkin BN, Ochoa O, Chedin F, Theoharis C, Sun LZ, Curiel TJ, Elledge R, Jin VX, Hu Y, Li R) Nat Commun 2017 Jun 26;8:15908 PMID: 28649985 PMCID: PMC5490191 SCOPUS ID: 2-s2.0-85021414427 06/27/2017       111 Citations
  • Integration of DNA methylation and gene transcription across nineteen cell types reveals cell type-specific and genomic region-dependent regulatory patterns. (Tang B, Zhou Y, Wang CM, Huang TH, Jin VX) Sci Rep 2017 Jun 15;7(1):3626 PMID: 28620196 PMCID: PMC5472622 SCOPUS ID: 2-s2.0-85020861990 06/18/2017       18 Citations
  • DNA Methylation Targets Influenced by Bisphenol A and/or Genistein Are Associated with Survival Outcomes in Breast Cancer Patients. (Jadhav RR, Santucci-Pereira J, Wang YV, Liu J, Nguyen TD, Wang J, Jenkins S, Russo J, Huang TH, Jin VX, Lamartiniere CA) Genes (Basel) 2017 May 15;8(5) PMID: 28505145 PMCID: PMC5448018 SCOPUS ID: 2-s2.0-85019255409 05/16/2017       31 Citations
  • Transcription factor-associated combinatorial epigenetic pattern reveals higher transcriptional activity of TCF7L2-regulated intragenic enhancers. (Liu Q, Bonneville R, Li T, Jin VX) BMC Genomics 2017 May 12;18(1):375 PMID: 28499350 PMCID: PMC5429574 SCOPUS ID: 2-s2.0-85038924082 05/14/2017       13 Citations
  • Integrative analysis identifies targetable CREB1/FoxA1 transcriptional co-regulation as a predictor of prostate cancer recurrence. (Sunkel B, Wu D, Chen Z, Wang CM, Liu X, Ye Z, Horning AM, Liu J, Mahalingam D, Lopez-Nicora H, Lin CL, Goodfellow PJ, Clinton SK, Jin VX, Chen CL, Huang TH, Wang Q) Nucleic Acids Res 2017 Jun 20;45(11):6993 PMID: 28419278 PMCID: PMC5499716 SCOPUS ID: 2-s2.0-85054776962 04/19/2017       7 Citations
  • COPAR: A ChIP-Seq Optimal Peak Analyzer. (Tang B, Wang X, Jin VX) Biomed Res Int 2017;2017:5346793 PMID: 28357402 PMCID: PMC5357551 SCOPUS ID: 2-s2.0-85015921256 03/31/2017    
  • EGFR-Dependent Regulated Intramembrane Proteolysis of EpCAM-Response. (Hsu YT, Osmulski P, Wang Y, Huang YW, Liu L, Ruan J, Jin VX, Kirma NB, Gaczynska ME, Huang TH) Cancer Res 2017 Apr 01;77(7):1777 PMID: 28330931 SCOPUS ID: 2-s2.0-85017351424 03/24/2017       3 Citations
  • Inference of hierarchical regulatory network of TCF7L2 binding sites in MCF7 cell line. (Wang Y, Wang R, Jin VX) Int J Comput Biol Drug Des 2016;9(1-2):25-53 PMID: 28066512 PMCID: PMC5218816 SCOPUS ID: 2-s2.0-84960124715 01/10/2017       2 Citations
  • Statistical challenges in analyzing methylation and long-range chromosomal interaction data. (Qin Z, Li B, Conneely KN, Wu H, Hu M, Ayyala D, Park Y, Jin VX, Zhang F, Zhang H, Li L, Lin S) Stat Biosci 2016 Oct;8(2):284-309 PMID: 28008337 PMCID: PMC5167536 SCOPUS ID: 2-s2.0-84960105545 12/23/2016       9 Citations
  • Methyl-binding DNA capture Sequencing for Patient Tissues. (Jadhav RR, Wang YV, Hsu YT, Liu J, Garcia D, Lai Z, Huang TH, Jin VX) J Vis Exp 2016 Oct 31(116) PMID: 27842364 PMCID: PMC5203769 SCOPUS ID: 2-s2.0-84994632278 11/15/2016       1 Citation
  • Computational Methods and Correlation of Exon-skipping Events with Splicing, Transcription, and Epigenetic Factors. (Wang J, Ye Z, Huang TH, Shi H, Jin VX) Methods Mol Biol 2017;1513:163-170 PMID: 27807836 PMCID: PMC5203767 SCOPUS ID: 2-s2.0-84994204366 11/04/2016       10 Citations
  • EpCAM-Regulated Transcription Exerts Influences on Nanomechanical Properties of Endometrial Cancer Cells That Promote Epithelial-to-Mesenchymal Transition. (Hsu YT, Osmulski P, Wang Y, Huang YW, Liu L, Ruan J, Jin VX, Kirma NB, Gaczynska ME, Huang TH) Cancer Res 2016 Nov 01;76(21):6171-6182 PMID: 27569206 PMCID: PMC5405773 SCOPUS ID: 2-s2.0-84995543447 11/03/2016       43 Citations
  • Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1. (Ye Z, Chen Z, Sunkel B, Frietze S, Huang TH, Wang Q, Jin VX) Nucleic Acids Res 2016 Sep 19;44(16):7540-54 PMID: 27458208 PMCID: PMC5027512 SCOPUS ID: 2-s2.0-84988944828 07/28/2016       11 Citations
  • Genetic suppression reveals DNA repair-independent antagonism between BRCA1 and COBRA1 in mammary gland development. (Nair SJ, Zhang X, Chiang HC, Jahid MJ, Wang Y, Garza P, April C, Salathia N, Banerjee T, Alenazi FS, Ruan J, Fan JB, Parvin JD, Jin VX, Hu Y, Li R) Nat Commun 2016 Mar 04;7:10913 PMID: 26941120 PMCID: PMC4785232 SCOPUS ID: 2-s2.0-84960158445 03/05/2016       17 Citations
  • 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 PMID: 26924343 PMCID: PMC4770430 SCOPUS ID: 2-s2.0-84979970470 03/01/2016       17 Citations
  • Integrative analysis identifies targetable CREB1/FoxA1 transcriptional co-regulation as a predictor of prostate cancer recurrence. (Sunkel B, Wu D, Chen Z, Wang CM, Liu X, Ye Z, Horning AM, Liu J, Mahalingam D, Lopez-Nicora H, Lin CL, Goodfellow PJ, Clinton SK, Jin VX, Chen CL, Huang TH, Wang Q) Nucleic Acids Res 2016 May 19;44(9):4105-22 PMID: 26743006 PMCID: PMC4872073 SCOPUS ID: 2-s2.0-84969832986 01/09/2016       30 Citations
  • Frontiers in Integrative Genomics and Translational Bioinformatics. (Zhao Z, Jin VX, Huang Y, Guda C, Ruan J) Biomed Res Int 2015;2015:725491 PMID: 26605336 PMCID: PMC4641167 SCOPUS ID: 2-s2.0-84947461310 11/26/2015       1 Citation
  • Ligand-dependent genomic function of glucocorticoid receptor in triple-negative breast cancer. (Chen Z, Lan X, Wu D, Sunkel B, Ye Z, Huang J, Liu Z, Clinton SK, Jin VX, Wang Q) Nat Commun 2015 Sep 16;6:8323 PMID: 26374485 PMCID: PMC4573460 SCOPUS ID: 2-s2.0-84941900818 09/17/2015       72 Citations
  • DNA methylation screening of primary prostate tumors identifies SRD5A2 and CYP11A1 as candidate markers for assessing risk of biochemical recurrence. (Horning AM, Awe JA, Wang CM, Liu J, Lai Z, Wang VY, Jadhav RR, Louie AD, Lin CL, Kroczak T, Chen Y, Jin VX, Abboud-Werner SL, Leach RJ, Hernandez J, Thompson IM, Saranchuk J, Drachenberg D, Chen CL, Mai S, Huang TH) Prostate 2015 Nov;75(15):1790-801 PMID: 26332453 SCOPUS ID: 2-s2.0-84942830759 09/04/2015       20 Citations
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  • Agonist and antagonist switch DNA motifs recognized by human androgen receptor in prostate cancer. (Chen Z, Lan X, Thomas-Ahner JM, Wu D, Liu X, Ye Z, Wang L, Sunkel B, Grenade C, Chen J, Zynger DL, Yan PS, Huang J, Nephew KP, Huang TH, Lin S, Clinton SK, Li W, Jin VX, Wang Q) EMBO J 2015 Feb 12;34(4):502-16 PMID: 25535248 PMCID: PMC4331004 SCOPUS ID: 2-s2.0-84923062755 12/24/2014       68 Citations
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  • Three-tiered role of the pioneer factor GATA2 in promoting androgen-dependent gene expression in prostate cancer. (Wu D, Sunkel B, Chen Z, Liu X, Ye Z, Li Q, Grenade C, Ke J, Zhang C, Chen H, Nephew KP, Huang TH, Liu Z, Jin VX, Wang Q) Nucleic Acids Res 2014 Apr;42(6):3607-22 PMID: 24423874 PMCID: PMC3973339 SCOPUS ID: 2-s2.0-84899017831 01/16/2014       101 Citations
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  • Fhit deficiency-induced global genome instability promotes mutation and clonal expansion. (Miuma S, Saldivar JC, Karras JR, Waters CE, Paisie CA, Wang Y, Jin V, Sun J, Druck T, Zhang J, Huebner K) PLoS One 2013;8(11):e80730 PMID: 24244712 PMCID: PMC3828255 SCOPUS ID: 2-s2.0-84893557882 11/19/2013       27 Citations
  • Amplification of distant estrogen response elements deregulates target genes associated with tamoxifen resistance in breast cancer. (Hsu PY, Hsu HK, Lan X, Juan L, Yan PS, Labanowska J, Heerema N, Hsiao TH, Chiu YC, Chen Y, Liu Y, Li L, Li R, Thompson IM, Nephew KP, Sharp ZD, Kirma NB, Jin VX, Huang TH) Cancer Cell 2013 Aug 12;24(2):197-212 PMID: 23948299 PMCID: PMC3890247 SCOPUS ID: 2-s2.0-84881510124 08/21/2013       44 Citations
  • MicroRNA-31 predicts the presence of lymph node metastases and survival in patients with lung adenocarcinoma. (Meng W, Ye Z, Cui R, Perry J, Dedousi-Huebner V, Huebner A, Wang Y, Li B, Volinia S, Nakanishi H, Kim T, Suh SS, Ayers LW, Ross P, Croce CM, Chakravarti A, Jin VX, Lautenschlaeger T) Clin Cancer Res 2013 Oct 01;19(19):5423-33 PMID: 23946296 PMCID: PMC3823052 SCOPUS ID: 2-s2.0-84886420851 08/16/2013       96 Citations
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  • ZBTB33 binds unmethylated regions of the genome associated with actively expressed genes. (Blattler A, Yao L, Wang Y, Ye Z, Jin VX, Farnham PJ) Epigenetics Chromatin 2013 May 21;6(1):13 PMID: 23693142 PMCID: PMC3663758 SCOPUS ID: 2-s2.0-84877877569 05/23/2013       54 Citations
  • Ultra-rare mutation in long-range enhancer predisposes to thyroid carcinoma with high penetrance. (He H, Li W, Wu D, Nagy R, Liyanarachchi S, Akagi K, Jendrzejewski J, Jiao H, Hoag K, Wen B, Srinivas M, Waidyaratne G, Wang R, Wojcicka A, Lattimer IR, Stachlewska E, Czetwertynska M, Dlugosinska J, Gierlikowski W, Ploski R, Krawczyk M, Jazdzewski K, Kere J, Symer DE, Jin V, Wang Q, de la Chapelle A) PLoS One 2013;8(5):e61920 PMID: 23690926 PMCID: PMC3653903 SCOPUS ID: 2-s2.0-84877788249 05/22/2013       37 Citations
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  • Cancer omics: from regulatory networks to clinical outcomes. (Tang B, Hsu PY, Huang TH, Jin VX) Cancer Lett 2013 Nov 01;340(2):277-83 PMID: 23201140 SCOPUS ID: 2-s2.0-84887616313 12/04/2012       9 Citations
  • Hierarchical 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 PMID: 23166858 PMCID: PMC3500769 SCOPUS ID: 2-s2.0-84870799141 11/21/2012       25 Citations
  • A hidden Markov model to identify combinatorial epigenetic regulation patterns for estrogen receptor α target genes. (Bonneville R, Jin VX) Bioinformatics 2013 Jan 01;29(1):22-8 PMID: 23104890 SCOPUS ID: 2-s2.0-84871756139 10/30/2012       8 Citations
  • Canonical and atypical E2Fs regulate the mammalian endocycle. (Chen HZ, Ouseph MM, Li J, Pécot T, Chokshi V, Kent L, Bae S, Byrne M, Duran C, Comstock G, Trikha P, Mair M, Senapati S, Martin CK, Gandhi S, Wilson N, Liu B, Huang YW, Thompson JC, Raman S, Singh S, Leone M, Machiraju R, Huang K, Mo X, Fernandez S, Kalaszczynska I, Wolgemuth DJ, Sicinski P, Huang T, Jin V, Leone G) Nat Cell Biol 2012 Nov;14(11):1192-202 PMID: 23064266 PMCID: PMC3616487 SCOPUS ID: 2-s2.0-84869079592 10/16/2012       119 Citations
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  • Uncovering transcription factor modules using one- and three-dimensional analyses. (Lan X, Farnham PJ, Jin VX) J Biol Chem 2012 Sep 07;287(37):30914-21 PMID: 22952238 PMCID: PMC3438924 SCOPUS ID: 2-s2.0-84866139176 09/07/2012       6 Citations
  • Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3. (Frietze S, Wang R, Yao L, Tak YG, Ye Z, Gaddis M, Witt H, Farnham PJ, Jin VX) Genome Biol 2012 Sep 26;13(9):R52 PMID: 22951069 PMCID: PMC3491396 SCOPUS ID: 2-s2.0-84865773113 09/07/2012       86 Citations
  • Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages. (Lan X, Witt H, Katsumura K, Ye Z, Wang Q, Bresnick EH, Farnham PJ, Jin VX) Nucleic Acids Res 2012 Sep;40(16):7690-704 PMID: 22675074 PMCID: PMC3439894 SCOPUS ID: 2-s2.0-84866120986 06/08/2012       83 Citations
  • Using ChIPMotifs for de novo motif discovery of OCT4 and ZNF263 based on ChIP-based high-throughput experiments. (Kennedy BA, Lan X, Huang TH, Farnham PJ, Jin VX) Methods Mol Biol 2012;802:323-34 PMID: 22130890 PMCID: PMC4160035 SCOPUS ID: 2-s2.0-84555196359 12/02/2011       3 Citations
  • ChIP-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 PMID: 21799915 PMCID: PMC3143154 SCOPUS ID: 2-s2.0-79960745768 07/30/2011       30 Citations
  • High resolution detection and analysis of CpG dinucleotides methylation using MBD-Seq technology. (Lan X, Adams C, Landers M, Dudas M, Krissinger D, Marnellos G, Bonneville R, Xu M, Wang J, Huang TH, Meredith G, Jin VX) PLoS One 2011;6(7):e22226 PMID: 21779396 PMCID: PMC3136941 SCOPUS ID: 2-s2.0-79960115813 07/23/2011       68 Citations
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  • Targeted methylation of two tumor suppressor genes is sufficient to transform mesenchymal stem cells into cancer stem/initiating cells. (Teng IW, Hou PC, Lee KD, Chu PY, Yeh KT, Jin VX, Tseng MJ, Tsai SJ, Chang YS, Wu CS, Sun HS, Tsai KD, Jeng LB, Nephew KP, Huang TH, Hsiao SH, Leu YW) Cancer Res 2011 Jul 01;71(13):4653-63 PMID: 21518779 SCOPUS ID: 2-s2.0-79959868249 04/27/2011       90 Citations
  • Functional analysis of KAP1 genomic recruitment. (Iyengar S, Ivanov AV, Jin VX, Rauscher FJ 3rd, Farnham PJ) Mol Cell Biol 2011 May;31(9):1833-47 PMID: 21343339 PMCID: PMC3133220 SCOPUS ID: 2-s2.0-79955410721 02/24/2011       90 Citations
  • Genome-wide analysis of transcription factor E2F1 mutant proteins reveals that N- and C-terminal protein interaction domains do not participate in targeting E2F1 to the human genome. (Cao AR, Rabinovich R, Xu M, Xu X, Jin VX, Farnham PJ) J Biol Chem 2011 Apr 08;286(14):11985-96 PMID: 21310950 PMCID: PMC3069401 SCOPUS ID: 2-s2.0-79953297708 02/12/2011       42 Citations
  • Epigenetic silencing mediated through activated PI3K/AKT signaling in breast cancer. (Zuo T, Liu TM, Lan X, Weng YI, Shen R, Gu F, Huang YW, Liyanarachchi S, Deatherage DE, Hsu PY, Taslim C, Ramaswamy B, Shapiro CL, Lin HJ, Cheng AS, Jin VX, Huang TH) Cancer Res 2011 Mar 01;71(5):1752-62 PMID: 21216892 PMCID: PMC3048165 SCOPUS ID: 2-s2.0-79952241034 01/11/2011       52 Citations
  • ZNF274 recruits the histone methyltransferase SETDB1 to the 3' ends of ZNF genes. (Frietze S, O'Geen H, Blahnik KR, Jin VX, Farnham PJ) PLoS One 2010 Dec 08;5(12):e15082 PMID: 21170338 PMCID: PMC2999557 SCOPUS ID: 2-s2.0-78650081714 12/21/2010       120 Citations
  • Inference 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 PMID: 21167036 PMCID: PMC3012048 SCOPUS ID: 2-s2.0-78650116700 12/21/2010       41 Citations
  • W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data. (Lan X, Bonneville R, Apostolos J, Wu W, Jin VX) Bioinformatics 2011 Feb 01;27(3):428-30 PMID: 21138948 PMCID: PMC3031039 SCOPUS ID: 2-s2.0-79551590211 12/09/2010       45 Citations
  • An improved profile-level domain linker propensity index for protein domain boundary prediction. (Zhang Y, Liu B, Dong Q, Jin VX) Protein Pept Lett 2011 Jan;18(1):7-16 PMID: 20955175 SCOPUS ID: 2-s2.0-78751536327 10/20/2010       15 Citations
  • DNA methylation of the Trip10 promoter accelerates mesenchymal stem cell lineage determination. (Hsiao SH, Lee KD, Hsu CC, Tseng MJ, Jin VX, Sun WS, Hung YC, Yeh KT, Yan PS, Lai YY, Sun HS, Lu YJ, Chang YS, Tsai SJ, Huang TH, Leu YW) Biochem Biophys Res Commun 2010 Sep 24;400(3):305-12 PMID: 20727853 SCOPUS ID: 2-s2.0-77956901192 08/24/2010       46 Citations
  • Multivalent epigenetic marks confer microenvironment-responsive epigenetic plasticity to ovarian cancer cells. (Bapat SA, Jin V, Berry N, Balch C, Sharma N, Kurrey N, Zhang S, Fang F, Lan X, Li M, Kennedy B, Bigsby RM, Huang TH, Nephew KP) Epigenetics 2010;5(8):716-29 PMID: 20676026 PMCID: PMC3052886 SCOPUS ID: 2-s2.0-78449231269 08/03/2010       41 Citations
  • Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263. (Frietze S, Lan X, Jin VX, Farnham PJ) J Biol Chem 2010 Jan 08;285(2):1393-403 PMID: 19887448 PMCID: PMC2801265 SCOPUS ID: 2-s2.0-74049139555 11/06/2009       81 Citations
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  • Epigenetic changes during disease progression in a murine model of human chronic lymphocytic leukemia. (Chen SS, Raval A, Johnson AJ, Hertlein E, Liu TH, Jin VX, Sherman MH, Liu SJ, Dawson DW, Williams KE, Lanasa M, Liyanarachchi S, Lin TS, Marcucci G, Pekarsky Y, Davuluri R, Croce CM, Guttridge DC, Teitell MA, Byrd JC, Plass C) Proc Natl Acad Sci U S A 2009 Aug 11;106(32):13433-8 PMID: 19666576 PMCID: PMC2726368 SCOPUS ID: 2-s2.0-69449100327 08/12/2009       76 Citations
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  • E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites. (Rabinovich A, Jin VX, Rabinovich R, Xu X, Farnham PJ) Genome Res 2008 Nov;18(11):1763-77 PMID: 18836037 PMCID: PMC2577861 SCOPUS ID: 2-s2.0-55549103719 10/07/2008       111 Citations
  • A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members. (Xu X, Bieda M, Jin VX, Rabinovich A, Oberley MJ, Green R, Farnham PJ) Genome Res 2007 Nov;17(11):1550-61 PMID: 17908821 PMCID: PMC2045138 SCOPUS ID: 2-s2.0-35949000033 10/03/2007       177 Citations
  • Frequent epigenetic inactivation of secreted frizzled-related protein 2 (SFRP2) by promoter methylation in human gastric cancer. (Cheng YY, Yu J, Wong YP, Man EP, To KF, Jin VX, Li J, Tao Q, Sung JJ, Chan FK, Leung WK) Br J Cancer 2007 Oct 08;97(7):895-901 PMID: 17848950 PMCID: PMC2360406 SCOPUS ID: 2-s2.0-34948898013 09/13/2007       116 Citations
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  • Identification of genes directly regulated by the oncogene ZNF217 using chromatin immunoprecipitation (ChIP)-chip assays. (Krig SR, Jin VX, Bieda MC, O'Geen H, Yaswen P, Green R, Farnham PJ) J Biol Chem 2007 Mar 30;282(13):9703-9712 PMID: 17259635 PMCID: PMC2269729 SCOPUS ID: 2-s2.0-34248198548 01/30/2007       70 Citations
  • Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. (Elnitski L, Jin VX, Farnham PJ, Jones SJ) Genome Res 2006 Dec;16(12):1455-64 PMID: 17053094 SCOPUS ID: 2-s2.0-33845341455 10/21/2006       184 Citations
  • A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1. (Jin VX, Rabinovich A, Squazzo SL, Green R, Farnham PJ) Genome Res 2006 Dec;16(12):1585-95 PMID: 17053090 PMCID: PMC1665642 SCOPUS ID: 2-s2.0-33845290262 10/21/2006       58 Citations
  • A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha. (Li L, Cheng AS, Jin VX, Paik HH, Fan M, Li X, Zhang W, Robarge J, Balch C, Davuluri RV, Kim S, Huang TH, Nephew KP) Bioinformatics 2006 Sep 15;22(18):2210-6 PMID: 16809387 SCOPUS ID: 2-s2.0-33748692896 07/01/2006       12 Citations
  • Suz12 binds to silenced regions of the genome in a cell-type-specific manner. (Squazzo SL, O'Geen H, Komashko VM, Krig SR, Jin VX, Jang SW, Margueron R, Reinberg D, Green R, Farnham PJ) Genome Res 2006 Jul;16(7):890-900 PMID: 16751344 PMCID: PMC1484456 SCOPUS ID: 2-s2.0-33745604636 06/06/2006       272 Citations
  • Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs. (Jin VX, Singer GA, Agosto-Pérez FJ, Liyanarachchi S, Davuluri RV) BMC Bioinformatics 2006 Mar 07;7:114 PMID: 16522199 PMCID: PMC1475891 SCOPUS ID: 2-s2.0-33847173310 03/09/2006       61 Citations
  • Combinatorial analysis of transcription factor partners reveals recruitment of c-MYC to estrogen receptor-alpha responsive promoters. (Cheng AS, Jin VX, Fan M, Smith LT, Liyanarachchi S, Yan PS, Leu YW, Chan MW, Plass C, Nephew KP, Davuluri RV, Huang TH) Mol Cell 2006 Feb 03;21(3):393-404 PMID: 16455494 SCOPUS ID: 2-s2.0-31544465230 02/04/2006       153 Citations
  • MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data. (Sun H, Palaniswamy SK, Pohar TT, Jin VX, Huang TH, Davuluri RV) Nucleic Acids Res 2006 Jan 01;34(Database issue):D98-103 PMID: 16381984 PMCID: PMC1347458 SCOPUS ID: 2-s2.0-33644878173 12/31/2005       35 Citations
  • ERTargetDB: an integral information resource of transcription regulation of estrogen receptor target genes. (Jin VX, Sun H, Pohar TT, Liyanarachchi S, Palaniswamy SK, Huang TH, Davuluri RV) J Mol Endocrinol 2005 Oct;35(2):225-30 PMID: 16216904 SCOPUS ID: 2-s2.0-27644480473 10/12/2005       25 Citations
  • Identifying estrogen receptor alpha target genes using integrated computational genomics and chromatin immunoprecipitation microarray. (Jin VX, Leu YW, Liyanarachchi S, Sun H, Fan M, Nephew KP, Huang TH, Davuluri RV) Nucleic Acids Res 2004;32(22):6627-35 PMID: 15608294 PMCID: PMC545447 SCOPUS ID: 2-s2.0-13544265659 12/21/2004       63 Citations
  • Loss of estrogen receptor signaling triggers epigenetic silencing of downstream targets in breast cancer. (Leu YW, Yan PS, Fan M, Jin VX, Liu JC, Curran EM, Welshons WV, Wei SH, Davuluri RV, Plass C, Nephew KP, Huang TH) Cancer Res 2004 Nov 15;64(22):8184-92 PMID: 15548683 SCOPUS ID: 2-s2.0-8544226964 11/19/2004       172 Citations
  • OMGProm: a database of orthologous mammalian gene promoters. (Palaniswamy SK, Jin VX, Sun H, Davuluri RV) Bioinformatics 2005 Mar;21(6):835-6 PMID: 15531605 SCOPUS ID: 2-s2.0-15944411332 11/09/2004       17 Citations
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