Department of Molecular Medicine
 

Jin, Victor Xinhua, Ph.D Victor  X. JinPh.D.

Associate Professor


Profile and Contact Information | Research | Laboratory


RESEARCH

 

Research Program

The main focus in our lab is on two aspects: 1) Computational Biology: to apply machine learning algorithms and statistical methods to decipher the transcriptional regulatory codes in eukaryotic genomes. By working closely with bench-scientists, specifically, we will a) identify functional elements in mammalian genomes using the ChIP-seq, MBD-seq, Hi-C and RNA-seq technologies; b) construct transcriptional regulatory networks from gene expression, protein-DNA interaction and protein-protein interaction data; and c) understand genetic/epigenetic regulatory mechanisms in cancers and cancer stem cells. Our investigation will not only fundamentally contribute to the understanding of genome/chromatin organization as well as gene/epigenetic regulation mechanisms, but also provide new approaches to the treatment of cancers. 2) Translational Bioinformatics: to develop computational pipelines to aid molecular biomarker discovery. We will utilize existing software tools developed in my lab and other labs for processing various disease related ‘omics data such as ChIP-seq, RNA-seq, miRNA-seq, Hi-C and MBD-seq and integrate them into an interactive and integrated platform. The predicted genes (loci) are further correlated with disease related gene signatures and performed for experimental validations in patient samples. One of the major applications will be cancers such as breast cancer, prostate cancer and lung cancer.

 

Selected Publications

  1. Zhang X, Chiang H-C, Wang Y, Zhang C, Smith S, Zhao X, Nair S, Michalek J, Jatoi J, Lautner M, Oliver B, Wang H, Petit A, Soler T, Brunet J, Mateo F, Pujana MA, Poggi E, Chaldekas K, Isaacs C, Peshkin BN, Ochoa O, Chedin F, Theoharis C, Sun L-Z, Curiel TJ, Elledge R, Jin VX*, Hu, Y*, Li R*. (2017) Attenuation of RNA Polymerase II Pausing Mitigates BRCA1-Associated R-loop Accumulation and Tumorigenesis. Nat Commun. In press. (*co-corresponding authors).

  2. Hsu YT, Osmulski P, Wang Y, Huang YW, Liu L, Ruan J, Jin VX, Kirma NB, Gaczynska ME, Huang TH. EpCAM-Regulated Transcription Exerts Influences on Nanomechanical Properties of Endometrial Cancer Cells that Promote Epithelial-to-Mesenchymal Transition. Cancer Res. 2016 Aug 28. pii: canres.0752.2016. [Epub ahead of print] PMID: 27569206

  3. Ye Z, Chen Z, Sunkel B, Frietze S, Huang TH, Wang Q, Jin VX. Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1. Nucleic Acids Res. 2016 Sep 19;44(16):7540-54. doi: 10.1093/nar/gkw659. Epub 2016 Jul 25. PMID: 27458208

  4. 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. Genetic suppression reveals DNA repair-independent antagonism between BRCA1 and COBRA1 in mammary gland development. Nat Commun. 2016 Mar 4;7:10913. doi: 10.1038/ncomms10913. PMID: 26941120

  5. Wang Y, Jadhav RR, Liu J, Wilson D, Chen Y, Thompson IM, Troyer DA, Hernandez J, Shi H, Leach RJ, Huang TH, Jin VX. Roles of Distal and Genic Methylation in the Development of Prostate Tumorigenesis Revealed by Genome-wide DNA Methylation Analysis. Sci Rep. 2016 Feb 29;6:22051. doi: 10.1038/srep22051. PMID: 26924343

  6. 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. Integrative analysis identifies targetable CREB1/FoxA1 transcriptional co-regulation as a predictor of prostate cancer recurrence. Nucleic Acids Res. 2016 May 19;44(9):4105-22. doi: 10.1093/nar/gkv1528. Epub 2016 Jan 6. PMID: 26743006

  7. Zhao Z, Jin VX, Huang Y, Guda C, Ruan J. Frontiers in Integrative Genomics and Translational Bioinformatics. Biomed Res Int. 2015;2015:725491. doi: 10.1155/2015/725491. Epub 2015 Oct 28. No abstract available. PMID: 26605336

  8. Chen Z, Lan X, Wu D, Sunkel B, Ye Z, Huang J, Liu Z, Clinton SK, Jin VX, Wang Q. Ligand-dependent genomic function of glucocorticoid receptor in triple-negative breast cancer. Nat Commun. 2015 Sep 16;6:8323. doi: 10.1038/ncomms9323. PMID: 26374485

  9. Cui R, Meng W, Sun HL, Kim T, Ye Z, Fassan M, Jeon YJ, Li B, Vicentini C, Peng Y, Lee TJ, Luo Z, Liu L, Xu D, Tili E, Jin V.X., Middleton J, Chakravarti A, Lautenschlaeger T, Croce CM. MicroRNA-224 promotes tumor progression in nonsmall cell lung cancer. Proc Natl Acad Sci U S A. 2015 Jul 17. pii: 201502068. [Epub ahead of print]

  10. Ruan J, Jin V.X., Huang Y, Xu H, Edwards JS, Chen Y, Zhao Z. Education, collaboration, and innovation: intelligent biology and medicine in the era of big data. BMC Genomics. 2015;16 Suppl 7:S1.

  11. He H, Li W, Liyanarachchi S, Srinivas M, Wang Y, Akagi K, Wang Y, Wu D, Wang Q, Jin V.X., Symer DE, Shen R, Phay J, Nagy R, de la Chapelle A. Multiple functional variants in long-range enhancer elements contribute to the risk of SNP rs965513 in thyroid cancer. Proc Natl Acad Sci U S A. 2015 May 12;112(19):6128-33.

  12. Wang J, Ye Z, Huang TH, Shi H, Jin V.X.. A survey of computational methods in transcriptome-wide alternative splicing analysis. Biomol Concepts. 2015 Mar;6(1):59-66.

  13. Jadhav RR, Ye Z, Huang RL, Liu J, Hsu PY, Huang YW, Rangel LB, Lai HC, Roa JC, Kirma NB, Huang TH, Jin V.X.. Genome-wide DNA methylation analysis reveals estrogen-mediated epigenetic repression of metallothionein-1 gene cluster in breast cancer. Clin Epigenetics. 2015 Feb 24;7(1):13.

  14. 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 V.X., Wang Q. Agonist and antagonist switch DNA motifs recognized by human androgen receptor in prostate cancer. EMBO J. 2015 Feb 12;34(4):502-16

  15. 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 V.X., Wang Q. Three-tiered role of the pioneer factor GATA2 in promoting androgen-dependent gene expression in prostate cancer. Nucleic Acids Res. 2014 Apr;42(6):3607-22.

  16. Ye Z, Chen Z, Lan X, Hara S, Sunkel B, Huang TH, Elnitski L, Wang Q, Jin V.X.. Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors. Nucleic Acids Res. 2014 Mar;42(5):2856-69.

  17. “A Hidden Markov Model to Identify Combinatorial Epigenetic Regulation Patterns for Estrogen Receptor α Target Genes” Bonneville, R. and Jin, V.X.* Bioinformatics, 29, 22-28 (2013).

  18. “Genome-wide analysis uncovers high frequency and strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation” Wang, J.#,*, Lan, X.#, Hsu, P.-Y., Huang, K., Parvin, J., Huang, T.H.-M., and Jin, V.X.* BMC Genomics, 14:70 (2013).
  19. “Cancer ‘omics: from regulatory networks to clinical outcomes” Tang, B., Hsu, P.-H., Huang, T.M. and Jin, V.X.* Cancer Letters (Invited review), 340:277-83 (2013).

  20. “Ultra-rare mutation in long-range enhancer predisposes to thyroid carcinoma with high penetrance: the “common disease-rare mutation” concept” 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., Stachlewska, E., Czetwertynska, M., Dlugosinska, J., Dymecka, K., Ploski, R., Krawczyk, M., Jazdzewski, K., Kere, J., Symer, D.E., Jin, V.X., Wang, Q., and de la Chapelle, A. PLoS ONE, 8:e61920 (2013).

  21. “ZBTB33 binds unmethylated regions of the genome associated with actively expressed genes”, Blattler, A., Yao, L., Wang, Y., Ye, Z., Jin, V.X., and Farnham, P.J. Epigenetics and Chromatin, 6:13 (2013).

  22. “Locate Non-unique matched tags (LONUT) to improve the detection of enriched regions for ChIP-seq and MBD-seq data” Wang, R., Hsu, H.-K., Blattler A., Wang, Y., Lan, X., Hsu, P.-Y., Huang, T.-H.M., Farnham, P.J. and Jin, V.X.* PLoS ONE, 8:e67788 (2013).

  23. “Amplification of Distant Estrogen Response Elements Deregulates Target Genes Associated with Tamoxifen Resistance in Breast Cancer” Hsu, P.-Y., Hsu, H.-K.., Lan, X., Juan, L., Yan, P.S., Labanowska, J., Heerema, N., Hsia, T.-H., Chiu, Y.-C., Chen, Y., Liu, Y., Li, L., Li, R., Thompson I.M., Nephew, K.P., Sharp, Z.D., Kirma, N.B., Jin, V.X., and Huang, T.H.-M. Cancer Cell, 24:197-212 (2013).

  24. “MicroRNA-31 predicts the presence of lymph node metastases and survival in lung adenocarcinoma patients” Meng, W., Ye, Z., Cui, R., Perry, J., Dedousi-Huebner, V.,  Huebner, A., Wang, Y., Li, B., Volinia, S., Nakanishi, H., Kim, T., Suh, S.-S., Ayers, L.W., Ross, P., Croce, C.M., Chakravarti, A., Jin, V.X.*, and Lautenschlaeger, T.* Clinical Cancer Research, 19:5423-33 (2013).

  25. “A quantitative method to identify distinct binding patterns for two biological related ChIP-seq samples” Liu, B., Yi, J., Lan, X., Ma, Y., Huang, T.H.-M., Leone, G. and Jin, V.X.* BMC Genomics, 14 (Suppl 8):S3 (2013).

  26. “Fhit Deficiency-Induced Global Genome Instability Promotes Mutation and Clonal Expansion” Miuma, S., Saldivar, J.C., Karras, J.R., Waters, C.E., Paisie, C.A., Wang, Y., Jin, V.X., Sun, J., Druck, T., Zhang, J., Huebner, K.. PLoS ONE, 8:e80730 (2013).

  27. “Summary of talks and papers at ISCB-Asia/SCCG 2012”, Tretyakov, K., Goldberg, T., Jin, V.X. and Horton, P. BMC Genomics, 14 (Suppl. 2), I1 (2013).

  28. “Loss of estrogen signaling triggers epigenetic silencing of its downstream targets in breast cancer” Leu, Y-W, Yan, P. S., Fan, M., Jin, V.X., Liu, J.C., Curran, E.M., Welshons, W.V., Wei,P .S.H., Davuluri, R.V., Plass, C., Nephew, K.P. and Huang, T.H.-M. Cancer Res., 64, 8184-8192 (2004). PMID: 15548683.

  29. “Identifying estrogen receptor α target genes using integrated computational genomics and chromatin immunoprecipitation microarray” Jin, V.X.,  Leu, Y.-W., Liyanarachchi, S., Sun, H., Huang T.H-M. and Davuluri, R.V. Nucleic Acid Res. 32, 6627-6635 (2004). PMID: 15608294.

  30. “ERTargetDB: an integral information resource of transcription regulation of ER target genes” Jin, V.X., Sun, H., Pohar, T.T., Liyanarachchi, S., Palaniswamy, S.K., Huang T.H-M. and Davuluri, R.V. Journal of Molecular Endocrinology 35, 225-230 (2005). PMID: 16216904.

  31. “Combinatorial Analysis of Transcription Factor Partners Reveals Recruitment of c-MYC to ERα-Responsive Promoters” Cheng, A.S., Jin, V.X., Yan, P.S., Fan, M., Leu, Y.W, Chan, M.W., Plass, C., Nephew, K.P., Davuluri, R.V. and Huang, T.H.-M. Molecular Cell 21, 393-404 (2006). PMID: 16455494.

  32. “Locating Mammalian Transcription Factor Binding Sites: A Survey of Computational and Experimental Techniques” Elnitski, L., Jin, V.X., Farnham, P.J. and Jones, S.J.M. P Genome Research (Review), 16, 1455-1464 (2006). PMID: 17053094.

  33. “A computational genomics approach to identify cis-regulatory modules for chromatin immunoprecipitation microarray data – a case study using E2F1 in cancers” Jin, V.X., Rabinovich, A., Squazzo, S.L., Green, R. and Farnham, P.J. Genome Research, 16, 1585-1595 (2006). PMID: 17053090.

  34. “Identification of genes directly regulated by the oncogene ZNF217 using ChIP-chip assays” Krig, S, Jin, V.X. (Co-1st), Bieda, M., O’Geen, H., Green, R. and Farnham, P.J. Journal of Biological Chemistry, 282, 9703-9712 (2007). PMID: 17259635.

  35. “Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches” Jin, V.X., O’Geen, H., Iyengar, S. Green, R. and Farnham, P.J. Genome Research, 17, 807-817 (2007) (ENCODE issue). PMID: 17567999.

  36. “N-Myc regulates a widespread euchromatic program in the human genome partially independent of its role as a classical transcription factor” Cotterman, R., Jin, V.X. (Co-1st), Krig, S., Lemen, J., Wey, A., Farnham, P.J. and Knoepfler., P. Cancer Research 68, 9654-9662 (2008). PMID: 19047142.

  37. “Epigenetic Changes During Disease Progression in a Murine Model of Human Chronic Lymphocytic Leukemia” Chen, S.-S., Raval, A., Johnson, A.J., Hertlein, E., Liu, T.-H., Jin, V.X., Sherman, M., Liu, S., Dawson, D.W., Williams, K.E., Lanasa, M., Liyanarachchi, S., Lin, T.S., Marcucci, G., Pekarsky, Y., Davuluri, R.V., Croce, C.M., Guttridge, D.C., Teitell, M.A., Byrd, J.C. and Plass, C. PNAS. 106, 13433-13438 (2009). PMID: 19666576.

  38. “W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high throughput data” Jin, V.X.*, Apostolos, J., Nagisetty, N.S.V., Farnham, P.J. Bioinformatics, 25, 3191-3193 (2009).  PMID: 19797408.

  39. “HRTBLDb: an informative data resource for Hormone Receptors Target Binding Loci” Kennedy, B., Gao, W., Huang, T.H.-M., Jin, V.X*. Nucleic Acids Res. 38, D676-D681 (2010). PMID: 19773424.

  40. “W-ChIPeaks: a comprehensive web application tool to process ChIP-chip and ChIP-seq data” Lan, X., Bonneville, R., Apostolos, J., Wang, W. and Jin, V.X.* Bioinformatics, 27, 428-430 (2011). PMID: 21138948.

  41. “Inference of hierarchal regulatory network of estrogen-dependent breast cancer through ChIP-based data” Gu, F., Wu, J., Parvin, J., Huang, T.H-M., Jin, V.X.* BMC Systems Biology, 4, 170 (2010). PMID: 21167036.

  42. “Epigenetic silencing mediated through activated PI3K/AKT signaling in breast cancer” Zuo, T., Liu, T.-M., Lan, X., Weng, Y.-I., Shen, R., Gu, F., Huang, Y.W., Liyanarachchi, S., Deatherage, D.E., Hsu, P.Y., Taslim, C., Ramaswamy, B., Shapiro, C.L., Lin, H.J., Cheng, A.S.L., Jin, V.X. and Huang, TH-M.  Cancer Research, 71, 1752-1762 (2011). PMID: 21216892.

  43. “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, T.H.-M., Meredith, G., and Jin, V.X.* PLoS One, 6, e22226 (2011). PMID: 21779396.

  44. “ChIP-seq defined genome-wide map of TGFβ/SMAD4 targets: implications with clinical outcome of ovarian cancer” Kennedy, B.A., Deatherage, D.E., Gu, F., Tang, B., Chan, M.W.Y., Nephew, K.P., Huang, T.H.-M. and Jin, V.X.* PLoS ONE, 6, e22606 (2011). PMID: 21799915.  

  45. “Integration of Hi-C and ChIP-seq data reveals the distinct types of transcriptional chromatin linkages” Lan, X., Witt, H., Katsumura, K., Ye, Z., Wang, Q., Huang, T.H.-M., Bresnick, E.H., Farnham, P.J.* and Jin, V.X.* Nucleic Acids Res., 40, 7690-7704 (2012). PMID: 22675074. ENCODE companion paper.

  46. “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, Y.G., Ye, Z., Gaddis, M., Witt, H., Farnham, P.J.* and Jin, V.X.* Genome Biology, 13, R52 (2012). PMID: 22951069. ENCODE companion paper.

  47. “Uncovering transcription factor modules using one-dimensional and three-dimensional analyses” Lan, X., Farnham, P.J. and Jin, V.X.* J. Biol. Chem., (Invited Review), 287, 30914-21 (2012). PMID: 22952238. ENCODE companion paper.

  48. “An integrated encyclopedia of DNA elements in the human genome” The ENCODE Project Consortium, Nature, 489, 57-74 (2012). PMID: 22955616.     

  49. “Atypical E2Fs Link Mammalian Endocycle Control to Cancer” Chen*, H.-Z., Ouseph,* M.M., Li, J., Pécot, T., Liu, B., Chokshi, V., Byrne, M., Duran, C., Comstock, G.,  Martin, C.K., Trikha, P., Senapati, S., Huang, Y.-W.,  Gandhi, S., Wilson, N., Thompson, J.C., Raman, S., Singh, S., Leone, M., Machiraju, R., Huang, K., Mo, X., Fernandez, S., Wolgemuth, D.J., Sicinski, P., Huang, T.H.-M., Jin, V.X.  and Leone, G. Nature Cell Biology, 14, 1192-1202 (2012). PMID: 23064266.

  50. “A Hidden Markov Model to Identify Combinatorial Epigenetic Regulation Patterns for Estrogen Receptor α Target Genes” Bonneville, R. and Jin, V.X.* Bioinformatics, 29, 22-28 (2013). PMID: 23104890.

  51. “Genome-wide analysis uncovers high frequency and strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation” Wang, J.#,*, Lan, X.#, Hsu, P.-Y., Huang, K., Parvin, J., Huang, T.H.-M., and Jin, V.X.* BMC Genomics, 14:70 (2013). PMID: 23368971.

  52. “Locate Non-unique matched tags (LONUT) to improve the detection of enriched regions for ChIP-seq and MBD-seq data” Wang, R., Hsu, H.-K., Blattler A., Wang, Y., Lan, X., Hsu, P.-Y., Huang, T.-H.M., Farnham, P.J. and Jin, V.X.* PLoS ONE, 8:e67788 (2013). PMID: 23825685.

  53. “Amplification of Distant Estrogen Response Elements Deregulates Target Genes Associated with Tamoxifen Resistance in Breast Cancer” Hsu, P.-Y., Hsu, H.-K.., Lan, X., Juan, L., Yan, P.S., Labanowska, J., Heerema, N., Hsia, T.-H., Chiu, Y.-C., Chen, Y., Liu, Y., Li, L., Li, R., Thompson I.M., Nephew, K.P., Sharp, Z.D., Kirma, N.B., Jin, V.X., and Huang, T.H.-M. Cancer Cell, 24:197-212 (2013). PMID: 23948299.

  54. “MicroRNA-31 predicts the presence of lymph node metastases and survival in lung adenocarcinoma patients” Meng, W., Ye, Z., Cui, R., Perry, J., Dedousi-Huebner, V.,  Huebner, A., Wang, Y., Li, B., Volinia, S., Nakanishi, H., Kim, T., Suh, S.-S., Ayers, L.W., Ross, P., Croce, C.M., Chakravarti, A., Jin, V.X.*, and Lautenschlaeger, T.* Clinical Cancer Research, 19:5423-33 (2013). PMID: 23946296.