Tim H M Huang

Summary

Affiliation: The Ohio State University
Country: USA

Publications

  1. pmc Identifying estrogen receptor alpha target genes using integrated computational genomics and chromatin immunoprecipitation microarray
    Victor X Jin
    Human Cancer Genetics Program, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA
    Nucleic Acids Res 32:6627-35. 2004
  2. pmc A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data
    Zhi Han
    College of Software, Nankai University, Tianjin, China
    BMC Bioinformatics 13:S2. 2012
  3. pmc Functional characterization of Trip10 in cancer cell growth and survival
    Chia Chen Hsu
    Human Epigenomics Center, Department of Life Science, Institute of Molecular Biology and Institute of Biomedical Science, National Chung Cheng University, Chia Yi, Taiwan
    J Biomed Sci 18:12. 2011
  4. pmc Identification of novel DNA methylation inhibitors via a two-component reporter gene system
    Yi Shiuan Lin
    Human Epigenomics Center, Department of Life Science, Institute of Molecular Biology, National Chung Cheng University, Chia Yi, 621, Taiwan
    J Biomed Sci 18:3. 2011
  5. pmc Preprocessing differential methylation hybridization microarray data
    Shuying Sun
    Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, 44106, USA
    BioData Min 4:13. 2011
  6. pmc A modulated empirical Bayes model for identifying topological and temporal estrogen receptor α regulatory networks in breast cancer
    Changyu Shen
    Center for Computational Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    BMC Syst Biol 5:67. 2011
  7. pmc An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules
    Huaxia Qin
    Human Cancer Genetics Program, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA
    BMC Syst Biol 3:73. 2009
  8. pmc An empirical Bayes model for gene expression and methylation profiles in antiestrogen resistant breast cancer
    Jaesik Jeong
    Department of Medicine Division of Biostatistics, Indiana University, Indianapolis, IN, USA
    BMC Med Genomics 3:55. 2010
  9. pmc Integrated analysis of DNA methylation and gene expression reveals specific signaling pathways associated with platinum resistance in ovarian cancer
    Meng Li
    Medical Sciences, Indiana University School of Medicine, Bloomington, IN 47405, USA
    BMC Med Genomics 2:34. 2009
  10. pmc A Poisson mixture model to identify changes in RNA polymerase II binding quantity using high-throughput sequencing technology
    Weixing Feng
    Division of Biostatistics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    BMC Genomics 9:S23. 2008

Collaborators

Detail Information

Publications81

  1. pmc Identifying estrogen receptor alpha target genes using integrated computational genomics and chromatin immunoprecipitation microarray
    Victor X Jin
    Human Cancer Genetics Program, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA
    Nucleic Acids Res 32:6627-35. 2004
    ..This integrated approach, therefore, sets a paradigm in which the iterative process of model refinement and experimental verification will continue until an accurate prediction of promoter target sequences is derived...
  2. pmc A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data
    Zhi Han
    College of Software, Nankai University, Tianjin, China
    BMC Bioinformatics 13:S2. 2012
    ..However, since PolII enriched regions in the genome can be very long, existing peak finding algorithms for ChIP-seq data are not adequate for identifying such long regions...
  3. pmc Functional characterization of Trip10 in cancer cell growth and survival
    Chia Chen Hsu
    Human Epigenomics Center, Department of Life Science, Institute of Molecular Biology and Institute of Biomedical Science, National Chung Cheng University, Chia Yi, Taiwan
    J Biomed Sci 18:12. 2011
    ..To test this hypothesis and evaluate whether Trip10 is epigenetically regulated by DNA methylation in other cancers, we evaluated DNA methylation of Trip10 in liver cancer, brain tumor, ovarian cancer, and breast cancer...
  4. pmc Identification of novel DNA methylation inhibitors via a two-component reporter gene system
    Yi Shiuan Lin
    Human Epigenomics Center, Department of Life Science, Institute of Molecular Biology, National Chung Cheng University, Chia Yi, 621, Taiwan
    J Biomed Sci 18:3. 2011
    ..Thus, our laboratories have embarked on the pharmacological exploitation of procainamide to develop potent DNA methylation inhibitors through lead optimization...
  5. pmc Preprocessing differential methylation hybridization microarray data
    Shuying Sun
    Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, 44106, USA
    BioData Min 4:13. 2011
    ..abstract:..
  6. pmc A modulated empirical Bayes model for identifying topological and temporal estrogen receptor α regulatory networks in breast cancer
    Changyu Shen
    Center for Computational Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    BMC Syst Biol 5:67. 2011
    ..Dynamic gene expression changes have been shown to characterize the breast cancer cell response to estrogens, the every molecular mechanism of which is still not well understood...
  7. pmc An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules
    Huaxia Qin
    Human Cancer Genetics Program, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA
    BMC Syst Biol 3:73. 2009
    ..The regulatory effect of SMAD complex likely depends on transcriptional modules, in which the SMAD binding elements and partner transcription factor binding sites (SMAD modules) are present in specific context...
  8. pmc An empirical Bayes model for gene expression and methylation profiles in antiestrogen resistant breast cancer
    Jaesik Jeong
    Department of Medicine Division of Biostatistics, Indiana University, Indianapolis, IN, USA
    BMC Med Genomics 3:55. 2010
    ....
  9. pmc Integrated analysis of DNA methylation and gene expression reveals specific signaling pathways associated with platinum resistance in ovarian cancer
    Meng Li
    Medical Sciences, Indiana University School of Medicine, Bloomington, IN 47405, USA
    BMC Med Genomics 2:34. 2009
    ..Finally, our results suggest that epigenetic therapies may facilitate the prevention or reversal of transcriptional repression responsible for chemoresistance and the restoration of sensitivity to platinum-based chemotherapeutics...
  10. pmc A Poisson mixture model to identify changes in RNA polymerase II binding quantity using high-throughput sequencing technology
    Weixing Feng
    Division of Biostatistics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    BMC Genomics 9:S23. 2008
    ..However, only approximately 0.7% (172) genes displayed significant Pol II binding changes in E2-treated antiestrogen-resistant cells. These results show that a Poisson mixture model can be used to analyze ChIP-seq data...
  11. pmc Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array
    Gregory A C Singer
    Human Cancer Genetics Program, Comprehensive Cancer Center, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH, USA
    BMC Genomics 9:349. 2008
    ..Understanding which promoter is employed in which cellular context is required to unravel gene regulatory networks within the cell...
  12. pmc STAT3 can be activated through paracrine signaling in breast epithelial cells
    Jacqueline C Lieblein
    Department of Pediatrics, The Ohio State University, Columbus, USA
    BMC Cancer 8:302. 2008
    ..However, whether the tumor microenvironment plays a role in this activation is still poorly understood...
  13. pmc Identifying hypermethylated CpG islands using a quantile regression model
    Shuying Sun
    Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
    BMC Bioinformatics 12:54. 2011
    ..However, we were unsure whether 75% was the best quantile level for identifying hypermethylated CGIs. In this paper, we attempt to determine which quantile level should be used to identify hypermethylated CGIs and their associated genes...
  14. pmc Identifying differentially methylated genes using mixed effect and generalized least square models
    Shuying Sun
    Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio 44106, USA
    BMC Bioinformatics 10:404. 2009
    ..However, patient samples or cell lines are heterogeneous, so their methylation pattern may be very different. In addition, neighboring probes at each CGI are correlated. How these factors affect the analysis of DMH data is unknown...
  15. pmc Cancer epigenetics: a perspective on the role of DNA methylation in acquired endocrine resistance
    Michael P Trimarchi
    Human Cancer Genetics Program, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, Ohio 43210, USA
    Chin J Cancer 30:749-56. 2011
    ....
  16. pmc Chromatin remodeling in mammary gland differentiation and breast tumorigenesis
    Tim H M Huang
    Human Cancer Genetics Program, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, Ohio 43220, USA
    Cold Spring Harb Perspect Biol 2:a004515. 2010
    ..Here we further discuss interactions between DNA methylation and histone modifications that have significant contributions to the differentiation of mammary stem/progenitor cells and to tumor initiation and progression...
  17. pmc Methods in DNA methylation profiling
    Tao Zuo
    Division of Human Cancer Genetics, Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
    Epigenomics 1:331-45. 2009
    ....
  18. pmc Epigenetic silencing mediated through activated PI3K/AKT signaling in breast cancer
    Tao Zuo
    Human Cancer Genetics Program, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA
    Cancer Res 71:1752-62. 2011
    ..These combined treatments synergistically relieve gene silencing and suppress cancer cell growth in vitro and in xenografts. The new finding has important implications for improving targeted cancer therapies in the future...
  19. pmc Estrogen-mediated epigenetic repression of the imprinted gene cyclin-dependent kinase inhibitor 1C in breast cancer cells
    Benjamin A T Rodriguez
    Human Cancer Genetics Program, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA
    Carcinogenesis 32:812-21. 2011
    ..Our findings suggest that in addition to promoter hypermethylation, epigenetic repression of tumor suppressor genes by CTCF and noncoding RNA transcripts could be more common and important than previously understood...
  20. pmc Estrogen-mediated epigenetic repression of large chromosomal regions through DNA looping
    Pei Yin Hsu
    Human Cancer Genetics Program, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, Ohio 43210, USA
    Genome Res 20:733-44. 2010
    ..Together with the acquisition of DNA methylation and repressive chromatin modifications at the 16p11.2 loci, an inflexible DNA scaffold may be a novel determinant used by breast cancer cells to reinforce estrogen-mediated repression...
  21. pmc Epigenetic influences of low-dose bisphenol A in primary human breast epithelial cells
    Yu I Weng
    Human Cancer Genetics Program, The Ohio State University, Columbus, OH 43210, USA
    Toxicol Appl Pharmacol 248:111-21. 2010
    ..Combination of our exposure model with epigenetic analysis and other biochemical assays can give insight into the heritable effect of low-dose BPA in human cells...
  22. pmc Diverse histone modifications on histone 3 lysine 9 and their relation to DNA methylation in specifying gene silencing
    Jiejun Wu
    Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
    BMC Genomics 8:131. 2007
    ..Here we use epigenomic tools to simultaneously interrogate chromatin modifications and DNA methylation in a mouse leukemia cell line, L1210...
  23. ncbi request reprint Hypermethylation of 18S and 28S ribosomal DNAs predicts progression-free survival in patients with ovarian cancer
    Michael W Y Chan
    Human Cancer Genetics Program, Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
    Clin Cancer Res 11:7376-83. 2005
    ..The aim of the study was to determine the methylation status of two rDNA subunits, the 18S and 28S genes, in ovarian tumors and to correlate methylation levels with clinicopathologic features in a cohort of ovarian cancer patients...
  24. ncbi request reprint Loss of estrogen receptor signaling triggers epigenetic silencing of downstream targets in breast cancer
    Yu Wei Leu
    Human Cancer Genetics Program, Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
    Cancer Res 64:8184-92. 2004
    ..The results imply, for the first time, the significance of epigenetic regulation on ERalpha target genes, providing new direction for research in this classical signaling pathway...
  25. pmc Breast cancer-associated fibroblasts confer AKT1-mediated epigenetic silencing of Cystatin M in epithelial cells
    Huey Jen L Lin
    Division of Medical Technology, School of Allied Medical Professions, Human Cancer Genetics Program, The Ohio State University, Columbus, Ohio 43210, USA
    Cancer Res 68:10257-66. 2008
    ..Because this two-way interaction is anticipated, the described coculture system can be used to determine the effect of epithelial factors on fibroblasts in future studies...
  26. ncbi request reprint Mapping geographic zones of cancer risk with epigenetic biomarkers in normal breast tissue
    Pearlly S Yan
    Department of Hematology and Oncology, Comprehensive Cancer Center, College of Medicine and Public Health, The Ohio State University, Columbus, Ohio 43210, USA, and Department of Pathology, Addenbrooks Hospital, Cambridge, UK
    Clin Cancer Res 12:6626-36. 2006
    ..The aim of this study was to determine DNA methylation in histologically normal tissues from multiple geographic zones adjacent to primary breast tumors...
  27. pmc MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data
    Hao Sun
    Department of Molecular Virology, Immunology and Medical Genetics, Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio Stage University, 420 W 12th Avenue, TMRF 524, Columbus, OH 43210, USA
    Nucleic Acids Res 34:D98-103. 2006
    ..MPromDb serves as a portal for genome-wide promoter analysis of data generated by ChIP-chip experimental studies. MPromDb can be accessed from http://bioinformatics.med.ohio-state.edu/MPromDb...
  28. doi request reprint Epithelial progeny of estrogen-exposed breast progenitor cells display a cancer-like methylome
    Alfred S L Cheng
    Human Cancer Genetics Program, Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
    Cancer Res 68:1786-96. 2008
    ..This finding also offers a mechanistic explanation as to why a tumor suppressor gene, such as RUNX3, can be heritably silenced by epigenetic mechanisms in breast cancer...
  29. pmc Epigenetic repression of the estrogen-regulated Homeobox B13 gene in breast cancer
    Benjamin A T Rodriguez
    Human Cancer Genetics Program, The Ohio State University, Columbus, OH 43210, USA
    Carcinogenesis 29:1459-65. 2008
    ..029) in cancer patients. These results suggest that hypermethylation of HOXB13 is a late event of breast tumorigenesis and a poor prognostic indicator of node-positive cancer patients...
  30. pmc Hierarchical modularity in ERα transcriptional network is associated with distinct functions and implicates clinical outcomes
    Binhua Tang
    Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
    Sci Rep 2:875. 2012
    ....
  31. pmc Epigenetic repression of microRNA-129-2 leads to overexpression of SOX4 oncogene in endometrial cancer
    Yi Wen Huang
    Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
    Cancer Res 69:9038-46. 2009
    ..Unlike the notion that promoter hypomethylation may upregulate an oncogene, we present a new paradigm in which hypermethylation-mediated silencing of a microRNA derepresses its oncogenic target in cancer cells...
  32. pmc Integrated analysis of genome-wide DNA methylation and gene expression profiles in molecular subtypes of breast cancer
    Je Keun Rhee
    Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151 742, Korea, Bioinformatics Institute, Seoul National University, Seoul 151 744, Korea, School of Informatics and Computing, Indiana University, Bloomington, IN 47408, USA, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA, The Ohio State University Comprehensive Cancer Center Nucleic Acid Shared Resource Illumina Core, Columbus, OH 43210, USA, School of Computer Science and Engineering, Seoul National University, Seoul 151 742, Korea, OHSU Knight Cancer Institute, Portland, OR 97239, USA, Department of Molecular Medicine Institute of Biotechnology, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 3900, USA, Medical Sciences, Indiana University School of Medicine, Bloomington, IN 47405, USA and Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Nucleic Acids Res 41:8464-74. 2013
    ..Our integrated analysis demonstrates that methylation status of different genomic regions may play a key role in establishing transcriptional patterns in molecular subtypes of human breast cancer. ..
  33. doi request reprint Differential methylation hybridization: profiling DNA methylation with a high-density CpG island microarray
    Pearlly S Yan
    Human Cancer Genetics Program, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
    Methods Mol Biol 507:89-106. 2009
    ..As we continue to update our analysis algorithm and approaches to integrate high-throughput methylation data with other large-scale data types, we will make these new computation protocols available through the GenePattern platform...
  34. pmc Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors
    Zhenqing Ye
    Departments of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, Department of Molecular and Cellular Biochemistry and the Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA, Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Rockville, MD 20852, USA and Deparment of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
    Nucleic Acids Res 42:2856-69. 2014
    ..Finally, our analysis suggested that different epigenetic factors may introduce a variable obstacle in the process of exon-intron boundary establishment leading to skipping events. ..
  35. pmc Three-tiered role of the pioneer factor GATA2 in promoting androgen-dependent gene expression in prostate cancer
    Dayong Wu
    Department of Molecular and Cellular Biochemistry and the Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH 43210, USA, Ohio State Biochemistry Graduate Program, The Ohio State University, Columbus, OH 43210, USA, Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA, State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China and Medical Sciences Program and Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Bloomington, IN 47405, USA
    Nucleic Acids Res 42:3607-22. 2014
    ..Identifying these determinants of AR transcriptional activity may provide a foundation for the development of future prostate cancer therapeutics that target pioneer factor function. ..
  36. ncbi request reprint Prognostic DNA methylation biomarkers in ovarian cancer
    Susan H Wei
    Human Cancer Genetics Program, Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
    Clin Cancer Res 12:2788-94. 2006
    ..Correspondingly, distinct combinations of methylated loci can function as biomarkers for numerous clinical correlates of ovarian and other cancers...
  37. doi request reprint Cancer omics: from regulatory networks to clinical outcomes
    Binhua Tang
    Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
    Cancer Lett 340:277-83. 2013
    ....
  38. pmc Heritable clustering and pathway discovery in breast cancer integrating epigenetic and phenotypic data
    Zailong Wang
    Mathematical Biosciences Institute, The Ohio State University, 231 W, 18th Avenue, Columbus, OH 43210, USA
    BMC Bioinformatics 8:38. 2007
    ..Furthermore, our likelihood-based clustering algorithm has great flexibility, allowing for incomplete epigenotype or clinical phenotype data and also permitting dependencies among variables...
  39. pmc Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data
    Fei Gu
    Department of Biomedical Informatics, The Ohio State University, Columbus, USA
    BMC Syst Biol 4:170. 2010
    ....
  40. pmc Promoter hypermethylation of CIDEA, HAAO and RXFP3 associated with microsatellite instability in endometrial carcinomas
    Yi Wen Huang
    Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
    Gynecol Oncol 117:239-47. 2010
    ..The purpose of this study is to identify novel hypermethylated loci associated with clinicopathologic variables in endometrioid endometrial carcinomas...
  41. ncbi request reprint Tilling the chromatin landscape: emerging methods for the discovery and profiling of protein-DNA interactions
    Benjamin A T Rodriguez
    Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA
    Biochem Cell Biol 83:525-34. 2005
    ..These methods have been used to assess transcription-factor binding and (or) histone modification. This review describes these global methods and illustrates their potential in answering biological questions...
  42. pmc Modulation of DNA methylation by a sesquiterpene lactone parthenolide
    Zhongfa Liu
    Division of Pharmaceutics, Colleges of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
    J Pharmacol Exp Ther 329:505-14. 2009
    ..Hence, our study established parthenolide as an effective DNA methylation inhibitor, representing a novel prototype for DNMT1 inhibitor discovery and development from natural structural-diversified sesquiterpene lactones...
  43. pmc Xenoestrogen-induced epigenetic repression of microRNA-9-3 in breast epithelial cells
    Pei Yin Hsu
    Human Cancer Genetics Program, Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
    Cancer Res 69:5936-45. 2009
    ..Promoter hypermethylation of this microRNA may be a hallmark for early breast cancer development, and restoration of its expression by epigenetic and microRNA-based therapies is another viable option for future treatment of this disease...
  44. pmc Probe signal correction for differential methylation hybridization experiments
    Dustin P Potter
    Human Cancer Genetics Program, OSU Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
    BMC Bioinformatics 9:453. 2008
    ..Hybridization effects related to probe-sequence composition and DNA dye-probe interactions have been observed in differential methylation hybridization (DMH) microarray experiments as well as other effects inherent to the DMH protocol...
  45. doi request reprint The role of parental and grandparental epigenetic alterations in familial cancer risk
    Jessica L Fleming
    Human Cancer Genetics Program and the Ohio State Comprehensive Cancer Center, Department of Molecular Virology, Immunology, and Medical Genetics, USA
    Cancer Res 68:9116-21. 2008
    ..Here, we will discuss Mendelian, non-Mendelian, and environmentally induced patterns of multigenerational epigenetic alterations as well as some possible mechanisms for how these events may be occurring...
  46. pmc Methylated DNA immunoprecipitation and microarray-based analysis: detection of DNA methylation in breast cancer cell lines
    Yu I Weng
    Human Cancer Genetics Program, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
    Methods Mol Biol 590:165-76. 2009
    ..Potential technical pitfalls and solutions are also provided to serve as workflow guidelines...
  47. pmc ChIP-seq defined genome-wide map of TGFβ/SMAD4 targets: implications with clinical outcome of ovarian cancer
    Brian A Kennedy
    Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, United States of America
    PLoS ONE 6:e22606. 2011
    ....
  48. ncbi request reprint ChIP-chip comes of age for genome-wide functional analysis
    Jiejun Wu
    Departments of Molecular Genetics and Molecular Virology, Immunology, and Medical Genetics, Division of Human Cancer Genetics, Comprehensive Cancer Center, Ohio State University, Columbus, Ohio 43210, USA
    Cancer Res 66:6899-902. 2006
    ....
  49. pmc FOXP3 is an X-linked breast cancer suppressor gene and an important repressor of the HER-2/ErbB2 oncogene
    Tao Zuo
    Program in Molecular, Cellular, and Developmental Biology and Department of Molecular Virology, Immunology, and Medical Genetics, Ohio State University Medical Center and Comprehensive Cancer Center, Columbus, OH 43210, USA
    Cell 129:1275-86. 2007
    ..Our data demonstrate that FOXP3 is an X-linked breast cancer suppressor gene and an important regulator of the HER-2/ErbB2 oncogene...
  50. pmc Activation of silenced tumor suppressor genes in prostate cancer cells by a novel energy restriction-mimetic agent
    Hsiang Yu Lin
    Division of Medicinal Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA
    Prostate 72:1767-78. 2012
    ..Targeting tumor metabolism by energy restriction-mimetic agents (ERMAs) has emerged as a strategy for cancer therapy/prevention. Evidence suggests a mechanistic link between ERMA-mediated antitumor effects and epigenetic gene regulation...
  51. doi request reprint Using ChIPMotifs for de novo motif discovery of OCT4 and ZNF263 based on ChIP-based high-throughput experiments
    Brian A Kennedy
    Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
    Methods Mol Biol 802:323-34. 2012
    ..In a separate study, we also use de novo motif discovery to suggest that ZNF263 binds to a 24-nt site that differs from the motif predicted by the zinc finger code in several positions...
  52. doi request reprint Detection of DNA methylation by MeDIP and MBDCap assays: an overview of techniques
    Hang Kai Hsu
    The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
    Methods Mol Biol 1105:61-70. 2014
    ..They are the most economical and effective methods to study DNA methylation either at a single locus or in genome-wide scale. ..
  53. pmc Methylation analysis by microarray
    Daniel E Deatherage
    Human Cancer Genetics Program, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
    Methods Mol Biol 556:117-39. 2009
    ..Issues regarding quality control are addressed as well...
  54. pmc Aberrant transforming growth factor beta1 signaling and SMAD4 nuclear translocation confer epigenetic repression of ADAM19 in ovarian cancer
    Michael Wy Chan
    Human Cancer Genetics Program, Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210 1234, USA
    Neoplasia 10:908-19. 2008
    ..Given the emerging role of ADAMs family proteins in growth factor regulation in normal cells, we suggest that epigenetic dysregulation of ADAM19 may contribute to the neoplastic process in ovarian cancer...
  55. pmc Seed in soil, with an epigenetic view
    Huey Jen L Lin
    Ohio State University, Columbus, USA
    Biochim Biophys Acta 1790:920-4. 2009
    ..It is believed that abrogation of these initiators could offer a promising therapeutic strategy...
  56. pmc Profiling DNA methylomes from microarray to genome-scale sequencing
    Yi Wei Huang
    The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
    Technol Cancer Res Treat 9:139-47. 2010
    ..With advances on next-generation sequencing technologies, it is now possible to globally map the DNA cytosine methylation at single-base resolution, providing new insights into the regulation and dynamics of DNA methylation in genomes...
  57. pmc Modulation of genetic and epigenetic biomarkers of colorectal cancer in humans by black raspberries: a phase I pilot study
    Li Shu Wang
    Department of Internal Medicine, Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43240, USA
    Clin Cancer Res 17:598-610. 2011
    ....
  58. pmc Identification of candidate epigenetic biomarkers for ovarian cancer detection
    Yi Wen Huang
    Molecular Biology and Cancer Genetics Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
    Oncol Rep 22:853-61. 2009
    ..Molecular therapies, by reversing the aberrant epigenomes using inhibitory agents or by abrogating the upstream signaling pathways that convey the epigenomic perturbations, may be developed into promising treatment regimens...
  59. doi request reprint The functional consequences of alternative promoter use in mammalian genomes
    Ramana V Davuluri
    Human Cancer Genetics Program, Comprehensive Cancer Center, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA
    Trends Genet 24:167-77. 2008
    ..Here we discuss the functional consequences of use and misuse of alternative promoters in normal and disease genomes and review the molecular mechanisms regulating alternative promoter use in mammalian genomes...
  60. pmc Definition of a FoxA1 Cistrome that is crucial for G1 to S-phase cell-cycle transit in castration-resistant prostate cancer
    Chunpeng Zhang
    Department of Molecular and Cellular Biochemistry and the Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, Ohio, USA
    Cancer Res 71:6738-48. 2011
    ..Our findings establish FoxA1 as a pivotal driver of the cell-cycle in CRPC which promotes G₁ to S-phase transit as well as G₂ to M-phase transit through two distinct mechanisms...
  61. pmc Epigenetic alterations in the breast: Implications for breast cancer detection, prognosis and treatment
    Amy M Dworkin
    Integrated Biomedical Science Graduate Program, The Ohio State University, Columbus, OH 43210, USA
    Semin Cancer Biol 19:165-71. 2009
    ..Here, we discuss the importance of epigenetics in breast cancer detection, prognosis, and therapy with an emphasis on mechanisms and epigenetic contributions to field cancerization effects...
  62. pmc High resolution detection and analysis of CpG dinucleotides methylation using MBD-Seq technology
    Xun Lan
    Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, United States of America
    PLoS ONE 6:e22226. 2011
    ..These results demonstrated the combination of MBD-seq and BALM could serve as a useful tool to investigate DNA methylome due to its low cost, high specificity, efficiency and resolution...
  63. pmc Quantification of regional DNA methylation by liquid chromatography/tandem mass spectrometry
    Zhongfa Liu
    College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
    Anal Biochem 391:106-13. 2009
    ....
  64. ncbi request reprint Combinatorial analysis of transcription factor partners reveals recruitment of c-MYC to estrogen receptor-alpha responsive promoters
    Alfred S L Cheng
    Division of Human Cancer Genetics, Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, Ohio State University, Columbus, Ohio 43210, USA
    Mol Cell 21:393-404. 2006
    ..These results suggest that ERalpha and c-MYC physically interact to stabilize the ERalpha-coactivator complex, thereby permitting other signal transduction pathways to fine-tune estrogen-mediated signaling networks...
  65. ncbi request reprint New anti-cancer strategies: epigenetic therapies and biomarkers
    Curtis Balch
    Medical Sciences, Indiana University, Bloomington, IN 47405, USA
    Front Biosci 10:1897-931. 2005
    ..Finally, future directions are addressed, including alternative epigenetic targets, gene-specific modifications, and the use of bioinformatics...
  66. ncbi request reprint Toward a human epigenome
    Romulo M Brena
    Nat Genet 38:1359-60. 2006
  67. ncbi request reprint Chromatin immunoprecipitation (ChIP) on chip experiments uncover a widespread distribution of NF-Y binding CCAAT sites outside of core promoters
    Anna Testa
    Dipartimento di Biologia Animale, Università di Modena e Reggio, Via Campi 213 D, 41100 Modena, Italy
    J Biol Chem 280:13606-15. 2005
    ..The abundance of "unorthodox" CCAAT positions highlights an unexpected complexity of the NF-Y-mediated transcriptional network...
  68. ncbi request reprint The androgen receptor gene is preferentially hypermethylated in follicular non-Hodgkin's lymphomas
    Hongyu Yang
    Department of Pathology and Anatomical Sciences, Fischel Cancer Center, University of Missouri School of Medicine, 115 Business Loop 70 West, Columbia, MO 65203, USA
    Clin Cancer Res 9:4034-42. 2003
    ..Full re-expression of AR requires both demethylation and reacetylation, a finding that may affect treatment decisions...
  69. ncbi request reprint Analysis of Myc bound loci identified by CpG island arrays shows that Max is essential for Myc-dependent repression
    Daniel Y L Mao
    Ontario Cancer Institute Princess Margaret Hospital, University of Toronto, Ontario M5G 2M9, Canada
    Curr Biol 13:882-6. 2003
    ..Taken together, the identification and analysis of Myc bound target genes supports a model whereby Max plays an essential and universal role in the mechanism of Myc-dependent transcriptional regulation...
  70. ncbi request reprint Use of CpG island microarrays to identify colorectal tumors with a high degree of concurrent methylation
    Pearlly S Yan
    Department of Pathology and Anatomical Sciences, Ellis Fischel Cancer Center, University of Missouri School of Medicine, Columbia, MO 65203, USA
    Methods 27:162-9. 2002
    ..The present study demonstrates that this microarray-based technique is useful in classifying tumors according to their methylation profiles...
  71. pmc High-throughput methylation profiling by MCA coupled to CpG island microarray
    Marcos R H Estecio
    Department of Leukemia, UT M D Anderson Cancer Center, Houston, Texas 77030, USA
    Genome Res 17:1529-36. 2007
    ..In summary, MCAM is a suitable technique to discover methylated genes and to profile methylation changes in clinical samples in a high-throughput fashion...
  72. ncbi request reprint Diverse gene expression and DNA methylation profiles correlate with differential adaptation of breast cancer cells to the antiestrogens tamoxifen and fulvestrant
    Meiyun Fan
    Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana 47405, USA
    Cancer Res 66:11954-66. 2006
    ..Such knowledge of resistance-associated mechanisms could allow for identification of therapy targets and strategies for resensitization to these well-established antihormonal agents...
  73. ncbi request reprint Antimitogenic and chemosensitizing effects of the methylation inhibitor zebularine in ovarian cancer
    Curtis Balch
    Medical Sciences Program, Indiana University, 302 Jordan Hall, 1001 East Third Street, Bloomington, IN 47405, USA
    Mol Cancer Ther 4:1505-14. 2005
    ..In summary, zebularine seems to be a promising clinical candidate, singly or combined with conventional regimens, for the therapy of drug-resistant ovarian cancer...
  74. ncbi request reprint T-bet binding to newly identified target gene promoters is cell type-independent but results in variable context-dependent functional effects
    Kristin M Beima
    Department of Immunology, University of Washington, Seattle, Washington 98195, USA
    J Biol Chem 281:11992-2000. 2006
    ..Thus, there is a high variability in the functional consequences, if any, that result from the association of T-bet with individual target promoters...
  75. ncbi request reprint Aberrant DNA methylation in ovarian cancer: is there an epigenetic predisposition to drug response?
    Susan H Wei
    Department of Pathology and Anatomical Sciences, Ellis Fischel Cancer Center, University of Missouri School of Medicine, Columbia, Missouri 65203, USA
    Ann N Y Acad Sci 983:243-50. 2003
    ..Methylation profiles of ovarian cancer might be useful for early cancer detection and prediction of chemotherapy outcome in a clinical context...
  76. ncbi request reprint Epigenetic "bivalently marked" process of cancer stem cell-driven tumorigenesis
    Curt Balch
    Medical Sciences Program, Indiana University, Bloomington, IN, USA
    Bioessays 29:842-5. 2007
    ..These results suggest a possible mechanism by which aberrant differentiation, mediated by histone and DNA methylation, instigates tumor progression...
  77. ncbi request reprint The epigenetics of ovarian cancer drug resistance and resensitization
    Curtis Balch
    Medical Sciences, Indiana University, Bloomington, Ind, USA
    Am J Obstet Gynecol 191:1552-72. 2004
    ..Moreover, when used in combination with conventional chemotherapeutic agents, epigenetic-based therapies may provide a means to resensitize ovarian tumors to the proven cytotoxic activities of conventional chemotherapeutics...
  78. ncbi request reprint A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha
    Lang Li
    Division of Biostatistics, Department of Medicine, Indiana University School of Medicine Indianapolis, IN 47405, USA
    Bioinformatics 22:2210-6. 2006
    ....
  79. ncbi request reprint Differential DNA methylation of gene promoters in small B-cell lymphomas
    Juyuan Guo
    Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia 65203, USA
    Am J Clin Pathol 124:430-9. 2005
    ..This study illustrates nonrandom epigenetic alterations in SBCLs that seem to preferentially involve lymphomas of germinal center derivation...
  80. pmc CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome
    Lawrence E Heisler
    Department of Laboratory Medicine and Pathobiology, Program in Proteomics and Bioinformatics, University of Toronto Toronto, ON M5S 1A8, Canada
    Nucleic Acids Res 33:2952-61. 2005
    ..A browsable database is available on-line to facilitate exploration of the CGIs in this library and their association with annotated genes or promoter elements...
  81. pmc Enriched transcription factor binding sites in hypermethylated gene promoters in drug resistant cancer cells
    Meng Li
    Medical Sciences, School of Medicine, Indiana University, Bloomington, IN 47404, USA
    Bioinformatics 24:1745-8. 2008
    ..To our knowledge, the potential relationship between CpG island hypermethylation, transcription factor (TF) binding in local promoter regions and transcriptional control has not been previously explored in a genome-wide context...

Research Grants18

  1. Novel Tool for Analysis of Promoter Hypermethylation
    Tim Huang; Fiscal Year: 2005
    ..The MSO assay will furnish digital profiles of promoter hypermethylation for individual tumors and offers an alternative to cDNA microarray approaches for molecular classification of different cancer subtypes. ..
  2. DNA HYPERMETHYLATION IN BREAST CANCER
    Tim Huang; Fiscal Year: 2002
    ..In contrast, the CpG island microarray uses DNA targets, which is more stable and easier to isolate from patients' specimens. ..
  3. CpG Island Methylator Phenotypes in Breast Cancer
    Tim H M Huang; Fiscal Year: 2010
    ..This type of epigenetic studies will be useful for identifying patients with resistant-CIMPs for alternative therapies in the future. ..
  4. Epigenomics of Bisphenol A Exposure and Disease Risk
    Tim Huang; Fiscal Year: 2009
    ..It is our hope that the result of this study supports an inclusion of the epigenetic effects of estrogenic plasticizers, like BPA, into risk assessment implemented by regulatory agencies. ..
  5. CpG Island Methylator Phenotypes in Breast Cancer
    Tim Huang; Fiscal Year: 2009
    ..This type of epigenetic studies will be useful for identifying patients with resistant-CIMPs for alternative therapies in the future. ..
  6. Environmental Epigenetics and Stem/Progenitor Cell Injury
    Tim Huang; Fiscal Year: 2007
    ..These loci are future biomarkers for early breast cancer detection and are putative biosensors to environmental estrogens. ..
  7. CpG Island Methylator Phenotypes in Breast Cancer
    Tim Huang; Fiscal Year: 2007
    ..This type of epigenetic studies will be useful for identifying patients with resistant-CIMPs for alternative therapies in the future. ..
  8. Epigenetic Biomarkers for Ovarian Cancer Progression
    Tim Huang; Fiscal Year: 2005
    ..Additionally, the study will give insights into the role of CpG island hypermethylation in drug-resistant ovarian cancer. ..
  9. DNA HYPERMETHYLATION IN BREAST CANCER
    Tim Huang; Fiscal Year: 2005
    ..In contrast, the CpG island microarray uses DNA targets, which is more stable and easier to isolate from patients' specimens. ..
  10. DNA HYPERMETHYLATION IN BREAST CANCER
    Tim Huang; Fiscal Year: 2004
    ..In contrast, the CpG island microarray uses DNA targets, which is more stable and easier to isolate from patients' specimens. ..
  11. DNA HYPERMETHYLATION IN BREAST CANCER
    Tim Huang; Fiscal Year: 2003
    ..In contrast, the CpG island microarray uses DNA targets, which is more stable and easier to isolate from patients' specimens. ..
  12. HIGH THROUGHPUT METHYLATION ANALYSIS IN CANCER
    Tim Huang; Fiscal Year: 2002
    ..Moreover, the characterization of the corresponding biological relevant cDNAs will open unforeseen avenues for investigating the pathology of cancer and for better treatment of the disease. ..
  13. Epigenomics of Bisphenol A Exposure and Disease Risk
    Tim H M Huang; Fiscal Year: 2010
    ..It is our hope that the result of this study supports an inclusion of the epigenetic effects of estrogenic plasticizers, like BPA, into risk assessment implemented by regulatory agencies. ..