Richard M Myers

Summary

Publications

  1. pmc Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation
    Jason Gertz
    HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
    PLoS Genet 7:e1002228. 2011
  2. pmc Functional analysis of transcription factor binding sites in human promoters
    Troy W Whitfield
    Program in Bioinformatics and Integrative Biology and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Genome Biol 13:R50. 2012
  3. pmc Characterization of X-linked SNP genotypic variation in globally distributed human populations
    Amanda M Casto
    Department of Genetics, Stanford University, Mail Stop 5120, Stanford, California 94305, USA
    Genome Biol 11:R10. 2010
  4. pmc Characterizing the admixed African ancestry of African Americans
    Fouad Zakharia
    Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
    Genome Biol 10:R141. 2009
  5. pmc Distinct properties of cell-type-specific and shared transcription factor binding sites
    Jason Gertz
    HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
    Mol Cell 52:25-36. 2013
  6. pmc Distinct gene regulatory programs define the inhibitory effects of liver X receptors and PPARG on cancer cell proliferation
    Daniel Savic
    HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
    Genome Med 8:74. 2016
  7. pmc Dynamic DNA methylation across diverse human cell lines and tissues
    Katherine E Varley
    HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
    Genome Res 23:555-67. 2013
  8. pmc Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/ enhancer-binding protein beta binding sites
    Daniel Savic
    HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
    Genome Res 25:1791-800. 2015
  9. pmc Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner
    Jason Gertz
    HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
    Genome Res 22:2153-62. 2012
  10. doi request reprint Genomic regulation of invasion by STAT3 in triple negative breast cancer
    Joy M McDaniel
    HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
    Oncotarget . 2016

Detail Information

Publications21

  1. pmc Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation
    Jason Gertz
    HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
    PLoS Genet 7:e1002228. 2011
    ..Overall, our results demonstrate that the influence of genotype on patterns of DNA methylation is widespread in the genome and greatly exceeds the influence of imprinting on genome-wide methylation patterns...
  2. pmc Functional analysis of transcription factor binding sites in human promoters
    Troy W Whitfield
    Program in Bioinformatics and Integrative Biology and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Genome Biol 13:R50. 2012
    ..We carried out functional tests on these sites in four different immortalized human cell lines using transient transfections with a luciferase reporter assay, primarily for the transcription factors CTCF, GABP, GATA2, E2F, STAT, and YY1...
  3. pmc Characterization of X-linked SNP genotypic variation in globally distributed human populations
    Amanda M Casto
    Department of Genetics, Stanford University, Mail Stop 5120, Stanford, California 94305, USA
    Genome Biol 11:R10. 2010
    ..Here we characterize the genomic variation represented by 16,297 X-linked SNPs genotyped in the CEPH human genome diversity project samples...
  4. pmc Characterizing the admixed African ancestry of African Americans
    Fouad Zakharia
    Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
    Genome Biol 10:R141. 2009
    ..To focus on African ancestry, we reduced the data to include only those genotypes in each African American determined statistically to be African in origin...
  5. pmc Distinct properties of cell-type-specific and shared transcription factor binding sites
    Jason Gertz
    HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
    Mol Cell 52:25-36. 2013
    ..The distinct properties of cell-specific binding were also observed with glucocorticoid receptor and for ER in primary mouse tissues, representing an elegant genomic encoding scheme for generating cell-type-specific gene regulation. ..
  6. pmc Distinct gene regulatory programs define the inhibitory effects of liver X receptors and PPARG on cancer cell proliferation
    Daniel Savic
    HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
    Genome Med 8:74. 2016
    ..However, a comprehensive temporal molecular characterization of the LXR and PPARG gene regulatory responses in tumor cells is still lacking...
  7. pmc Dynamic DNA methylation across diverse human cell lines and tissues
    Katherine E Varley
    HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
    Genome Res 23:555-67. 2013
    ..This study provides an atlas of DNA methylation across diverse and well-characterized samples and enables new discoveries about DNA methylation and its role in gene regulation and disease...
  8. pmc Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/ enhancer-binding protein beta binding sites
    Daniel Savic
    HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
    Genome Res 25:1791-800. 2015
    ..Collectively, our functional assay results indicate that RNAP2 occupancy can be used as a key genomic marker that can distinguish active from inactive TF bound sites. ..
  9. pmc Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner
    Jason Gertz
    HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
    Genome Res 22:2153-62. 2012
    ....
  10. doi request reprint Genomic regulation of invasion by STAT3 in triple negative breast cancer
    Joy M McDaniel
    HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
    Oncotarget . 2016
    ..Functional analysis revealed that STAT3 has a key role regulating invasion and metastasis, a characteristic often associated with TNBC. Our findings suggest therapies targeting STAT3 may be important for preventing TNBC metastasis...
  11. pmc The hypersensitive glucocorticoid response specifically regulates period 1 and expression of circadian genes
    Timothy E Reddy
    HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
    Mol Cell Biol 32:3756-67. 2012
    ..These findings show that hypersensitive GR binding occurs throughout the genome, drives targeted gene expression, and may be important to endocrine mediation of peripheral circadian rhythms...
  12. pmc CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins
    Daniel Savic
    HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
    Genome Res 25:1581-9. 2015
    ....
  13. doi request reprint RNA sequencing of pancreatic adenocarcinoma tumors yields novel expression patterns associated with long-term survival and reveals a role for ANGPTL4
    Marie K Kirby
    HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
    Mol Oncol 10:1169-82. 2016
    ..It is important to understand the molecular characteristics associated with survival differences in pancreatic adenocarcinoma tumors that may inform patient care...
  14. pmc Decoding transcriptional enhancers: Evolving from annotation to functional interpretation
    Krysta L Engel
    HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
    Semin Cell Dev Biol 57:40-50. 2016
    ..Additionally, we discuss the crucial role of novel techniques in deciphering the complex gene regulatory landscape and how these studies will shape future research. ..
  15. doi request reprint aRNApipe: A balanced, efficient and distributed pipeline for processing RNA-seq data in high performance computing environments
    Arnald Alonso
    HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
    Bioinformatics . 2017
    ..Availability and documentation: https://github.com/HudsonAlpha/aRNAPipe; DOI: 10.5281/zenodo.202950 CONTACT: rmyers@hudsonalpha.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online...
  16. pmc Blocking of targeted microRNAs from next-generation sequencing libraries
    Brian S Roberts
    HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
    Nucleic Acids Res 43:e145. 2015
    ..For small RNA sequencing, this technique could fill a similar role as do ribosomal or globin removal technologies in messenger RNA sequencing. ..
  17. pmc Recurrent read-through fusion transcripts in breast cancer
    Katherine E Varley
    HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
    Breast Cancer Res Treat 146:287-97. 2014
    ..Both breast cancer associated fusion transcripts identified in this study involve membrane proteins (SCNN1A-TNFRSF1A and CTSD-IFITM10), which raises the possibility that they could be breast cancer-specific cell surface markers...
  18. pmc Transposase mediated construction of RNA-seq libraries
    Jason Gertz
    HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
    Genome Res 22:134-41. 2012
    ..Our results show that high-quality RNA-seq libraries can be constructed efficiently and in an automatable fashion using transposition technology...
  19. pmc Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation
    Timothy E Reddy
    HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
    Genome Res 19:2163-71. 2009
    ..Overall, the genome-wide determination and analysis of GR:DNA binding and transcriptional response to hormone reveals new insights into the complexities of gene regulatory activities managed by GR...
  20. pmc Effects of sequence variation on differential allelic transcription factor occupancy and gene expression
    Timothy E Reddy
    HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
    Genome Res 22:860-9. 2012
    ..Our results have the potential to increase the power and interpretability of association studies by targeting functional intergenic variants in addition to protein coding sequences...