Matthew D Simon

Summary

Affiliation: Yale University
Country: USA

Publications

  1. doi request reprint Insight into lncRNA biology using hybridization capture analyses
    Matthew D Simon
    Dept of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06516, USA Chemical Biology Institute, Yale West Campus, West Haven, CT, 06511, USA Electronic address
    Biochim Biophys Acta 1859:121-7. 2016
  2. pmc Multiplexed Illumina sequencing libraries from picogram quantities of DNA
    Sarah K Bowman
    Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
    BMC Genomics 14:466. 2013
  3. doi request reprint A method to site-specifically incorporate methyl-lysine analogues into recombinant proteins
    Matthew D Simon
    Department of Molecular Biophysics and Biochemistry, Chemical Biology Institute, Yale University, New Haven, Connecticut, USA
    Methods Enzymol 512:57-69. 2012
  4. pmc High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation
    Matthew D Simon
    1 Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA 2 Department of Molecular Biophysics and Biochemistry, and Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA 3
    Nature 504:465-9. 2013
  5. doi request reprint Probing Xist RNA Structure in Cells Using Targeted Structure-Seq
    Rui Fang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
    PLoS Genet 11:e1005668. 2015
  6. doi request reprint Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry
    Erin E Duffy
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
    Mol Cell 59:858-66. 2015

Collaborators

  • Jeannie T Lee
  • Erin E Duffy
  • Rui Fang
  • Michael Rutenberg-Schoenberg
  • Sarah K Bowman
  • Walter N Moss
  • Mark B Gerstein
  • Robert R Kitchen
  • Catherine D Stark
  • Robert E Kingston
  • Mark L Borowsky
  • Aimée M Deaton
  • Michael Tolstorukov

Detail Information

Publications6

  1. doi request reprint Insight into lncRNA biology using hybridization capture analyses
    Matthew D Simon
    Dept of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06516, USA Chemical Biology Institute, Yale West Campus, West Haven, CT, 06511, USA Electronic address
    Biochim Biophys Acta 1859:121-7. 2016
    ..This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa. ..
  2. pmc Multiplexed Illumina sequencing libraries from picogram quantities of DNA
    Sarah K Bowman
    Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
    BMC Genomics 14:466. 2013
    ..Existing protocols for picogram-scale libraries require concomitant fragmentation of DNA, pre-amplification, or long overnight steps...
  3. doi request reprint A method to site-specifically incorporate methyl-lysine analogues into recombinant proteins
    Matthew D Simon
    Department of Molecular Biophysics and Biochemistry, Chemical Biology Institute, Yale University, New Haven, Connecticut, USA
    Methods Enzymol 512:57-69. 2012
    ..These MLA histones have been used to construct well-defined chromatin templates to study the direct biochemical consequences of histone lysine methylation in a variety of contexts...
  4. pmc High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation
    Matthew D Simon
    1 Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA 2 Department of Molecular Biophysics and Biochemistry, and Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA 3
    Nature 504:465-9. 2013
    ..We conclude that Xist spreading takes distinct stage-specific forms. During initial establishment, Xist follows a two-step mechanism, but during maintenance, Xist spreads rapidly to both gene-rich and gene-poor regions. ..
  5. doi request reprint Probing Xist RNA Structure in Cells Using Targeted Structure-Seq
    Rui Fang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
    PLoS Genet 11:e1005668. 2015
    ..This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function. ..
  6. doi request reprint Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry
    Erin E Duffy
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
    Mol Cell 59:858-66. 2015
    ..This improved chemistry will enhance methods that depend on tracking different populations of RNA, such as 4-thiouridine tagging to study tissue-specific transcription and dynamic transcriptome analysis (DTA) to study RNA turnover...