Li Shen

Summary

Affiliation: Mount Sinai School of Medicine
Country: USA

Publications

  1. pmc ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases
    Li Shen
    Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
    BMC Genomics 15:284. 2014
  2. pmc diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates
    Li Shen
    Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
    PLoS ONE 8:e65598. 2013
  3. pmc Prediction of quantitative phenotypes based on genetic networks: a case study in yeast sporulation
    Li Shen
    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, San Diego, CA 92093, USA
    BMC Syst Biol 4:128. 2010
  4. pmc Essential role of SIRT1 signaling in the nucleus accumbens in cocaine and morphine action
    Deveroux Ferguson
    Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, Texas 78229, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, Maryland 20892
    J Neurosci 33:16088-98. 2013
  5. pmc Morphine epigenomically regulates behavior through alterations in histone H3 lysine 9 dimethylation in the nucleus accumbens
    Haosheng Sun
    Fishberg Department of Neuroscience and Friedman Brain Institute, Mount Sinai School of Medicine, New York, New York 10029, USA
    J Neurosci 32:17454-64. 2012
  6. doi request reprint SIRT1-FOXO3a Regulate Cocaine Actions in the Nucleus Accumbens
    Deveroux Ferguson
    Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, Department of Basic Medical Sciences, University of Arizona College of Medicine Phoenix, Phoenix, Arizona 85004, and
    J Neurosci 35:3100-11. 2015
  7. pmc Cocaine dynamically regulates heterochromatin and repetitive element unsilencing in nucleus accumbens
    Ian Maze
    Fishberg Department of Neuroscience, Mount Sinai School of Medicine, New York, NY 10029, USA
    Proc Natl Acad Sci U S A 108:3035-40. 2011
  8. pmc Essential role of poly(ADP-ribosyl)ation in cocaine action
    Kimberly N Scobie
    Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
    Proc Natl Acad Sci U S A 111:2005-10. 2014
  9. doi request reprint Analytical tools and current challenges in the modern era of neuroepigenomics
    Ian Maze
    1 Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York, USA 2 Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
    Nat Neurosci 17:1476-90. 2014
  10. doi request reprint β-catenin mediates stress resilience through Dicer1/microRNA regulation
    Caroline Dias
    Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
    Nature 516:51-5. 2014

Collaborators

Detail Information

Publications17

  1. pmc ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases
    Li Shen
    Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
    BMC Genomics 15:284. 2014
    ..As the cost of DNA sequencing continues to fall, the interpretation of the ever increasing amount of data generated represents a considerable challenge...
  2. pmc diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates
    Li Shen
    Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
    PLoS ONE 8:e65598. 2013
    ..The results indicated that diffReps is a highly sensitive program in detecting differential sites from ChIP-seq data...
  3. pmc Prediction of quantitative phenotypes based on genetic networks: a case study in yeast sporulation
    Li Shen
    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, San Diego, CA 92093, USA
    BMC Syst Biol 4:128. 2010
    ..However, de novo prediction for quantitative phenotypes based on network topology is always a challenging task...
  4. pmc Essential role of SIRT1 signaling in the nucleus accumbens in cocaine and morphine action
    Deveroux Ferguson
    Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, Texas 78229, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, Maryland 20892
    J Neurosci 33:16088-98. 2013
    ....
  5. pmc Morphine epigenomically regulates behavior through alterations in histone H3 lysine 9 dimethylation in the nucleus accumbens
    Haosheng Sun
    Fishberg Department of Neuroscience and Friedman Brain Institute, Mount Sinai School of Medicine, New York, New York 10029, USA
    J Neurosci 32:17454-64. 2012
    ..These data provide novel insight into the epigenomic regulation of H3K9me2 by chronic morphine and suggest novel chromatin-based mechanisms through which morphine-induced addictive-like behaviors arise...
  6. doi request reprint SIRT1-FOXO3a Regulate Cocaine Actions in the Nucleus Accumbens
    Deveroux Ferguson
    Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, Department of Basic Medical Sciences, University of Arizona College of Medicine Phoenix, Phoenix, Arizona 85004, and
    J Neurosci 35:3100-11. 2015
    ..The discovery of these two actions of SIRT1 in NAc in the context of behavioral adaptations to cocaine represents an important step forward in advancing our understanding of the molecular adaptations underlying cocaine action. ..
  7. pmc Cocaine dynamically regulates heterochromatin and repetitive element unsilencing in nucleus accumbens
    Ian Maze
    Fishberg Department of Neuroscience, Mount Sinai School of Medicine, New York, NY 10029, USA
    Proc Natl Acad Sci U S A 108:3035-40. 2011
    ..Such increases likely reflect global patterns of genomic destabilization in this brain region after repeated cocaine administration and open the door for future investigations into the epigenetic and genetic basis of drug addiction...
  8. pmc Essential role of poly(ADP-ribosyl)ation in cocaine action
    Kimberly N Scobie
    Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
    Proc Natl Acad Sci U S A 111:2005-10. 2014
    ..These findings establish the involvement of PARP-1 and PARylation in the long-term actions of cocaine...
  9. doi request reprint Analytical tools and current challenges in the modern era of neuroepigenomics
    Ian Maze
    1 Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York, USA 2 Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
    Nat Neurosci 17:1476-90. 2014
    ..This will be critical to the development of future diagnostic and therapeutic strategies aimed at alleviating the vast array of heterogeneous and genetically distinct disorders of the CNS. ..
  10. doi request reprint β-catenin mediates stress resilience through Dicer1/microRNA regulation
    Caroline Dias
    Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
    Nature 516:51-5. 2014
    ..We thus present a foundation for the development of novel therapeutic targets to promote stress resilience...
  11. pmc G9a influences neuronal subtype specification in striatum
    Ian Maze
    Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York, USA
    Nat Neurosci 17:533-9. 2014
    ....
  12. pmc An integrated approach to identifying cis-regulatory modules in the human genome
    Kyoung Jae Won
    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
    PLoS ONE 4:e5501. 2009
    ..Incorporating histone signature information successfully penalized false prediction and improved the whole performance. The dataset we used and the software are available at http://nash.ucsd.edu/CIS/...
  13. pmc GBNet: deciphering regulatory rules in the co-regulated genes using a Gibbs sampler enhanced Bayesian network approach
    Li Shen
    Department of Chemistry and Biochemistry, University of California, San Diego, California, USA
    BMC Bioinformatics 9:395. 2008
    ..Deciphering regulatory rules between cooperative TFs is a critical step towards understanding the mechanisms of combinatorial regulation...
  14. pmc Distinct epigenomic landscapes of pluripotent and lineage-committed human cells
    R David Hawkins
    Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
    Cell Stem Cell 6:479-91. 2010
    ..Our results provide new insights into epigenetic mechanisms underlying properties of pluripotency and cell fate commitment...
  15. doi request reprint Locus-specific epigenetic remodeling controls addiction- and depression-related behaviors
    Elizabeth A Heller
    Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
    Nat Neurosci 17:1720-7. 2014
    ..This approach allowed us to relate the epigenetic landscape at a given gene directly to regulation of its expression and to its subsequent effects on reward behavior. ..
  16. pmc HDAC2 regulates atypical antipsychotic responses through the modulation of mGlu2 promoter activity
    Mitsumasa Kurita
    Department of Psychiatry, Mount Sinai School of Medicine, New York, New York, USA
    Nat Neurosci 15:1245-54. 2012
    ..These observations support the view of HDAC2 as a promising new target for schizophrenia treatment...
  17. pmc STAR: an integrated solution to management and visualization of sequencing data
    Tao Wang
    Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA, The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia 6009, Australia, Key Laboratory for Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China, Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA, Department of Cellular and Molecular Medicine, University of California, San Diego, CA 92093, USA and Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
    Bioinformatics 29:3204-10. 2013
    ..We developed STAR, an integrated web application that enables online management, visualization and track-based analysis of NGS data...