Chaolin Zhang

Summary

Affiliation: The Rockefeller University
Country: USA

Publications

  1. pmc Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data
    Chaolin Zhang
    Laboratory of Molecular Neuro Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
    Nat Biotechnol 29:607-14. 2011
  2. pmc Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain
    Donny D Licatalosi
    Laboratory of Molecular Neuro Oncology, The Rockefeller University, New York, New York 10065, USA
    Genes Dev 26:1626-42. 2012
  3. pmc Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls
    Chaolin Zhang
    Laboratory of Molecular Neuro Oncology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Science 329:439-43. 2010
  4. pmc Prediction of clustered RNA-binding protein motif sites in the mammalian genome
    Chaolin Zhang
    Laboratory of Molecular Neuro Oncology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Nucleic Acids Res 41:6793-807. 2013
  5. doi mCarts: Genome-Wide Prediction of Clustered Sequence Motifs as Binding Sites for RNA-Binding Proteins
    Sebastien M Weyn-Vanhentenryck
    Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, P and S Building, Room 4 448, 630 W 168th Street, New York, NY, 10032, USA
    Methods Mol Biol 1421:215-26. 2016
  6. pmc NOVA-dependent regulation of cryptic NMD exons controls synaptic protein levels after seizure
    Taesun Eom
    Laboratory of Molecular Neuro Oncology, Rockefeller University, New York, United States
    elife 2:e00178. 2013
  7. pmc Neuronal Elav-like (Hu) proteins regulate RNA splicing and abundance to control glutamate levels and neuronal excitability
    Gulayse Ince-Dunn
    Laboratory of Molecular Neuro Oncology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Neuron 75:1067-80. 2012
  8. pmc Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis
    Michael J Moore
    1 Laboratory of Molecular Neuro Oncology, The Rockefeller University, New York, New York, USA 2
    Nat Protoc 9:263-93. 2014
  9. ncbi CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data
    Ankeeta Shah
    Department of Systems BiologyDepartment of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
    Bioinformatics . 2016
  10. pmc FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism
    Jennifer C Darnell
    Laboratory of Molecular Neuro Oncology, The Rockefeller University, New York, NY 10065, USA
    Cell 146:247-61. 2011

Collaborators

  • Robert B Darnell
  • Jennifer C Darnell
  • Hideyuki Okano
  • Jernej Ule
  • Masato Yano
  • Sebastien M Weyn-Vanhentenryck
  • Aldo Mele
  • Ankeeta Shah
  • Michael J Moore
  • Taesun Eom
  • Jeffrey L Noebels
  • Donny D Licatalosi
  • Gulayse Ince-Dunn
  • John J Fak
  • Yingzhi Qian
  • Emily Conn Gantman
  • John Fak
  • Kenneth Lay
  • Huidong Wang
  • Chingwen Yang
  • Kirk B Jensen
  • Margaret Herre
  • Jong Yoo
  • Ru Zhong
  • Sarah E Grabinski
  • Woong Yang Park

Detail Information

Publications10

  1. pmc Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data
    Chaolin Zhang
    Laboratory of Molecular Neuro Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
    Nat Biotechnol 29:607-14. 2011
    ..CIMS analysis provides a general and more precise means of mapping protein-RNA interactions than currently available methods and insight into the biochemical properties of such interactions in living tissues...
  2. pmc Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain
    Donny D Licatalosi
    Laboratory of Molecular Neuro Oncology, The Rockefeller University, New York, New York 10065, USA
    Genes Dev 26:1626-42. 2012
    ..Thus, Ptbp2 inhibition of a discrete set of adult neuronal exons underlies early brain development prior to neuronal differentiation and is essential for postnatal survival...
  3. pmc Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls
    Chaolin Zhang
    Laboratory of Molecular Neuro Oncology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Science 329:439-43. 2010
    ..Thus, we have developed a general approach to understanding mammalian RNA regulation at the systems level...
  4. pmc Prediction of clustered RNA-binding protein motif sites in the mammalian genome
    Chaolin Zhang
    Laboratory of Molecular Neuro Oncology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Nucleic Acids Res 41:6793-807. 2013
    ..This algorithm can be readily applied to other RBPs to infer their RNA-regulatory networks. The software is freely available at http://zhanglab.c2b2.columbia.edu/index.php/MCarts. ..
  5. doi mCarts: Genome-Wide Prediction of Clustered Sequence Motifs as Binding Sites for RNA-Binding Proteins
    Sebastien M Weyn-Vanhentenryck
    Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, P and S Building, Room 4 448, 630 W 168th Street, New York, NY, 10032, USA
    Methods Mol Biol 1421:215-26. 2016
    ..A probabilistic model is learned from bona fide binding sites determined by CLIP and applied genome wide to generate high specificity binding site predictions. ..
  6. pmc NOVA-dependent regulation of cryptic NMD exons controls synaptic protein levels after seizure
    Taesun Eom
    Laboratory of Molecular Neuro Oncology, Rockefeller University, New York, United States
    elife 2:e00178. 2013
    ..The data reveal a hidden means of dynamic RNA regulation linking electrical activity to splicing and protein output, and of mediating homeostatic excitation/inhibition balance in neurons.DOI:http://dx.doi.org/10.7554/eLife.00178.001...
  7. pmc Neuronal Elav-like (Hu) proteins regulate RNA splicing and abundance to control glutamate levels and neuronal excitability
    Gulayse Ince-Dunn
    Laboratory of Molecular Neuro Oncology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Neuron 75:1067-80. 2012
    ..The genome-wide analysis of nElavl targets reveals that one function of neuron-specific RNABPs is to control excitation-inhibition balance in the brain...
  8. pmc Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis
    Michael J Moore
    1 Laboratory of Molecular Neuro Oncology, The Rockefeller University, New York, New York, USA 2
    Nat Protoc 9:263-93. 2014
    ..Once IP conditions are established, HITS-CLIP takes ∼8 d to prepare RNA for sequencing. Established pipelines for data analysis, including those for CIMS, take 3-4 d. ..
  9. ncbi CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data
    Ankeeta Shah
    Department of Systems BiologyDepartment of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
    Bioinformatics . 2016
    ..The CLIP Tool Kit (CTK) aims at providing a set of tools for flexible, streamlined and comprehensive CLIP data analysis. This software package extends the scope of our original CIMS package...
  10. pmc FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism
    Jennifer C Darnell
    Laboratory of Molecular Neuro Oncology, The Rockefeller University, New York, NY 10065, USA
    Cell 146:247-61. 2011
    ..In addition, they provide insight into the molecular basis of the cognitive and allied defects in FXS and ASD and suggest multiple targets for clinical intervention...