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{{#meta: keywords | computational biology; systems biology; RNA splicing and regulatory networks; gene expression }}{{#meta: description | The Chaolin Zhang Laboratory Home Page at Columbia University}}{{#meta: Content-Type | text/html; charset=utf-8 }}
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__NOTOC__
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[[Publications|Papers]] | [[Talks]]
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['''*''' co-first authors; '''†''' co-corresponding authors]
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=2015=
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==MBNL sequestration by toxic RNAs and RNA misprocessing in the myotonic dystrophy brain==
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Goodwin, M., Mohan, A. Batra, R., Lee, K.-Y., Charizanis, K., Francisco Jose Fernandez-Gomez, F.J., Eddarkaoui, S., Sergeant, N., Buee, L., Kimura, T., Clark, H.B., Dalton, J., Takamura, K., <b>Weyn-Vanhentenryck, S.M. </b>, <b>Zhang, C.</b>, Reid, T., Ranum, L.P.W., Day, J.W., Swanson, M.S. 2015.
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''Cell Rep.'' http://dx.doi.org/10.1016/j.celrep.2015.07.029.
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[http://www.ncbi.nlm.nih.gov/pubmed/26257173" PubMed]
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[http://www.cell.com/cell-reports/pdf/S2211-1247(15)00789-5.pdf">PDF]
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<div class="title">mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA sequencing data. </div>
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<b>Feng, H.</b>, Zhang, X., <b>Zhang, C.† </b>, 2015.
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<p>
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<i>Nat Comm.</i> <b>6</b>:7816. doi: 10.1038/ncomms8816.
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[<a href="http://www.ncbi.nlm.nih.gov/pubmed/26234653">PubMed</a>]
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[<a href="http://www.pnas.org/content/early/2015/03/02/1502849112.full.pdf">PDF</a>]
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[<a href="http://zhanglab.c2b2.columbia.edu/index.php/mRIN">Software</a>]
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<p>
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- Research highlights, “How good are those RNA-seq data?”, <i>Nature Methods</i>, <b>12</b>:910 (2015).
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<div class="title">Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators.</div>
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<b>Yan, Q.*</b>, <b>Weyn-Vanhentenryck, S.M.*</b>,<b>Wu, J.</b>, Sloan, S.A., Zhang, Y., Chen, K., Wu, J.-Q., Barres, B.A.†, <b>Zhang, C.†</b>, 2015.
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<p>
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<i>Proc. Nat. Acad. Sci. USA. </i> Mar 3. pii: 201502849.
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[<a href="http://www.ncbi.nlm.nih.gov/pubmed/25737549">PubMed</a>]
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[<a href="http://www.nature.com/ncomms/2015/150803/ncomms8816/pdf/ncomms8816.pdf">PDF</a>]
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[<a href="http://zhanglab.c2b2.columbia.edu/index.php/Cortex_AS">Supp Info</a>]
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==2014==
  
 
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<div class="title">Loss of MBNL function leads to disruption of developmentally regulated alternative polyadenylation in RNA-mediated disease. </div>  
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Batra, R., Charizanis, K., Manchanda, M., Mohan, A., Li, M., Finn, D.J., Goodwin, <b>Zhang, C.</b>, Sobczak,K., Thornton, C.A., Swanson, M.S. 2014.
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<i>Mol Cell. </i> 56: 311-322.
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[<a href="http://www.ncbi.nlm.nih.gov/pubmed/25263597">PubMed</a>]
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[<a href="http://www.sciencedirect.com/science/article/pii/S1097276514006820/pdfft?md5=c81d51c9f97e8d76d1e21a5c75941edd&pid=1-s2.0-S1097276514006820-main.pdf">PDF</a>]
  
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<div class="title">An RNA-Sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex.</div>
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Zhang, Y., Chen, K., Sloan, S., Bennett, M.L., Scholze, A.R., O’Keeffe, S., Phatnani, H.P., Guarnieri, P., Caneda, C., Ruderisch, N., Deng, S., Liddelow, S.A., <b>Zhang, C.</b>, Daneman, R., Maniatis, T., Barres, B.A., Wu, J.-Q. 2014. 
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<i>J Neurosci.</i> 34:11929-11947.
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[<a href="http://www.ncbi.nlm.nih.gov/pubmed/25186741">PubMed</a>]
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<div class="title">HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. </div>
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<b>Weyn-Vanhentenryck, S.M.</b>*, Mele,A.*, <b>Yan,Q.</b>*, Sun,S., Farny,N., Zhang,Z., Xue,C., Herre,M., Silver,P.A., Zhang,M.Q., Krainer,A.R., Darnell,R.B. †, <b>Zhang,C.</b> † 2014. 
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<i>Cell Rep.</i> 10.1016/j.celrep.2014.02.005.
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[<a href="http://www.ncbi.nlm.nih.gov/pubmed/24613350">PubMed</a>]
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[<a href="http://download.cell.com/cell-reports/pdf/PIIS2211124714000849.pdf">PDF</a>]
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[<a href="http://zhanglab.c2b2.columbia.edu/index.php/CIMS">software</a>]
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<div class="title">Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. </div>
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Moore, M.*, <b>Zhang, C.</b>*, Gantman, E.C., Mele, A., Darnell, J.C., Darnell, R.B. 2014.
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<p>
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<i>Nat Protocols</i>, 9:263-293.
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[<a href="http://www.ncbi.nlm.nih.gov/pubmed/24407355?dopt=Abstract">PubMed</a>]
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[<a href="http://www.nature.com/nprot/journal/v9/n2/pdf/nprot.2014.012.pdf">PDF</a>]
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[<a href="http://zhanglab.c2b2.columbia.edu/index.php/CIMS">software</a>]
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==2013==
  
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'''Introduction of the Zhang Laboratory'''
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We are part of the [http://systemsbiology.columbia.edu Department of Systems Biology], the [http://cpmcnet.columbia.edu/dept/gsas/biochem/ Department of Biochemistry and Molecular Biophysics], and the [http://www.columbiamnc.org/ Motor Neuron Center] at [http://http://www.cumc.columbia.edu Columbia University Medical Center].
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We are fascinated by the complexity of the mammalian nervous system and its underlying molecular mechanisms. While mammals have a similar number of genes compared to phenotypically simpler organisms (such as worms), one apparent feature of mammalian genes is their more complicated gene structures, providing an opportunity for sophisticated regulation at the RNA level. 
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<div class="title">Progressive impairment of muscle regeneration in Muscleblind-like 3 isoform knockout mice. </div>
  
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The focus of the Zhang lab is to dissect RNA regulatory networks in the nervous system as a way to understand the mammalian complexity manifested in evolutionary-developmental (evo-devo) processes and in several neuronal disorders. We work on a range of problems towards the goal, including mechanistic understanding of the specificity of protein-RNA interactions, organizational principles of RNA regulatory networks, and functional implication of RNA regulation in neural development and in certain pathologic contexts (such as autism and neurodegenerative disorders).  The Zhang lab has a mixed dry and wet setup. We take advantage of different model systems, including mouse models and in vitro neural differentiation of embryonic stem cells, and a combination of high-throughput data-driven and hypothesis-driven approaches.
 
  
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Poulos, M.G., Batra, R., Li, M., Yuan, Y., <b>Zhang, C.</b>, Darnell, R.B., Swanson, M.S. 2013.
  
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'''Lab News'''
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<p>
  
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* 03/01/2016. Congratulate Ankeeta Shah on winning the 2016 SURF/Amgen fellowship!
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<i>Hum Mol Genet.</i> 22:3547-3558.
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* 06/19/2105. Chaolin Zhang received an R01 award from NIH/NINDS
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* 03/06/2015. Discovery of new AS exons in the brain published on PNAS
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[<a href="http://www.ncbi.nlm.nih.gov/pubmed/23660517?dopt=Abstract">PubMed</a>][<a href="http://hmg.oxfordjournals.org/content/early/2013/05/08/hmg.ddt209.full.pdf+html">PDF</a>]
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* 07/29/2014. Chaolin Zhang received a 3 year Research Award from Simons Foundation
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* 03/06/2014. Rbfox CLIP and integrative modeling paper published on Cell Reports
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</LI>
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* 01/10/2014. Step by step guide of CIMS analysis published on Nature Protocols
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* 09/24/2013. Chaolin Zhang received an Explorer Award from Simons Foundation
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<p>
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* 04/26/2013. mCarts paper published on NAR
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* 04/26/2013. OLego paper published on NAR
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<LI>
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<div class="title">Prediction of clustered RNA-binding protein motif sites in the mammalian genome. </div>
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<b>Zhang, C.</b> †, Lee, K.-Y., Swanson, M.S., Darnell, R.B. † 2013.
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<p>
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<i>Nucleic Acids Res.  </i> 41:6793-6807.  
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[<a href="http://nar.oxfordjournals.org/content/early/2013/05/17/nar.gkt421.full.pdf">PDF</a>]
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[<a href="http://zhanglab.c2b2.columbia.edu/index.php/MCarts_Documentation">software</a>]
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<div class="title">OLego: Fast and sensitive mapping of spliced mRNA-Seq reads using small seeds.</div>
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<b>Wu,J.</b>, Anczukow,O., Krainer,A.R., Zhang,M.Q. †, <b>Zhang,C.</b> †, 2013.  
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<p>
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<i>Nucleic Acids Res.  </i> 41:5149-5163.  
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[<a href="http://www.ncbi.nlm.nih.gov/pubmed/23571760?dopt=Abstract">PubMed</a>][<a href="http://nar.oxfordjournals.org/content/early/2013/04/08/nar.gkt216.full.pdf+html">PDF</a>][<a href="http://zhanglab.c2b2.columbia.edu/index.php/OLego">software</a>]
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[Publications before my own lab]
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==2012==
  
  
  
 
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<a href="http://sbi.c2b2.columbia.edu/"><img src="/data/images/CSB.png" width="147" height="40" /></a>
 
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<a href="http://www.columbiamnc.org/"><img src="/data/images/mnc_logo.gif" width="122" height="35" /></a>
 
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<a href="http://www.c2b2.columbia.edu"><img src="/data/images/C2B2_logo.png" width="215" height="60" /></a> <p>
 
  
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<div class="title">NOVA-dependent regulation of cryptic NMD exons controls synaptic protein levels after seizure. </div>
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Eom,T., <b>Zhang,C.</b>, Wang,H., Lay,K., Fak,J., Noebels,J.L., Darnell,R.B. 2012.
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<p>
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<i>eLife</i>, 2:e00178.
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[<a href="http://www.ncbi.nlm.nih.gov/pubmed/23359859‎?dopt=Abstract">PubMed</a>][<a href="http://elife.elifesciences.org/content/elife/2/e00178.full.pdf">PDF</a>]
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<div class="title">Neuronal Elav-like (Hu) Proteins Regulate RNA Splicing and Abundance to Control Glutamate Levels and Neuronal Excitability. </div>
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Ince-Dunn, G., Okano, H.J., Jensen, K.B., Park, W.Y., Zhong, R., Ule, J., Mele,A., Fak, J.J., Yang, C., <b>Zhang,C.</b>, Yoo, J., Herre, M., Okano, H., Noebels, J.L., Darnell, R.B., 2012. 
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<i>Neuron</i>, 75:1067-1080.
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[<a href="http://www.ncbi.nlm.nih.gov/pubmed/22998874?dopt=Abstract">PubMed</a>][<a href="http://ac.els-cdn.com/S0896627312006587/1-s2.0-S0896627312006587-main.pdf?_tid=4b5c6686-28eb-11e2-af58-00000aacb35f&acdnat=1352300362_a80f3a1435a1357a9a6b45a3918673c5">PDF</a>]
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<div class="title">The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult.  </div>
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Zhang,B.,  Arun,G., Mao,Y.S., Lazar,Z., Hung,G., Bhattacharjee,G., Xiao,X., Booth,C.J., Wu,J., <b>Zhang,C.</b>, Spector,D.L., 2012. 
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<p>
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<i>Cell Reports</i>, 2:111-123.
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[<a href="http://pdn.sciencedirect.com/science?_ob=MiamiImageURL&_cid=280959&_user=276325&_pii=S2211124712001635&_check=y&_origin=article&_zone=toolbar&_coverDate=26-Jul-2012&view=c&originContentFamily=serial&wchp=dGLbVlS-zSkWb&md5=8fe31b35ab69517df50fb38ff54ee1ad&pid=1-s2.0-S2211124712001635-main.pdf&sqtrkid=0.7794181457720697">PubMed</a>][<a href="http://genesdev.cshlp.org/content/26/14/1626.full.pdf">PDF</a>]
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<div class="title">Muscleblind-like 2 mediated alternative splicing in the developing brain and dysregulation in myotonic dystrophy. </div>
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Charizanis, K., Lee, K.-Y., Batra, R., Goodwin, M., <b>Zhang,C.</b>, Yuan, Y., Shuie, L., Cline, M., Scotti, M.M., Xia, G., Kumar,A., Ashizawa, T., Clark, H.B., Kimura, T., Takahashi, M.P., Fujimura, H., Jinnai, K., Yoshikawa, H., Pereira,M.G., Gourdon,G., Sakai,N., Nishino,S., Foster,T.C., Ares, M. Jr, Darnell, R.B. Swanson, M.S., 2012. 
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<i>Neuron</i>, 75:437-450.
 +
[<a href="http://www.ncbi.nlm.nih.gov/pubmed/22884328?dopt=Abstract">PubMed</a>][<a href="http://pdn.sciencedirect.com/science?_ob=MiamiImageURL&_cid=272195&_user=276325&_pii=S0896627312005259&_check=y&_origin=article&_zone=toolbar&_coverDate=09-Aug-2012&view=c&originContentFamily=serial&wchp=dGLzVBA-zSkWb&md5=5e68e7ef32a60388a706be10de84c960&pid=1-s2.0-S0896627312005259-main.pdf&sqtrkid=0.5248918924480677&sqtrkid=0.14140767510980368&sqtrkid=0.7367502509150654&sqtrkid=0.6107530847657472&sqtrkid=0.8712234853301197&sqtrkid=0.9306223317980766&sqtrkid=0.6240476940292865&sqtrkid=0.5726298945955932&sqtrkid=0.4283553180284798&sqtrkid=0.6780585322994739&sqtrkid=0.9059713387396187&sqtrkid=0.30562901636585593">PDF</a>]
 +
 
 +
<p>
 +
 
 +
</LI>
 +
 
 +
<LI>
 +
 
 +
<div class="title">Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain. </div>
 +
 
 +
Licatalosi,D.D., Yano,M., Fak,J.J., Mele,A., Grabinski,S.E., <b>Zhang,C.</b>, Darnell,R.B., 2012. 
 +
 
 +
<p>
 +
 
 +
<i>Genes Dev</i>, 26:1626-1642.
 +
[<a href="http://www.ncbi.nlm.nih.gov/pubmed/22802532?dopt=Abstract">PubMed</a>][<a href="http://genesdev.cshlp.org/content/26/14/1626.full.pdf">PDF</a>]
 +
 
 +
<p>
 +
 
 +
</LI>
 +
</html>
 +
 
 +
==2011==
 +
 
 +
<html>
 +
<LI>
 +
 
 +
<div class="title">Identification of novel androgen-regulated pathways and mRNA isoforms through genome-wide exon-specific profiling of the LNCaP transcriptome. </div>
 +
 
 +
Rajan P., Dalgliesh, C., Carling, P., Buist, T., <b>Zhang,C.</b>, Grellscheid, S., Armstrong, K., Stockley, J., Simillion, C., Gaughan, L., Kalna, G., Zhang, M.Q., Robson, C., Leung, H., Elliott, D. 2011. 
 +
 
 +
<br>
 +
 
 +
<i>PLoS One</i>, 6: e29088.
 +
[<a href="http://www.ncbi.nlm.nih.gov/pubmed/22194994?dopt=Abstract">PubMed</a>][<a href="http://www.plosone.org/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0029088&representation=PDF">PDF</a>]
 +
 
 +
<p>
 +
 
 +
</LI>
 +
 
 +
 
 +
<LI>
 +
 
 +
<div class="title">Study of FoxA pioneer factor at silent genes reveals Rfx-repressed enhancer at Cdx2 and a potential indicator of esophageal adenocarcinoma development. </div>
 +
 
 +
 
 +
Watts, J.A., <b>Zhang,C.</b>, Klein-Szanto, A.J., Kormish, J.D., Fu, J., Zhang, M.Q., Zaret, K.S. 2011.
 +
 
 +
<p>
 +
 
 +
<i>PLoS Genet</i>, 7: e1002277.
 +
[<a href="http://www.ncbi.nlm.nih.gov/pubmed/21935353?dopt=Abstract">PubMed</a>][<a href="http://www.plosgenetics.org/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pgen.1002277&representation=PDF">PDF</a>]
 +
 
 +
<p>
 +
 
 +
</LI>
 +
 
 +
 
 +
<LI>
 +
 
 +
<div>FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism. </div>
 +
 
 +
 
 +
Darnell, J.C., Van Driesche, S.J., <b>Zhang,C.</b>, Hung, K.Y.S., Mele, A., Fraser, C.E., Stone, E.F., Chen, C., Fak, J.J., Chi, S.W., Licatalosi, D.D., Richter, J.D., Darnell, R.B., 2011.
 +
 
 +
<br>
 +
 
 +
<i>Cell</i>, 146:247-261.
 +
 
 +
[<a href="http://www.ncbi.nlm.nih.gov/pubmed/21784246?dopt=Abstract">PubMed</a>][<a href="http://download.cell.com/pdf/PIIS0092867411006556.pdf">PDF</a>]
 +
<p>
 +
</LI>
 +
 
 +
 
 +
<LI>
 +
 
 +
<div class="title">Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data.  </div>
 +
 
 +
 
 +
<b>Zhang,C.</b>†, Darnell, R.B.† 2011.
 +
 
 +
<p>
 +
<i>Nat. Biotech.</i> 29:607-614.
 +
[<a href="http://www.ncbi.nlm.nih.gov/pubmed/21633356?dopt=Abstract">PubMed</a>][<a href="http://www.nature.com/nbt/journal/v29/n7/pdf/nbt.1873.pdf">PDF</a>]
 +
[<a href="http://zhanglab.c2b2.columbia.edu/index.php/CIMS">software</a>]
 +
<p>
 +
</LI>
 +
 
 +
</html>
 +
 
 +
==2010==
 +
 
 +
<html>
 +
<LI>
 +
 
 +
<div class="title">Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls.</div>
 +
 
 +
 
 +
<b>Zhang,C.</b>†, Frias, M.A., Mele, A., Ruggiu, M., Eom, T., Marney, C.B., Wang, H.,  Licatalosi, D.D., Fak, J.J., Darnell, R.B.† 2010.
 +
 
 +
<p>
 +
 
 +
<i>Science.</i> 329: 439-443.
 +
[<a href="http://www.ncbi.nlm.nih.gov/pubmed/20558669?dopt=Abstract">PubMed</a>][<a href="http://www.sciencemag.org/cgi/rapidpdf/science.1191150v1.pdf">PDF</a>]
 +
<br>
 +
- Editor’s choice, Pickersgill, H. 2010. Making the Final Cut. <i>Sci. Signal.</i> 3:ec234; <br>
 +
- Nominated by leading researchers as one of the 33 papers that represent breakthroughs in computational biology in 2010. Mak H.C., 2011. Trends in computational biology-2010. <i>Nat Biotech.</i> 29, doi:10.1038/nbt.1747.
 +
 
 +
<p>
 +
</LI>
 +
 
 +
<LI>
 +
<div class="title">Dissecting the unique role of the retinoblastoma tumor suppressor during cellular senescence.</div>
 +
 
 +
Chicas, A., Wang, X., <b>Zhang,C.</b>, McCurrach, M., Zhao Z., Ozlem, M., Dickins, R., Narita, M., Zhang, M.Q., and Lowe, S.W. 2010.
 +
 
 +
<br>
 +
 
 +
<i>Cancer Cell.</i> 17:376-387. [Comment in <i>Cancer Cell.</i> 2010 Apr 13;17(4):313-4.]
 +
[<a href="http://www.ncbi.nlm.nih.gov/pubmed/20385362?dopt=Abstract">PubMed</a>][<a href="http://www.sciencedirect.com/science/article/pii/S1535610810000723/pdfft?md5=a191ed96242c05f575dfa856697ecbab&pid=1-s2.0-S1535610810000723-main.pdf">PDF</a>]
 +
<p>
 +
</LI>
 +
 
 +
<p>
 +
<p>
 +
 
 +
</html>
 +
 
 +
==2008 or earlier==
 +
 
 +
<html>
 +
<LI>
 +
 
 +
<div class="title">Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines.</div>
 +
 
 +
Castle, J.C., <b>Zhang,C.</b>, Shah, J.K., Kulkarni, A.V., Cooper, T.A., Johnson, J.M. 2008.
 +
 
 +
<p>
 +
 
 +
<i>Nature Genet.</i> 40:1416-1425.
 +
[<a href="http://www.ncbi.nlm.nih.gov/pubmed/18978788?dopt=Abstract">PubMed</a>][<a href="http://www.nature.com/ng/journal/v40/n12/pdf/ng.264.pdf">PDF</a>]
 +
<p>
 +
</LI>
 +
 
 +
<LI>
 +
 
 +
<div class="title">Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. </div>
 +
 
 +
 
 +
<b>Zhang,C.</b>*, Zhang, Z.*, Castle, J., Sun, S., Johnson, J., Krainer, A.R. and Zhang, M.Q. 2008.
 +
<br>
 +
<i>Genes Dev.</i> 22:2550-2563.
 +
[<a href="http://www.ncbi.nlm.nih.gov/pubmed/18794351?dopt=Abstract">PubMed</a>][<a href="http://genesdev.cshlp.org/cgi/reprint/22/18/2550">PDF</a>]
 +
<p>
 +
</LI>
 +
 
 +
<LI>
 +
 
 +
<div class="title">An RNA landscape of evolution for optimal exon and intron discrimination. </div>
 +
 
 +
<b>Zhang,C.</b>, Li, W.-H., Krainer, A.R. and Zhang, M.Q. 2008.
 +
<br>
 +
<i>Proc. Nat. Acad. Sci. USA</i>. 105:5797-802.
 +
[<a href="http://www.ncbi.nlm.nih.gov/pubmed/18391195?dopt=Abstract">PubMed</a>][<a href="http://www.pnas.org/content/105/15/5797.full.pdf+html">PDF</a>]
 +
<p>
 +
</LI>
 +
 
 +
<LI>
 +
<div class="title">Dual-specificity splice sites function alternatively as 5&#39; and 3&#39; splice sites. </div>
 +
 
 +
<b>Zhang,C.</b>, Hasting, M.L., Krainer, A.R., Zhang, M.Q. 2007.
 +
 +
<br>
 +
<i>Proc. Nat. Acad. Sci. USA.</i> 104(38): 15028-15033
 +
[<a href="http://portal.isiknowledge.com/portal.cgi?DestApp=XS_FORM&amp;Func=Frame">PubMed</a>][<a href="http://www.pnas.org/cgi/content/full/104/38/15028">PDF</a>].
 +
 
 +
<p>
 +
</LI>
 +
 
 +
 
 +
<LI>
 +
<div class="title">Evolutionary impact of limited splicing fidelity in mammalian genes. </div>
 +
 
 +
<b>Zhang,C.</b>, Krainer A.R., Zhang, M.Q. 2007.
 +
 
 +
<br>
 +
 
 +
<i>Trends Genet.</i> 23(10): 484-488.
 +
[<a href="http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17719121&amp;ordinalpos=1&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum">PubMed</a>][<a href="http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6TCY-4PGXF12-1&_user=429752&amp;_coverDate=08/24/2007&amp;_rdoc=1&amp;_fmt=&amp;_orig=search&amp;_sort=d&amp;view=c&amp;_acct=C000020578&amp;_version=1&amp;_urlVersion=0&amp;_userid=429752&amp;md5=18d53f024a0cc53702a98f6b14a7b154">PDF</a>]
 +
 
 +
<p>
 +
</LI>
 +
 
 +
<LI>
 +
 
 +
<div class="title">An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers. </div>
 +
 
 +
Smith, P.J., <b>Zhang,C.</b>, Wang, J., Chew, S.L., Zhang, M.Q., Krainer, A.R. 2006.
 +
 
 +
<br>
 +
<i>Hum Mol Genet</i>, 15:16):2490-2508.
 +
[<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16825284&amp;query_hl=2&amp;itool=pubmed_docsum">PubMed</a>][<a href="http://hmg.oxfordjournals.org/cgi/reprint/ddl171v1">PDF</a>]
 +
<p>
 +
</LI>
 +
 
 +
<LI>
 +
<div class="title">Profiling alternatively spliced mRNA isoforms for prostate cancer classification. </div>
 +
 
 +
 
 +
<b>Zhang,C.</b>, Li, H.-R., Fan, J.-B., Wang-Rodriguez, J., Downs, T., Fu, X.-D. and Zhang, M.Q. 2006.
 +
<br>
 +
<i>BMC Bioinformatics, </i>7:202.
 +
[<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=16608523">PubMed</a>][<a href="http://www.biomedcentral.com/content/pdf/1471-2105-7-202.pdf">PDF</a>]
 +
 
 +
<p>
 +
</LI>
 +
 
 +
<LI><b>
 +
 
 +
<div class="title">Neighbor Number, Valley Seeking and Clustering. </div>
 +
 
 +
Zhang,C.</b>, Zhang, X., Zhang, M.Q. and Li, Y. 2007.
 +
<i>Pattern Recognition Letters, </i>28:173-180.
 +
 
 +
<p>
 +
 
 +
 
 +
<LI>
 +
 
 +
<div class="title">A Clustering property of highly-degenerate transcription factor binding sites in the mammalian genome. </div>
 +
 
 +
 
 +
<b>Zhang,C.</b>, Xuan, Z., Otto, S., Hover, J.R., McCorkle, S.R., Mandel, G. and Zhang, M.Q. 2006.
 +
<br>
 +
 
 +
<i>Nucl Acids Res, </i>34: 2238-2246.
 +
[<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16670430&query_hl=1&itool=pubmed_docsum">PubMed</a>] [<a href="http://nar.oxfordjournals.org/cgi/reprint/34/8/2238">PDF</a>]
 +
 
 +
<p>
 +
 
 +
</LI>
 +
 
 +
<LI>
 +
 
 +
<div class="title">Significance of Gene Ranking for Classification of Microarray Samples. </div>
 +
 
 +
<b>Zhang,C.</b>*, Lu, X.* and Zhang, X. 2005.
 +
<br>
 +
 
 +
<i>IEEE/ACM Transactions on Computational Biology and Bioinformatics</i>, 3(3): 312-320.
 +
[<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17048468&query_hl=2&itool=pubmed_docsum">PubMed</a>]
 +
<p>
 +
 
 +
</LI>
 +
 
 +
 
 +
</html>
 +
 
 +
==Book Chapters==
 +
 
 +
<html>
 +
 
 +
 
 +
<LI>
 +
 
 +
 
 +
<div class="title">Identification of Splicing Factor Target Genes by High-Throughput Sequencing. </div>
 +
 
 +
 
 +
 
 +
<b>Zhang,C.</b>, Zhang,M.Q. 2012.
 +
<br>
 +
Chapter 51 <i>in Alternative pre-mRNA Splicing: Theory and Protocols. </i>(S. Stamm, C.W. J. Smith, R. Lührmann, ed). Wiley-VCH Verlag GmbH & Co.
 +
 
 +
<p>
 +
</LI>
 +
 
 +
 
 +
<LI>
 +
 
 +
<div class="title">Functional <i>in sillico</i> analysis of gene regulatory polymorphism.</div>
 +
 
 +
 
 +
<b>Zhang,C.</b>, Zhao,X. and Zhang,M.Q. 2006. <br>
 +
 
 +
Chapter 12. In <i>Bioinformatics for Geneticists: A Bioinformatics primer for the analysis of genetic data</i>.&nbsp; 2nd Ed. (M.R. Barnes, ed.) &nbsp;John Wiley &amp; Sons, LTD.
 +
[<a style="color: blue; text-decoration: underline; text-underline: single" href="http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470026197,descCd-tableOfContents.html">Wiley-VCH</a>]
 +
[<a style="color: blue; text-decoration: underline; text-underline: single" href="http://rulai.cshl.edu/reprints/bioinfo4gen_chapter12_zhang.pdf">PDF</a>]
 +
 
 +
<p>
 +
 
 +
</LI>
 +
 
 +
<LI>
 +
 
 +
<div class="title">Biomedical literature mining. </div>
 +
 
 +
<b>Zhang,C.</b>, Zhang,M.Q. 2007. <br>
 +
 
 +
Chap 10. in <i>Introduction to Bioinformatics: A workbook approach</i>. (V. Mathura ed) Elsevier.
 +
 
 +
<p>
 +
</LI>
 +
</UL>
 +
 
 +
 
 
</html>
 
</html>

Revision as of 18:19, 10 March 2016


Papers | Talks

[* co-first authors; † co-corresponding authors]


2015

MBNL sequestration by toxic RNAs and RNA misprocessing in the myotonic dystrophy brain

Goodwin, M., Mohan, A. Batra, R., Lee, K.-Y., Charizanis, K., Francisco Jose Fernandez-Gomez, F.J., Eddarkaoui, S., Sergeant, N., Buee, L., Kimura, T., Clark, H.B., Dalton, J., Takamura, K., Weyn-Vanhentenryck, S.M. , Zhang, C., Reid, T., Ranum, L.P.W., Day, J.W., Swanson, M.S. 2015.

Cell Rep. http://dx.doi.org/10.1016/j.celrep.2015.07.029. " PubMed ">PDF


mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA sequencing data.

Feng, H., Zhang, X., Zhang, C.† , 2015.

Nat Comm. 6:7816. doi: 10.1038/ncomms8816. [<a href="http://www.ncbi.nlm.nih.gov/pubmed/26234653">PubMed</a>] [<a href="http://www.pnas.org/content/early/2015/03/02/1502849112.full.pdf">PDF</a>] [<a href="http://zhanglab.c2b2.columbia.edu/index.php/mRIN">Software</a>] <p> - Research highlights, “How good are those RNA-seq data?”, Nature Methods, 12:910 (2015). </LI> <p>

  • Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators.

    Yan, Q.*, Weyn-Vanhentenryck, S.M.*,Wu, J., Sloan, S.A., Zhang, Y., Chen, K., Wu, J.-Q., Barres, B.A.†, Zhang, C.†, 2015.

    <p> Proc. Nat. Acad. Sci. USA. Mar 3. pii: 201502849. [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25737549">PubMed</a>] [<a href="http://www.nature.com/ncomms/2015/150803/ncomms8816/pdf/ncomms8816.pdf">PDF</a>] [<a href="http://zhanglab.c2b2.columbia.edu/index.php/Cortex_AS">Supp Info</a>]

    • <p> </html>

    2014

  • Loss of MBNL function leads to disruption of developmentally regulated alternative polyadenylation in RNA-mediated disease.
    Batra, R., Charizanis, K., Manchanda, M., Mohan, A., Li, M., Finn, D.J., Goodwin, Zhang, C., Sobczak,K., Thornton, C.A., Swanson, M.S. 2014.

    Mol Cell. 56: 311-322. [PubMed] [PDF]

  • An RNA-Sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex.
    Zhang, Y., Chen, K., Sloan, S., Bennett, M.L., Scholze, A.R., O’Keeffe, S., Phatnani, H.P., Guarnieri, P., Caneda, C., Ruderisch, N., Deng, S., Liddelow, S.A., Zhang, C., Daneman, R., Maniatis, T., Barres, B.A., Wu, J.-Q. 2014.

    J Neurosci. 34:11929-11947. [PubMed] [PDF]

  • HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism.
    Weyn-Vanhentenryck, S.M.*, Mele,A.*, Yan,Q.*, Sun,S., Farny,N., Zhang,Z., Xue,C., Herre,M., Silver,P.A., Zhang,M.Q., Krainer,A.R., Darnell,R.B. †, Zhang,C. † 2014.

    Cell Rep. 10.1016/j.celrep.2014.02.005. [PubMed] [PDF] [software]

  • Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis.
    Moore, M.*, Zhang, C.*, Gantman, E.C., Mele, A., Darnell, J.C., Darnell, R.B. 2014.

    Nat Protocols, 9:263-293. [PubMed] [PDF] [software]

    • 2013

  • Progressive impairment of muscle regeneration in Muscleblind-like 3 isoform knockout mice.
    Poulos, M.G., Batra, R., Li, M., Yuan, Y., Zhang, C., Darnell, R.B., Swanson, M.S. 2013.

    Hum Mol Genet. 22:3547-3558. [PubMed][PDF]

  • Prediction of clustered RNA-binding protein motif sites in the mammalian genome.
    Zhang, C. †, Lee, K.-Y., Swanson, M.S., Darnell, R.B. † 2013.

    Nucleic Acids Res. 41:6793-6807. [PDF] [software]

  • OLego: Fast and sensitive mapping of spliced mRNA-Seq reads using small seeds.
    Wu,J., Anczukow,O., Krainer,A.R., Zhang,M.Q. †, Zhang,C. †, 2013.

    Nucleic Acids Res. 41:5149-5163. [PubMed][PDF][software]





    • [Publications before my own lab]

      <p>

      2012

    • NOVA-dependent regulation of cryptic NMD exons controls synaptic protein levels after seizure.
      Eom,T., Zhang,C., Wang,H., Lay,K., Fak,J., Noebels,J.L., Darnell,R.B. 2012.

      eLife, 2:e00178. [PubMed][PDF]

    • Neuronal Elav-like (Hu) Proteins Regulate RNA Splicing and Abundance to Control Glutamate Levels and Neuronal Excitability.
      Ince-Dunn, G., Okano, H.J., Jensen, K.B., Park, W.Y., Zhong, R., Ule, J., Mele,A., Fak, J.J., Yang, C., Zhang,C., Yoo, J., Herre, M., Okano, H., Noebels, J.L., Darnell, R.B., 2012.

      Neuron, 75:1067-1080. [PubMed][PDF]

    • The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult.
      Zhang,B., Arun,G., Mao,Y.S., Lazar,Z., Hung,G., Bhattacharjee,G., Xiao,X., Booth,C.J., Wu,J., Zhang,C., Spector,D.L., 2012.

      Cell Reports, 2:111-123. [PubMed][PDF]

    • Muscleblind-like 2 mediated alternative splicing in the developing brain and dysregulation in myotonic dystrophy.
      Charizanis, K., Lee, K.-Y., Batra, R., Goodwin, M., Zhang,C., Yuan, Y., Shuie, L., Cline, M., Scotti, M.M., Xia, G., Kumar,A., Ashizawa, T., Clark, H.B., Kimura, T., Takahashi, M.P., Fujimura, H., Jinnai, K., Yoshikawa, H., Pereira,M.G., Gourdon,G., Sakai,N., Nishino,S., Foster,T.C., Ares, M. Jr, Darnell, R.B. Swanson, M.S., 2012.

      Neuron, 75:437-450. [PubMed][PDF]

    • Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain.
      Licatalosi,D.D., Yano,M., Fak,J.J., Mele,A., Grabinski,S.E., Zhang,C., Darnell,R.B., 2012.

      Genes Dev, 26:1626-1642. [PubMed][PDF]

      • 2011

    • Identification of novel androgen-regulated pathways and mRNA isoforms through genome-wide exon-specific profiling of the LNCaP transcriptome.
      Rajan P., Dalgliesh, C., Carling, P., Buist, T., Zhang,C., Grellscheid, S., Armstrong, K., Stockley, J., Simillion, C., Gaughan, L., Kalna, G., Zhang, M.Q., Robson, C., Leung, H., Elliott, D. 2011.
      PLoS One, 6: e29088. [PubMed][PDF]

    • Study of FoxA pioneer factor at silent genes reveals Rfx-repressed enhancer at Cdx2 and a potential indicator of esophageal adenocarcinoma development.
      Watts, J.A., Zhang,C., Klein-Szanto, A.J., Kormish, J.D., Fu, J., Zhang, M.Q., Zaret, K.S. 2011.

      PLoS Genet, 7: e1002277. [PubMed][PDF]

    • FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism.
      Darnell, J.C., Van Driesche, S.J., Zhang,C., Hung, K.Y.S., Mele, A., Fraser, C.E., Stone, E.F., Chen, C., Fak, J.J., Chi, S.W., Licatalosi, D.D., Richter, J.D., Darnell, R.B., 2011.
      Cell, 146:247-261. [PubMed][PDF]

    • Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data.
      Zhang,C.†, Darnell, R.B.† 2011.

      Nat. Biotech. 29:607-614. [PubMed][PDF] [software]

      • 2010

    • Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls.
      Zhang,C.†, Frias, M.A., Mele, A., Ruggiu, M., Eom, T., Marney, C.B., Wang, H., Licatalosi, D.D., Fak, J.J., Darnell, R.B.† 2010.

      Science. 329: 439-443. [PubMed][PDF]
      - Editor’s choice, Pickersgill, H. 2010. Making the Final Cut. Sci. Signal. 3:ec234;
      - Nominated by leading researchers as one of the 33 papers that represent breakthroughs in computational biology in 2010. Mak H.C., 2011. Trends in computational biology-2010. Nat Biotech. 29, doi:10.1038/nbt.1747.

    • Dissecting the unique role of the retinoblastoma tumor suppressor during cellular senescence.
      Chicas, A., Wang, X., Zhang,C., McCurrach, M., Zhao Z., Ozlem, M., Dickins, R., Narita, M., Zhang, M.Q., and Lowe, S.W. 2010.
      Cancer Cell. 17:376-387. [Comment in Cancer Cell. 2010 Apr 13;17(4):313-4.] [PubMed][PDF]

      • 2008 or earlier

    • Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines.
      Castle, J.C., Zhang,C., Shah, J.K., Kulkarni, A.V., Cooper, T.A., Johnson, J.M. 2008.

      Nature Genet. 40:1416-1425. [PubMed][PDF]

    • Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2.
      Zhang,C.*, Zhang, Z.*, Castle, J., Sun, S., Johnson, J., Krainer, A.R. and Zhang, M.Q. 2008.
      Genes Dev. 22:2550-2563. [PubMed][PDF]

    • An RNA landscape of evolution for optimal exon and intron discrimination.
      Zhang,C., Li, W.-H., Krainer, A.R. and Zhang, M.Q. 2008.
      Proc. Nat. Acad. Sci. USA. 105:5797-802. [PubMed][PDF]

    • Dual-specificity splice sites function alternatively as 5' and 3' splice sites.
      Zhang,C., Hasting, M.L., Krainer, A.R., Zhang, M.Q. 2007.
      Proc. Nat. Acad. Sci. USA. 104(38): 15028-15033 [PubMed][PDF].

    • Evolutionary impact of limited splicing fidelity in mammalian genes.
      Zhang,C., Krainer A.R., Zhang, M.Q. 2007.
      Trends Genet. 23(10): 484-488. [PubMed][PDF]

    • An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers.
      Smith, P.J., Zhang,C., Wang, J., Chew, S.L., Zhang, M.Q., Krainer, A.R. 2006.
      Hum Mol Genet, 15:16):2490-2508. [PubMed][PDF]

    • Profiling alternatively spliced mRNA isoforms for prostate cancer classification.
      Zhang,C., Li, H.-R., Fan, J.-B., Wang-Rodriguez, J., Downs, T., Fu, X.-D. and Zhang, M.Q. 2006.
      BMC Bioinformatics, 7:202. [PubMed][PDF]

    • Neighbor Number, Valley Seeking and Clustering.
      Zhang,C.      , Zhang, X., Zhang, M.Q. and Li, Y. 2007. Pattern Recognition Letters, 28:173-180.

    • A Clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.
      Zhang,C., Xuan, Z., Otto, S., Hover, J.R., McCorkle, S.R., Mandel, G. and Zhang, M.Q. 2006.
      Nucl Acids Res, 34: 2238-2246. [PubMed] [PDF]

    • Significance of Gene Ranking for Classification of Microarray Samples.
      Zhang,C.*, Lu, X.* and Zhang, X. 2005.
      IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3(3): 312-320. [PubMed]

      • Book Chapters

    • Identification of Splicing Factor Target Genes by High-Throughput Sequencing.
      Zhang,C., Zhang,M.Q. 2012.
      Chapter 51 in Alternative pre-mRNA Splicing: Theory and Protocols. (S. Stamm, C.W. J. Smith, R. Lührmann, ed). Wiley-VCH Verlag GmbH & Co.

    • Functional in sillico analysis of gene regulatory polymorphism.
      Zhang,C., Zhao,X. and Zhang,M.Q. 2006.
      Chapter 12. In Bioinformatics for Geneticists: A Bioinformatics primer for the analysis of genetic data.  2nd Ed. (M.R. Barnes, ed.)  John Wiley & Sons, LTD. [Wiley-VCH] [PDF]

    • Biomedical literature mining.
      Zhang,C., Zhang,M.Q. 2007.
      Chap 10. in Introduction to Bioinformatics: A workbook approach. (V. Mathura ed) Elsevier.

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