Difference between revisions of "Publications"

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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>,  
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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>,  
 
Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators.
 
Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators.
 
<i>Proc. Nat. Acad. Sci. USA. </i> Mar 3. pii: 201502849.
 
<i>Proc. Nat. Acad. Sci. USA. </i> Mar 3. pii: 201502849.

Revision as of 17:32, 17 March 2015


Papers | Talks


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


    2015

  • Yan, Q.*, Weyn-Vanhentenryck, S.M.*,Wu, J., Sloan, S.A., Zhang, Y., Chen, K., Wu, J.-Q., Barres, B.A.†, Zhang, C.†, Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators. Proc. Nat. Acad. Sci. USA. Mar 3. pii: 201502849. [PubMed] [PDF] [Supp Info]

    • 2014

  • 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. Loss of MBNL function leads to disruption of developmentally regulated alternative polyadenylation in RNA-mediated disease. Mol Cell. 56: 311-322.
    • [PubMed] [PDF]

  • 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. An RNA-Sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex. J Neurosci. 34:11929-11947. [PubMed] [PDF]

  • 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. HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. Cell Rep. 10.1016/j.celrep.2014.02.005. [PubMed] [PDF] [software]

  • Moore, M.*, Zhang, C.*, Gantman, E.C., Mele, A., Darnell, J.C., Darnell, R.B. 2014. Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. Nat Protocols, 9:263-293. [PubMed] [PDF] [software]

    • 2013

  • Poulos, M.G., Batra, R., Li, M., Yuan, Y., Zhang, C., Darnell, R.B., Swanson, M.S. 2013. Progressive impairment of muscle regeneration in Muscleblind-like 3 isoform knockout mice. Hum Mol Genet. 22:3547-3558. [PubMed][PDF]

  • Zhang, C. †, Lee, K.-Y., Swanson, M.S., Darnell, R.B. † 2013. Prediction of clustered RNA-binding protein motif sites in the mammalian genome. Nucleic Acids Res. 41:6793-6807. [PDF] [software]

  • Wu,J., Anczukow,O., Krainer,A.R., Zhang,M.Q. †, Zhang,C. †, 2013. OLego: Fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. Nucleic Acids Res. 41:5149-5163. [PubMed][PDF][software]

    • 2012

  • Eom,T., Zhang,C., Wang,H., Lay,K., Fak,J., Noebels,J.L., Darnell,R.B. 2012. NOVA-dependent regulation of cryptic NMD exons controls synaptic protein levels after seizure. eLife, 2:e00178. [PubMed][PDF]

  • 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. Neuronal Elav-like (Hu) Proteins Regulate RNA Splicing and Abundance to Control Glutamate Levels and Neuronal Excitability. Neuron, 75:1067-1080. [PubMed][PDF]

  • 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. The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult. Cell Reports, 2:111-123. [PubMed][PDF]

  • 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. Muscleblind-like 2 mediated alternative splicing in the developing brain and dysregulation in myotonic dystrophy. Neuron, 75:437-450. [PubMed][PDF]

  • Licatalosi,D.D., Yano,M., Fak,J.J., Mele,A., Grabinski,S.E., Zhang,C., Darnell,R.B., 2012. Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain. Genes Dev, 26:1626-1642. [PubMed][PDF]

    • 2011

  • 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. Identification of novel androgen-regulated pathways and mRNA isoforms through genome-wide exon-specific profiling of the LNCaP transcriptome. PLoS One, 6: e29088. [PubMed][PDF]

  • Watts, J.A., Zhang,C., Klein-Szanto, A.J., Kormish, J.D., Fu, J., Zhang, M.Q., Zaret, K.S. 2011. Study of FoxA pioneer factor at silent genes reveals Rfx-repressed enhancer at Cdx2 and a potential indicator of esophageal adenocarcinoma development. PLoS Genet, 7: e1002277. [PubMed][PDF]

  • 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. FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism. Cell, 146:247-261. [PubMed][PDF]

  • Zhang,C.†, Darnell, R.B.† 2011. Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat. Biotech. 29:607-614. [PubMed][PDF] [software]

    • 2010

  • 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. Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls. 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.

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

    • 2008 or earlier

  • Castle, J.C., Zhang,C., Shah, J.K., Kulkarni, A.V., Cooper, T.A., Johnson, J.M. 2008. Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines. Nature Genet. 40:1416-1425. [PubMed][PDF]

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

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

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

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

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

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

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

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

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


    • Book Chapters

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

  • Zhang,C., Zhao,X. and Zhang,M.Q. 2006. Functional in sillico analysis of gene regulatory polymorphism. 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]

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

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