Publications

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Recent papers

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

    [2013]

    • Wu,J., Krainer,A.R., Zhang,M.Q. †, Zhang,C. †, 2012. Fast and sensitive mapping of deep mRNA-seq data with OLego reveals many novel micro-exons.

    Nucleic Acids Res., In press. [ 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.
    • 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]

    • [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]

  • 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 MQ. 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 MQ. 2007. Biomedical literature mining. Chap 10. in Introduction to Bioinformatics: A workbook approach. (V. Mathura ed) Elsevier.


Invited talks

  • Zhang, C. 2012. Global RNA regulatory networks in the mammalian brain: insights from an integrative systems biology approach. Oct 16. Bioinformatics Division, TNLIST, Tsinghua University, Beijing, China.

  • Zhang, C. 2012. Searching for the specificity of RNA-binding proteins. 2012 CSHA RNA Biology. Oct 8-12. Suzhou. China.

  • Zhang, C. 2012. Global RNA regulatory networks in the mammalian brain: insights from an integrative systems biology approach. Sept 28, CAS-MPG Partner Institute for Computational Biology. Shanghai, China.

  • Zhang, C. 2011. Mapping microRNA target networks: HITS-CLIP and beyond. ASN Annual meeting Advances in Research Conference: MicroRNA. Nov 8-9. Philadelphia. PA.

  • Zhang, C. 2011. HITS-CLIP analysis of protein-RNA interactions: four computational challenges & two applications. Rockefeller Bioinformatics/Biostatistics Collaborative Group meeting. Oct 21. Rockefeller University.

  • Zhang, C. 2011. Elucidating global mammalian RNA-regulatory networks—an integrative systems biology approach Rockefeller University. May 31 (special seminar).

  • Zhang, C. 2010. Elucidating RNA-regulatory networks in the brain. FASEB Posttranscriptional Control of Gene Expression: Mechanisms of mRNA Decay. July 11-16. Carefree, AZ. .

  • Zhang, C. 2009. HITS-CLIP defines in vivo protein-RNA interactions in mouse brain. New York Illumina Genome Analyzer User Group Meeting. Nov. 18.

  • Zhang, C. 2009. From Bayesian network to gene regulatory network: a strategy of information fusion. Integrative Statistical Analysis of Genome Scale Data. Cold Spring Harbor. June 20. (invited lecture).

  • Zhang, C. 2007. Genome evolution and signals for fidelity and regulation of pre-mRNA splicing. Cold Spring Harbor Laboratory In-House Seminar. Oct. 26. CSHL.

  • Zhang, C. 2006. Profiling alternatively spliced mRNA isoforms for prostate cancer classification. Cambridge Healthtech Institute 6th Annual Workshop: Microarray Data and Interpretation. Aug23-25. Washington, DC.


Conference and Poster Presentations

  • Zhang, C., Darnell, R.B. 2012. Searching for the specificity of non-specific RNA-binding proteins 2012 Annual Meeting of the RNA Society. May 29-June 3. Ann Arbor. MI. (selected talk).

  • Zhang, C., Mele, A., Yano, M., Darnell, R.B. 2011. Single-nucleotide-resolution mapping of protein-RNA interactions using cross-linking induced mutation site (CIMS) analysis of HITS-CLIP data and its applications. Eukaryotic mRNA Processing. Aug 23-27. Cold Spring Harbor, NY (poster).

  • Zhang, C. 2011. Mapping the exact base of in vivo protein-RNA interactions. Rockefeller University Postdoctoral Retreat. August 03-04 (selected talk).

  • 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. Gordon Research Conference: Biology of Post-transcriptional Gene Regulation. Newport, RI (poster, RNA Society Poster Award).

  • Zhang, C., Frias, M., Ruggiu, M., Eom, T., Marney, C., Wang, H., Licatalosi, D., Mele., A., Fak, J., and Darnell, R.B., 2010. Integrative discovery and analysis of a global splicing-regulatory network in mouse brain. Systems Biology: Global Regulation of Gene Expression. Mar 23-27. Cold Spring Harbor, NY (poster).

  • Zhang, C. 2009. Integrative discovery and analysis of a global splicing-regulatory network in mouse brain. Postdoctoral retreat, Rockefeller University, Sep. 21-22.(selected talk).

  • Zhang, C., Ruggiu, M., Frias, M., Eom, T., Marney, C., Wang, H., Licatalosi, D., Mele., A., Fak, J., Darnell, J., and Darnell, R.B., 2009. Integrative discovery and analysis of a global splicing-regulatory network in mouse brain. Eukaryotic mRNA processing. Aug 18-22. Cold Spring Harbor, NY (selected talk).

  • Zhang, C., Li, W.-H., Krainer, A.R. and Zhang, M.Q. 2008. RNA landscape of evolution for optimal exon and intron discrimination. Systems Biology: Global Regulation of Gene Expression. Mar27-30. Cold Spring Harbor, NY (poster).

  • Zhang, C., Zhang Z., Castle, J., Sun, S., Johnson, J., Krainer, A.R. and Zhang, M.Q. 2007. Comprehensive prediction and characterization of pre-mRNA targets of the tissue-specific alternative splicing factors Fox-1/2. RECOMB Regulatory Genomics 2007. Oct 11-13. MIT/Broad Institute, Boston, NY (selected talk).

  • Zhang, C., Zhang Z., Castle, J., Sun, S., Johnson, J., Krainer, A.R., and Zhang, M.Q. 2007. Comprehensive prediction and characterization of pre-mRNA targets of the tissue-specific alternative splicing factors Fox-1/2. Eukaryotic mRNA Processing. Aug 22-26. Cold Spring Harbor, NY (selected talk).

  • Hasting, M.L.*, Krainer, A.R., and Zhang, M.Q. 2007. Dual-specificity splice sites are used as 3' and 5' splice sites. RNA 2007 Annual Meeting. May 29-June3. Madison WI. (selected oral presentation, *presenter)

  • Zhang, C., Krainer, A.R., and Zhang, M.Q. 2006. Comparative genomics evidence for frequent splicing errors in mammals. RNA 2006 Annual Meeting. June 20-25. Seattle, WA.

  • Zhang, C., Xuan, Z., and Zhang M.Q. 2005. Weak transcription factor binding sites enrich the genomes. Mechanisms of Eukaryotic Transcription. Aug 31-Sep4. Cold Spring Harbor Laboratory. NY 11724.

  • Zhang, C., and Li S. 2004. Modeling of neuro-endoimmune network via subject oriented literature mining. The Fourth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2004). Novosibirsk, Russia, July 25-30. [PDF]

  • Zhang, C., Li, Y., and Zhang, X. 2004. gMap: extracting and interactively visualizing nonlinear relationships of genes from expression. Proc. RECOMB 2004, March 2004, pp.228-229. [PDF]

  • Zhang, C., Zhang, X., Ma, X., and Li, Y. 2003. Establishing gene relevant networks about breast cancer via automatic literature mining” (in Chinese). China National Computer Congress (CNCC) 2003 [PDF]

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