Difference between revisions of "Test"
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− | + | __NOTOC__ | |
− | + | [[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] | |
− | + | [http://www.cell.com/cell-reports/pdf/S2211-1247(15)00789-5.pdf PDF] | |
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− | + | =====mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA sequencing data===== | |
− | + | <b>Feng, H.</b>, Zhang, X., <b>Zhang, C.† </b>, 2015. | |
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− | + | ''Nat Comm.'' '''6''':7816. doi: 10.1038/ncomms8816. | |
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+ | [http://www.ncbi.nlm.nih.gov/pubmed/26234653 PubMed] | ||
+ | [http://www.pnas.org/content/early/2015/03/02/1502849112.full.pdf PDF] | ||
+ | [http://zhanglab.c2b2.columbia.edu/index.php/mRIN Software] | ||
− | + | - Research highlights, “How good are those RNA-seq data?”, ''Nature Methods'', <b>12</b>:910 (2015). | |
− | < | + | |
+ | =====Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators.===== | ||
− | + | <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. | |
− | + | ''Proc. Nat. Acad. Sci. USA.'' Mar 3. pii: 201502849. | |
− | + | [http://www.ncbi.nlm.nih.gov/pubmed/25737549 PubMed] | |
+ | [http://www.nature.com/ncomms/2015/150803/ncomms8816/pdf/ncomms8816.pdf PDF] | ||
+ | [http://zhanglab.c2b2.columbia.edu/index.php/Cortex_AS Supp Info] | ||
− | + | ==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, <b>Zhang, C.</b>, Sobczak,K., Thornton, C.A., Swanson, M.S. 2014. | ||
+ | ''Mol Cell.'' 56: 311-322. | ||
+ | [http://www.ncbi.nlm.nih.gov/pubmed/25263597 PubMed] | ||
+ | [http://www.sciencedirect.com/science/article/pii/S1097276514006820/pdfft?md5=c81d51c9f97e8d76d1e21a5c75941edd&pid=1-s2.0-S1097276514006820-main.pdf 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., <b>Zhang, C.</b>, Daneman, R., Maniatis, T., Barres, B.A., Wu, J.-Q. 2014. | ||
+ | ''J Neurosci.'' 34:11929-11947. | ||
+ | [http://www.ncbi.nlm.nih.gov/pubmed/25186741 PubMed] | ||
+ | [http://www.jneurosci.org/content/34/36/11929.full.pdf+html PDF] | ||
− | + | =====HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism===== | |
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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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− | </ | + | ''Cell Rep.'' 10.1016/j.celrep.2014.02.005. |
− | </html> | + | |
+ | [http://www.ncbi.nlm.nih.gov/pubmed/24613350 PubMed] | ||
+ | [http://download.cell.com/cell-reports/pdf/PIIS2211124714000849.pdf PDF] | ||
+ | [http://zhanglab.c2b2.columbia.edu/index.php/CIMS software] | ||
+ | |||
+ | =====Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis===== | ||
+ | |||
+ | Moore, M.*, <b>Zhang, C.</b>*, Gantman, E.C., Mele, A., Darnell, J.C., Darnell, R.B. 2014. | ||
+ | |||
+ | ''Nat Protocols'', 9:263-293. | ||
+ | |||
+ | [http://www.ncbi.nlm.nih.gov/pubmed/24407355?dopt=Abstract PubMed] | ||
+ | [http://www.nature.com/nprot/journal/v9/n2/pdf/nprot.2014.012.pdf PDF] | ||
+ | [http://zhanglab.c2b2.columbia.edu/index.php/CIMS software] | ||
+ | |||
+ | ==2013== | ||
+ | |||
+ | =====Progressive impairment of muscle regeneration in Muscleblind-like 3 isoform knockout mice===== | ||
+ | |||
+ | Poulos, M.G., Batra, R., Li, M., Yuan, Y., <b>Zhang, C.</b>, Darnell, R.B., Swanson, M.S. 2013. | ||
+ | |||
+ | ''Hum Mol Genet.'' 22:3547-3558. | ||
+ | |||
+ | [http://www.ncbi.nlm.nih.gov/pubmed/23660517?dopt=Abstract PubMed] | ||
+ | [http://hmg.oxfordjournals.org/content/early/2013/05/08/hmg.ddt209.full.pdf+html PDF] | ||
+ | |||
+ | =====Prediction of clustered RNA-binding protein motif sites in the mammalian genome===== | ||
+ | |||
+ | <b>Zhang, C.</b> †, Lee, K.-Y., Swanson, M.S., Darnell, R.B. † 2013. | ||
+ | |||
+ | ''Nucleic Acids Res.'' 41:6793-6807. | ||
+ | [http://nar.oxfordjournals.org/content/early/2013/05/17/nar.gkt421.full.pdf PDF] | ||
+ | [http://zhanglab.c2b2.columbia.edu/index.php/MCarts_Documentation software] | ||
+ | |||
+ | =====OLego: Fast and sensitive mapping of spliced mRNA-Seq reads using small seeds===== | ||
+ | |||
+ | <b>Wu,J.</b>, Anczukow,O., Krainer,A.R., Zhang,M.Q. †, <b>Zhang,C.</b> †, 2013. | ||
+ | |||
+ | ''Nucleic Acids Res.'' 41:5149-5163. | ||
+ | |||
+ | [http://www.ncbi.nlm.nih.gov/pubmed/23571760?dopt=Abstract PubMed] | ||
+ | [http://nar.oxfordjournals.org/content/early/2013/04/08/nar.gkt216.full.pdf+html PDF] | ||
+ | [http://zhanglab.c2b2.columbia.edu/index.php/OLego software] | ||
+ | |||
+ | |||
+ | |||
+ | |||
+ | [Publications before my own lab] | ||
+ | |||
+ | ==2012== | ||
+ | |||
+ | |||
+ | |||
+ | =====NOVA-dependent regulation of cryptic NMD exons controls synaptic protein levels after seizure===== | ||
+ | |||
+ | Eom,T., <b>Zhang,C.</b>, Wang,H., Lay,K., Fak,J., Noebels,J.L., Darnell,R.B. 2012. | ||
+ | |||
+ | ''eLife'', 2:e00178. | ||
+ | |||
+ | [http://www.ncbi.nlm.nih.gov/pubmed/23359859?dopt=Abstract PubMed] | ||
+ | [http://elife.elifesciences.org/content/elife/2/e00178.full.pdf 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., <b>Zhang,C.</b>, Yoo, J., Herre, M., Okano, H., Noebels, J.L., Darnell, R.B., 2012. | ||
+ | |||
+ | ''Neuron'', 75:1067-1080. | ||
+ | |||
+ | [http://www.ncbi.nlm.nih.gov/pubmed/22998874?dopt=Abstract PubMed] | ||
+ | [http://ac.els-cdn.com/S0896627312006587/1-s2.0-S0896627312006587-main.pdf?_tid=4b5c6686-28eb-11e2-af58-00000aacb35f&acdnat=1352300362_a80f3a1435a1357a9a6b45a3918673c5 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., <b>Zhang,C.</b>, Spector,D.L., 2012. | ||
+ | |||
+ | ''Cell Reports'', 2:111-123. | ||
+ | |||
+ | [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] | ||
+ | [http://genesdev.cshlp.org/content/26/14/1626.full.pdf 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., <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. | ||
+ | |||
+ | ''Neuron'', 75:437-450. | ||
+ | |||
+ | [http://www.ncbi.nlm.nih.gov/pubmed/22884328?dopt=Abstract PubMed] | ||
+ | [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] | ||
+ | |||
+ | =====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., <b>Zhang,C.</b>, Darnell,R.B., 2012. | ||
+ | |||
+ | ''Genes Dev'', 26:1626-1642. | ||
+ | |||
+ | [http://www.ncbi.nlm.nih.gov/pubmed/22802532?dopt=Abstract PubMed] | ||
+ | [http://genesdev.cshlp.org/content/26/14/1626.full.pdf 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., <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. | ||
+ | |||
+ | ''PLoS One'', 6: e29088. | ||
+ | |||
+ | [http://www.ncbi.nlm.nih.gov/pubmed/22194994?dopt=Abstract PubMed] | ||
+ | [http://www.plosone.org/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0029088&representation=PDF 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., <b>Zhang,C.</b>, Klein-Szanto, A.J., Kormish, J.D., Fu, J., Zhang, M.Q., Zaret, K.S. 2011. | ||
+ | |||
+ | ''PLoS Genet'', 7: e1002277. | ||
+ | |||
+ | [http://www.ncbi.nlm.nih.gov/pubmed/21935353?dopt=Abstract PubMed] | ||
+ | [http://www.plosgenetics.org/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pgen.1002277&representation=PDF PDF] | ||
+ | |||
+ | =====FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism===== | ||
+ | |||
+ | 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. | ||
+ | |||
+ | ''Cell'', 146:247-261. | ||
+ | |||
+ | [http://www.ncbi.nlm.nih.gov/pubmed/21784246?dopt=Abstract PubMed] | ||
+ | [http://download.cell.com/pdf/PIIS0092867411006556.pdf PDF] | ||
+ | |||
+ | =====Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data===== | ||
+ | |||
+ | <b>Zhang,C.</b>†, Darnell, R.B.† 2011. | ||
+ | |||
+ | ''Nat. Biotech.'' 29:607-614. | ||
+ | |||
+ | [http://www.ncbi.nlm.nih.gov/pubmed/21633356?dopt=Abstract PubMed] | ||
+ | [http://www.nature.com/nbt/journal/v29/n7/pdf/nbt.1873.pdf PDF] | ||
+ | [http://zhanglab.c2b2.columbia.edu/index.php/CIMS software] | ||
+ | |||
+ | ==2010== | ||
+ | |||
+ | =====Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls===== | ||
+ | |||
+ | <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. | ||
+ | |||
+ | ''Science''. 329: 439-443. | ||
+ | [http://www.ncbi.nlm.nih.gov/pubmed/20558669?dopt=Abstract PubMed] | ||
+ | [http://www.sciencemag.org/cgi/rapidpdf/science.1191150v1.pdf PDF] | ||
+ | |||
+ | - 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. | ||
+ | |||
+ | =====Dissecting the unique role of the retinoblastoma tumor suppressor during cellular senescence===== | ||
+ | |||
+ | 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. | ||
+ | |||
+ | ''Cancer Cell''. 17:376-387. | ||
+ | |||
+ | [http://www.ncbi.nlm.nih.gov/pubmed/20385362?dopt=Abstract PubMed] | ||
+ | [http://www.sciencedirect.com/science/article/pii/S1535610810000723/pdfft?md5=a191ed96242c05f575dfa856697ecbab&pid=1-s2.0-S1535610810000723-main.pd PDF] | ||
+ | |||
+ | - Comment in <i>Cancer Cell.</i> 2010 Apr 13;17(4):313-4. | ||
+ | |||
+ | ==2008 or earlier== | ||
+ | |||
+ | =====Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines===== | ||
+ | |||
+ | Castle, J.C., <b>Zhang,C.</b>, Shah, J.K., Kulkarni, A.V., Cooper, T.A., Johnson, J.M. 2008. | ||
+ | |||
+ | ''Nature Genet.'' 40:1416-1425. | ||
+ | |||
+ | [http://www.ncbi.nlm.nih.gov/pubmed/18978788?dopt=Abstract PubMed] | ||
+ | [http://www.nature.com/ng/journal/v40/n12/pdf/ng.264.pdf PDF] | ||
+ | |||
+ | =====Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2===== | ||
+ | |||
+ | <b>Zhang,C.</b>*, Zhang, Z.*, Castle, J., Sun, S., Johnson, J., Krainer, A.R. and Zhang, M.Q. 2008. | ||
+ | |||
+ | ''Genes Dev''. 22:2550-2563. | ||
+ | |||
+ | [http://www.ncbi.nlm.nih.gov/pubmed/18794351?dopt=Abstract PubMed] | ||
+ | [http://genesdev.cshlp.org/cgi/reprint/22/18/2550 PDF] | ||
+ | |||
+ | =====An RNA landscape of evolution for optimal exon and intron discrimination===== | ||
+ | |||
+ | <b>Zhang,C.</b>, Li, W.-H., Krainer, A.R. and Zhang, M.Q. 2008. | ||
+ | |||
+ | ''Proc. Nat. Acad. Sci. USA''. 105:5797-802. | ||
+ | |||
+ | [http://www.ncbi.nlm.nih.gov/pubmed/18391195?dopt=Abstract PubMed] | ||
+ | [http://www.pnas.org/content/105/15/5797.full.pdf+html PDF] | ||
+ | |||
+ | =====Dual-specificity splice sites function alternatively as 5' and 3' splice sites===== | ||
+ | |||
+ | <b>Zhang,C.</b>, Hasting, M.L., Krainer, A.R., Zhang, M.Q. 2007. | ||
+ | |||
+ | ''Proc. Nat. Acad. Sci. USA.'' 104(38): 15028-15033 | ||
+ | |||
+ | [http://www.ncbi.nlm.nih.gov/pubmed/17848517?dopt=Abstract PubMed] | ||
+ | [http://www.pnas.org/cgi/content/full/104/38/15028 PDF]. | ||
+ | |||
+ | =====Evolutionary impact of limited splicing fidelity in mammalian genes===== | ||
+ | |||
+ | <b>Zhang,C.</b>, Krainer A.R., Zhang, M.Q. 2007. | ||
+ | |||
+ | ''Trends Genet.'' 23(10): 484-488. | ||
+ | |||
+ | [http://www.ncbi.nlm.nih.gov/pubmed/17719121?dopt=Abstract PubMed] | ||
+ | [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCY-4PGXF12-1&_user=429752&_coverDate=08/24/2007&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000020578&_version=1&_urlVersion=0&_userid=429752&md5=18d53f024a0cc53702a98f6b14a7b154 PDF] | ||
+ | |||
+ | =====An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers===== | ||
+ | |||
+ | Smith, P.J., <b>Zhang,C.</b>, Wang, J., Chew, S.L., Zhang, M.Q., Krainer, A.R. 2006. | ||
+ | |||
+ | ''Hum Mol Genet'', 15:16):2490-2508. | ||
+ | |||
+ | [http://www.ncbi.nlm.nih.gov/pubmed/16825284?dopt=Abstract PubMed] | ||
+ | [http://hmg.oxfordjournals.org/cgi/reprint/ddl171v1 PDF] | ||
+ | |||
+ | =====Profiling alternatively spliced mRNA isoforms for prostate cancer classification===== | ||
+ | |||
+ | <b>Zhang,C.</b>, Li, H.-R., Fan, J.-B., Wang-Rodriguez, J., Downs, T., Fu, X.-D. and Zhang, M.Q. 2006. | ||
+ | |||
+ | ''BMC Bioinformatics'', 7:202. | ||
+ | |||
+ | [http://www.ncbi.nlm.nih.gov/pubmed/16608523?dopt=Abstract PubMed] | ||
+ | [http://www.biomedcentral.com/content/pdf/1471-2105-7-202.pdf PDF] | ||
+ | |||
+ | =====Neighbor Number, Valley Seeking and Clustering===== | ||
+ | |||
+ | Zhang,C.</b>, 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===== | ||
+ | |||
+ | <b>Zhang,C.</b>, Xuan, Z., Otto, S., Hover, J.R., McCorkle, S.R., Mandel, G. and Zhang, M.Q. 2006. | ||
+ | |||
+ | ''Nucl Acids Res'', 34: 2238-2246. | ||
+ | |||
+ | [http://www.ncbi.nlm.nih.gov/pubmed/16670430?dopt=Abstract PubMed] | ||
+ | [http://nar.oxfordjournals.org/cgi/reprint/34/8/2238 PDF] | ||
+ | |||
+ | =====Significance of Gene Ranking for Classification of Microarray Samples===== | ||
+ | |||
+ | <b>Zhang,C.</b>*, Lu, X.* and Zhang, X. 2005. | ||
+ | |||
+ | ''IEEE/ACM Transactions on Computational Biology and Bioinformatics'', 3(3): 312-320. | ||
+ | |||
+ | [http://www.ncbi.nlm.nih.gov/pubmed/17048468?dopt=Abstract PubMed] | ||
+ | |||
+ | ==Book Chapters== | ||
+ | |||
+ | =====Identification of Splicing Factor Target Genes by High-Throughput Sequencing===== | ||
+ | |||
+ | <b>Zhang,C.</b>, Zhang,M.Q. 2012. | ||
+ | |||
+ | 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. | ||
+ | |||
+ | =====Functional <i>in sillico</i> analysis of gene regulatory polymorphism===== | ||
+ | |||
+ | <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>. 2nd Ed. (M.R. Barnes, ed.) John Wiley & Sons, LTD. | ||
+ | |||
+ | =====Biomedical literature mining===== | ||
+ | |||
+ | <b>Zhang,C.</b>, Zhang,M.Q. 2007. <br> | ||
+ | |||
+ | Chap 10. in <i>Introduction to Bioinformatics: A workbook approach</i>. (V. Mathura ed) Elsevier. |
Latest revision as of 22:00, 10 March 2016
[* 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.
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.
- Research highlights, “How good are those RNA-seq data?”, Nature Methods, 12:910 (2015).
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.
Proc. Nat. Acad. Sci. USA. Mar 3. pii: 201502849.
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.
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.
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.
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.
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.
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.
[Publications before my own lab]
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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
Evolutionary impact of limited splicing fidelity in mammalian genes
Zhang,C., Krainer A.R., Zhang, M.Q. 2007.
Trends Genet. 23(10): 484-488.
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.
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.
Neighbor Number, Valley Seeking and Clustering
Zhang,C.</b>, 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.
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.
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.
Biomedical literature mining
Zhang,C., Zhang,M.Q. 2007.
Chap 10. in Introduction to Bioinformatics: A workbook approach. (V. Mathura ed) Elsevier.