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Difference between revisions of "Test"
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| + | ==2015== |
| | | |
− | [[File:olego.logo.png|link=OLego|center|300px]]
| + | =====MBNL sequestration by toxic RNAs and RNA misprocessing in the myotonic dystrophy brain===== |
− | <center>[[OLego| OLego, published online]]</center>
| + | |
| | | |
| + | 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. |
| | | |
− | '''Introduction of the Zhang Laboratory''' | + | ''Cell Rep.'' http://dx.doi.org/10.1016/j.celrep.2015.07.029. |
| | | |
− | We are part of [http://cpmcnet.columbia.edu/dept/gsas/biochem/ Department of Biochemistry and Molecular Biophysics], [http://sbi.c2b2.columbia.edu/ Columbia Initiative in Systems Biology], [http://www.columbiamnc.org/ Motor Neuron Center], [http://stemcell.columbia.edu/ Columbia Stem Cell Initiative], and [http://hiccc.columbia.edu Herbert Irving Comprehensive Cancer Center] at [http://http://www.cumc.columbia.edu Columbia University Medical Center].
| + | [http://www.ncbi.nlm.nih.gov/pubmed/26257173 PubMed] |
| + | [http://www.cell.com/cell-reports/pdf/S2211-1247(15)00789-5.pdf PDF] |
| | | |
− | We are fascinated by the complexity of the mammalian brain and the underlying molecular mechanisms. While mammals have a similar number of genes compared to phenotypically simpler organisms (such as worm), one apparent feature of mammalian genes is their more complicated gene structures, providing opportunity of sophisticated regulation at the RNA level.
| + | =====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. |
| | | |
− | The vision of my lab is to infer RNA regulatory networks in the nervous system, as a way to understand the mammlian complexity manifested in evolutionary-developmental (evo-devo) processes and in several neuronal disorders. Specifically we are interested in obtaining fundamental understanding how neuronal cell types are specified during the normal development process, how this process can be reversed in certain pathologic contexts (such as brain tumors), and why they die abnormally in neurodegenerative diseases. My lab will have a mixed dry and wet lab setup (a.k.a. "humid" lab). We use different model systems and a combination of high-throughput data driven and hypothesis driven approaches.
| + | ''Nat Comm.'' '''6''':7816. doi: 10.1038/ncomms8816. |
| | | |
| + | [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===== |
| | | |
− | <html> | + | 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. |
− | <div align="center"> | + | |
| | | |
− | <a href="http://sbi.c2b2.columbia.edu/"><img src="/data/images/sbi_logo.png" width="223" height="56" /></a>
| + | ''Mol Cell.'' 56: 311-322. |
− | <a href="http://www.columbiamnc.org/"><img src="/data/images/mnc_logo.gif" width="122" height="35" /></a>
| + | |
− | <a href="http://www.c2b2.columbia.edu"><img src="/data/images/C2B2_logo.png" width="215" height="60" /></a> <p>
| + | |
| | | |
− | </div> | + | [http://www.ncbi.nlm.nih.gov/pubmed/25263597 PubMed] |
− | </html> | + | [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===== |
| + | |
| + | <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. |
| + | |
| + | ''Cell Rep.'' 10.1016/j.celrep.2014.02.005. |
| + | |
| + | [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
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.
PubMed
PDF
Software
- 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.
PubMed
PDF
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, 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]
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.
PubMed
PDF
- 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.
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.</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.
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.
Biomedical literature mining
Zhang,C., Zhang,M.Q. 2007.
Chap 10. in Introduction to Bioinformatics: A workbook approach. (V. Mathura ed) Elsevier.
|