Difference between revisions of "Test"

From Zhang Laboratory

Jump to: navigation, search
(→‎An RNA-Sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex)
(→‎2012)
Line 125: Line 125:
  
  
−
<html>
+
=====NOVA-dependent regulation of cryptic NMD exons controls synaptic protein levels after seizure=====
−
 
+
−
 
+
−
 
+
−
<LI>
+
−
 
+
−
<div class="title">NOVA-dependent regulation of cryptic NMD exons controls synaptic protein levels after seizure. </div>
+
−
 
+
−
 
+
  
 
Eom,T., <b>Zhang,C.</b>, Wang,H., Lay,K., Fak,J., Noebels,J.L., Darnell,R.B. 2012.
 
Eom,T., <b>Zhang,C.</b>, Wang,H., Lay,K., Fak,J., Noebels,J.L., Darnell,R.B. 2012.
  
−
<p>
+
''eLife'', 2:e00178.
−
 
+
−
<i>eLife</i>, 2:e00178.
+
  
−
[<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>]
+
[http://www.ncbi.nlm.nih.gov/pubmed/23359859‎?dopt=Abstract PubMed]
 +
[http://elife.elifesciences.org/content/elife/2/e00178.full.pdf PDF]
  
−
<p>
 
  
−
</LI>
+
=====Neuronal Elav-like (Hu) Proteins Regulate RNA Splicing and Abundance to Control Glutamate Levels and Neuronal Excitability=====
−
 
+
−
 
+
−
<LI>
+
−
 
+
−
<div class="title">Neuronal Elav-like (Hu) Proteins Regulate RNA Splicing and Abundance to Control Glutamate Levels and Neuronal Excitability. </div>
+
  
 
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.   
 
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.   
  
−
<p>
+
''Neuron'', 75:1067-1080.
 +
[http://www.ncbi.nlm.nih.gov/pubmed/22998874?dopt=Abstract PubMed]
 +
[href="http://ac.els-cdn.com/S0896627312006587/1-s2.0-S0896627312006587-main.pdf?_tid=4b5c6686-28eb-11e2-af58-00000aacb35f&acdnat=1352300362_a80f3a1435a1357a9a6b45a3918673c5 PDF]
  
−
<i>Neuron</i>, 75:1067-1080.
 
−
[<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>]
 
  
−
<p>
+
=====The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult=====
−
 
+
−
</LI>
+
−
 
+
−
<LI>
+
−
 
+
−
<div class="title">The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult.  </div>
+
  
 
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.   
 
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.   
  
−
<p>
+
''Cell Reports'', 2:111-123.
  
−
<i>Cell Reports</i>, 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]
−
[<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>]
+
[http://genesdev.cshlp.org/content/26/14/1626.full.pdf PDF]
  
−
<p>
 
  
−
</LI>
+
=====Muscleblind-like 2 mediated alternative splicing in the developing brain and dysregulation in myotonic dystrophy=====
−
 
+
−
<LI>
+
−
 
+
−
<div class="title">Muscleblind-like 2 mediated alternative splicing in the developing brain and dysregulation in myotonic dystrophy. </div>
+
  
 
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.   
 
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.   
  
−
<p>
+
''Neuron'', 75:437-450.
−
<i>Neuron</i>, 75:437-450.
+
[http://www.ncbi.nlm.nih.gov/pubmed/22884328?dopt=Abstract PubMed]
−
[<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>]
+
[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]
  
−
<p>
 
  
−
</LI>
+
=====Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain=====
−
 
+
−
<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.   
 
Licatalosi,D.D., Yano,M., Fak,J.J., Mele,A., Grabinski,S.E., <b>Zhang,C.</b>, Darnell,R.B., 2012.   
  
−
<p>
+
''Genes Dev'', 26:1626-1642.  
−
 
+
[http://www.ncbi.nlm.nih.gov/pubmed/22802532?dopt=Abstract PubMed]
−
<i>Genes Dev</i>, 26:1626-1642.  
+
[http://genesdev.cshlp.org/content/26/14/1626.full.pdf PDF]
−
[<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==
 
==2011==

Revision as of 21:34, 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 [href="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., 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.

    • Retrieved from "https://zhanglab.c2b2.columbia.edu/index.php?title=Test&oldid=1271"