Difference between revisions of "Publications"
From Zhang Laboratory
(→2010) |
(→2008 or earlier) |
||
Line 377: | Line 377: | ||
[http://www.ncbi.nlm.nih.gov/pubmed/18978788?dopt=Abstract PubMed] | [http://www.ncbi.nlm.nih.gov/pubmed/18978788?dopt=Abstract PubMed] | ||
[http://www.nature.com/ng/journal/v40/n12/pdf/ng.264.pdf PDF] | [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===== | =====Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2===== | ||
Line 386: | Line 388: | ||
[http://www.ncbi.nlm.nih.gov/pubmed/18794351?dopt=Abstract PubMed] | [http://www.ncbi.nlm.nih.gov/pubmed/18794351?dopt=Abstract PubMed] | ||
[http://genesdev.cshlp.org/cgi/reprint/22/18/2550 PDF] | [http://genesdev.cshlp.org/cgi/reprint/22/18/2550 PDF] | ||
+ | |||
+ | |||
=====An RNA landscape of evolution for optimal exon and intron discrimination===== | =====An RNA landscape of evolution for optimal exon and intron discrimination===== | ||
Line 395: | Line 399: | ||
[http://www.ncbi.nlm.nih.gov/pubmed/18391195?dopt=Abstract PubMed] | [http://www.ncbi.nlm.nih.gov/pubmed/18391195?dopt=Abstract PubMed] | ||
[http://www.pnas.org/content/105/15/5797.full.pdf+html PDF] | [http://www.pnas.org/content/105/15/5797.full.pdf+html PDF] | ||
+ | |||
+ | |||
=====Dual-specificity splice sites function alternatively as 5' and 3' splice sites===== | =====Dual-specificity splice sites function alternatively as 5' and 3' splice sites===== | ||
Line 404: | Line 410: | ||
[http://www.ncbi.nlm.nih.gov/pubmed/17848517?dopt=Abstract PubMed] | [http://www.ncbi.nlm.nih.gov/pubmed/17848517?dopt=Abstract PubMed] | ||
[http://www.pnas.org/cgi/content/full/104/38/15028 PDF]. | [http://www.pnas.org/cgi/content/full/104/38/15028 PDF]. | ||
+ | |||
+ | |||
=====Evolutionary impact of limited splicing fidelity in mammalian genes===== | =====Evolutionary impact of limited splicing fidelity in mammalian genes===== | ||
Line 413: | Line 421: | ||
[http://www.ncbi.nlm.nih.gov/pubmed/17719121?dopt=Abstract PubMed] | [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] | [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===== | =====An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers===== | ||
Line 422: | Line 432: | ||
[http://www.ncbi.nlm.nih.gov/pubmed/16825284?dopt=Abstract PubMed] | [http://www.ncbi.nlm.nih.gov/pubmed/16825284?dopt=Abstract PubMed] | ||
[http://hmg.oxfordjournals.org/cgi/reprint/ddl171v1 PDF] | [http://hmg.oxfordjournals.org/cgi/reprint/ddl171v1 PDF] | ||
+ | |||
+ | |||
=====Profiling alternatively spliced mRNA isoforms for prostate cancer classification===== | =====Profiling alternatively spliced mRNA isoforms for prostate cancer classification===== | ||
Line 431: | Line 443: | ||
[http://www.ncbi.nlm.nih.gov/pubmed/16608523?dopt=Abstract PubMed] | [http://www.ncbi.nlm.nih.gov/pubmed/16608523?dopt=Abstract PubMed] | ||
[http://www.biomedcentral.com/content/pdf/1471-2105-7-202.pdf PDF] | [http://www.biomedcentral.com/content/pdf/1471-2105-7-202.pdf PDF] | ||
+ | |||
+ | |||
=====Neighbor Number, Valley Seeking and Clustering===== | =====Neighbor Number, Valley Seeking and Clustering===== | ||
Line 437: | Line 451: | ||
''Pattern Recognition Letters'',28:173-180. | ''Pattern Recognition Letters'',28:173-180. | ||
+ | |||
+ | |||
=====A Clustering property of highly-degenerate transcription factor binding sites in the mammalian genome===== | =====A Clustering property of highly-degenerate transcription factor binding sites in the mammalian genome===== | ||
Line 446: | Line 462: | ||
[http://www.ncbi.nlm.nih.gov/pubmed/16670430?dopt=Abstract PubMed] | [http://www.ncbi.nlm.nih.gov/pubmed/16670430?dopt=Abstract PubMed] | ||
[http://nar.oxfordjournals.org/cgi/reprint/34/8/2238 PDF] | [http://nar.oxfordjournals.org/cgi/reprint/34/8/2238 PDF] | ||
+ | |||
+ | |||
=====Significance of Gene Ranking for Classification of Microarray Samples===== | =====Significance of Gene Ranking for Classification of Microarray Samples===== |
Revision as of 22:04, 25 May 2018
Papers | Talks
[* co-first authors; † co-corresponding authors]
2018
LIN28 selectively modulates a subclass of let-7 microRNAs
Ustianenko,D.*, Chiu,H-S*, Treiber, T.*, Weyn-Vanhentenryck, S.M., Treiber, N., Meister, G., Sumazin,P.†, Zhang, C.† 2018.
Mol Cell, in press.
Precise temporal regulation of alternative splicing during neural development
Weyn-Vanhentenryck, S. M.*, Feng, H.*, Ustianenko, D., Duffié, R., Yan, Q., Jacko, M., Martinez, J. C., Goodwin, M., Zhang, X., Hengst, U., Lomvardas, S., Swanson, M. S. & Zhang, C. 2018.
Nat Commun, in press.
Systematic reconstruction of autism biology from massive genetic mutation profiles
Luo,W., Zhang,C., Jiang,Y., Brouwer,C.R. 2018.
Science Advances, 4:e1701799.
Rbfox splicing factors promote neuronal maturation and axon initial segment assembly
Jacko, M., Weyn-Vanhentenryck, S. M., Smerdon, J. W., Yan, R., Feng, H., Williams, D. J., Pai, J., Xu, K., Wichterle, H.† & Zhang, C.† 2018.
Neuron, 97: 853-868.e6.
-Issue highlight.
-Press release: “Research Unveils a Developmental Splicing Program Controlling Neuronal Maturation and Excitability”. CUMC News Room. http://newsroom.cumc.columbia.edu/blog/2018/02/08/new-insights-neurons-become-mature-excitable/.
Capturing the interactome of newly transcribed RNA
Bao, X., Guo, X., Yin, M., Tariq, M., Lai, Y., Kanwal, S., Zhou, J., Li, N., Lv, Y., Pulido-Quetglas, C., Wang, X., Ji, L., Khan, M. J., Zhu, X., Luo, Z., Shao, C., Lim, D.-H., Liu, X., Li, N., Wang, W., He, M., Liu, Y.-L., Ward, C., Wang, T., Zhang, G., Wang, D., Yang, J., Chen, Y., Zhang, C., Jauch, R., Yang, Y.-G., Wang, Y., Qin, B., Anko, M.-L., Hutchins, A. P., Sun, H., Wang, H., Fu, X.-D., Zhang, B. & Esteban, M. A. 2018.
Nat Meth, 15:213-220.
Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons
Yuan, Y., Xie, S., Darnell, J. C., Darnell, A. J., Saito, Y., Phatnani, H., Murphy, E. A., Zhang, C., Maniatis, T. & Darnell, R. B. 2018.
bioRxiv, DOI: http://doi.org/10.1101/237347 (preprint)
2017
Microexons: discovery, regulation, and function
Ustianenko,D., Weyn-Vanhentenryck, S.M., Zhang, C. 2017.
WIRES RNA, e1418. DOI: 10.1002/wrna.1418 (review)
A cell type-specific expression signature predicts haploinsufficient autism-susceptibility genes
Zhang,C.*,†, Shen,Y.*,† 2017.
Human Mutation, 38: 204-215.
PubMed PDF preprint at bioRxiv
-News release: “Third-party gene scores added to SFARI Gene”. SFARI. https://www.sfari.org/2017/12/14/third-party-gene-scores-added-to-sfari-gene/.
CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data
Shah,A., Qian,Y., Weyn-Vanhentenryck,S.M., Zhang,C. 2017.
Bioinformatics. 33:566-567. DOI: 10.1093/bioinformatics/btw653.
2016
mCarts: genome-wide prediction of clustered sequence motifs as binding sites for RNA-binding proteins
Weyn-Vanhentenryck,S.M., Zhang,C. 2016.
Methods Mol Biol. 1421:215-226.
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. 12:1159-1168.
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. 112:3445-3450.
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. 6:1139-1152.
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.
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., 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.