Test
From Zhang Laboratory
[* 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
eLife, 2:e00178. [PubMed][PDF]
Neuron, 75:1067-1080. [PubMed][PDF]
Cell Reports, 2:111-123. [PubMed][PDF]
Neuron, 75:437-450. [PubMed][PDF]
Genes Dev, 26:1626-1642. [PubMed][PDF]
2011
PLoS One, 6: e29088. [PubMed][PDF]
PLoS Genet, 7: e1002277. [PubMed][PDF]
Cell, 146:247-261. [PubMed][PDF]
Nat. Biotech. 29:607-614. [PubMed][PDF] [software]
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.
Cancer Cell. 17:376-387. [Comment in Cancer Cell. 2010 Apr 13;17(4):313-4.] [PubMed][PDF]
2008 or earlier
Nature Genet. 40:1416-1425. [PubMed][PDF]
Genes Dev. 22:2550-2563. [PubMed][PDF]
Proc. Nat. Acad. Sci. USA. 105:5797-802. [PubMed][PDF]
Proc. Nat. Acad. Sci. USA. 104(38): 15028-15033 [PubMed][PDF].
Trends Genet. 23(10): 484-488. [PubMed][PDF]
Hum Mol Genet, 15:16):2490-2508. [PubMed][PDF]
BMC Bioinformatics, 7:202. [PubMed][PDF]
Nucl Acids Res, 34: 2238-2246. [PubMed] [PDF]
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3(3): 312-320. [PubMed]
Book Chapters
Chapter 51 in Alternative pre-mRNA Splicing: Theory and Protocols. (S. Stamm, C.W. J. Smith, R. Lührmann, ed). Wiley-VCH Verlag GmbH & Co.
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]
Chap 10. in Introduction to Bioinformatics: A workbook approach. (V. Mathura ed) Elsevier.