Difference between revisions of "Publications"
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| − | + | [http://scholar.google.com/citations?user=hWYleB8AAAAJ&hl=en&oi=ao Search Google Scholar] (citations: 12,729; h-index: 40, i10-index: 49; as of Dec 22, 2022) | |
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| + | <div> | ||
| + | <a u=image href="http://www.pnas.org/doi/10.1073/pnas.2013056118" rel="nofollow"><img data-u="image" src="/data/images/pub_slideshow/pnas_feng2021.jpg" title="Feng, H., Moakley, D.F., Chen, S., McKenzie, M.G., Menon, V., Zhang, C. 2021. Complexity and graded regulation of neuronal cell type-specific alternative splicing revealed by single-cell RNA sequencing. Proc. Nat. Acad. Sci. USA. 118: e2013056118." width="196" height="238" /></a> | ||
| + | </div> | ||
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| + | <div> | ||
| + | <a u=image href="http://www.cell.com/molecular-cell/fulltext/S1097-2765(20)30147-7" rel="nofollow"><img data-u="image" src="/data/images/pub_slideshow/molcell_ustianenko_preview2020.gif" title="Ustianenko, D., McKenzie, M.G., Zhang, C. 2020. Brain translation – a feather tips the scale. Mol Cell. 77:1155-1156 (preview)." width="196" height="238" /> </a> | ||
| + | </div> | ||
| + | <div> | ||
| + | <a u=image href="http://www.cell.com/molecular-cell/fulltext/S1097-2765(19)30092-9" rel="nofollow"><img data-u="image" src="/data/images/pub_slideshow/molcell_feng2019.jpg" title="Feng, H.*, Bao, S.*, Rahman, M.,A., Weyn-Vanhentenryck, S.M., Khan, A., Wong, J., Shah, A., Flynn, E.D., Krainer, A.R., Zhang, C., 2019. Modeling RNA-binding protein specificity in vivo by precisely registering protein-RNA crosslink sites. Mol Cell. 74:1189-1204.E6." width="196" height="238" /> </a> | ||
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| + | <div> | ||
| + | <a u=image href="http://www.cell.com/cell/fulltext/S0092-8674(19)30046-7" rel="nofollow"><img data-u="image" src="/data/images/pub_slideshow/cell_bao2019.jpg" title="Bao, S., Moakley, D.,F., Zhang, C., 2019. The splicing code goes deep. Cell, 176:414-416 (Leading Edge Preview)." width="196" height="238" /> </a> | ||
| + | </div> | ||
| + | <div> | ||
| + | <a u=image href="http://www.cell.com/molecular-cell/fulltext/S1097-2765(18)30504-5" rel="nofollow"><img data-u="image" src="/data/images/pub_slideshow/molcell_ustianenko2018.jpg" title="Ustianenko, D.*, Chiu, H.-S.*, Treiber, T.*, Weyn-Vanhentenryck, S.M., Treiber, N., Meister, G., Sumazin, P. †, Zhang, C. † 2018. LIN28 selectively modulates a subclass of let-7 microRNAs. Mol. Cell. 71: 271-283.e5. (cover story)" width="196" height="238" /> </a> | ||
| + | </div> | ||
| + | <div> | ||
| + | <a u=image href="http://www.nature.com/articles/s41467-018-04559-0" rel="nofollow"><img data-u="image" src="/data/images/pub_slideshow/natcomm_weyn2018.png" title="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. Precise temporal regulation of alternative splicing during neural development. Nat Commun, 9:2189" width="196" height="238" /> </a> | ||
| + | </div> | ||
| + | <div> | ||
| + | <a u=image href="http://www.cell.com/neuron/fulltext/S0896-6273(18)30023-0" rel="nofollow"><img data-u="image" src="/data/images/pub_slideshow/neuron_jacko_2018.jpg" title="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. Rbfox splicing factors promote neuronal maturation and axon initial segment assembly. Neuron, 97: 853-868.e6" width="196" height="238" /> </a> | ||
| + | </div> | ||
| + | <div> | ||
| + | <a u=image href="http://wires.onlinelibrary.wiley.com/doi/10.1002/wrna.1418" rel="nofollow"><img data-u="image" src="/data/images/pub_slideshow/wiresrna_ustiannenko2017.png" title="Ustianenko, D., Weyn-Vanhentenryck, S.M., Zhang, C. 2017. Microexons: discovery, regulation, and function. WIREs RNA. e1418. doi: 10.1002/wrna.1418 (review)." width="196" height="238" /> </a> | ||
| + | </div> | ||
| + | <div> | ||
| + | <a u=image href="http://onlinelibrary.wiley.com/doi/10.1002/humu.23147" rel="nofollow"><img data-u="image" src="/data/images/pub_slideshow/hummut_zhang2017.jpg" title="Zhang, C.*,†, Shen, Y.*,† 2017. A cell type-specific expression signature predicts haploinsufficient autism-susceptibility genes. Hum Mut. 38: 204-215." width="196" height="238" /> </a> | ||
| + | </div> | ||
| + | <div> | ||
| + | <a u=image href="http://academic.oup.com/bioinformatics/article/33/4/566/2593905" rel="nofollow"><img data-u="image" src="/data/images/pub_slideshow/bioinfo_shah2017.jpeg" title="Shah, A., Qian, Y., Weyn-Vanhentenryck, S.M., Zhang, C. 2017. CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data. Bioinformatics, 33:566-567. DOI: 10.1093/bioinformatics/btw653." width="196" height="238" /> </a> | ||
| + | </div> | ||
| + | <div> | ||
| + | <a u=image href="http://www.nature.com/articles/ncomms8816" rel="nofollow"><img data-u="image" src="/data/images/pub_slideshow/natcomm_weyn2018.png" title="Feng, H., Zhang, X., Zhang, C. , 2015. mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data. Nat Comm. 6:7816." width="196" height="238" /> </a> | ||
| + | </div> | ||
| + | <div> | ||
| + | <a u=image href="http://www.pnas.org/doi/abs/10.1073/pnas.1502849112" rel="nofollow"><img data-u="image" src="/data/images/pub_slideshow/pnas_yan2015.jpg" title="Yan, Q.* , Weyn-Vanhentenrycka, S.M.*,Wu, J., Sloan, S.A., Zhang, Y., Chen, K., Wu, J.-Q., Barres, B.A.† , Zhang, C.† 2015. Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators. Proc. Nat. Acad. Sci. USA. 112:3445-3450." width="196" height="238" /> </a> | ||
| + | </div> | ||
| + | <div> | ||
| + | <a u=image href="https://www.cell.com/cell-reports/fulltext/S2211-1247(14)00084-9" rel="nofollow"><img data-u="image" src="/data/images/pub_slideshow/cellrep_weyn2014.jpg" title="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. HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. Cell Rep. 6:1139-1152." width="196" height="238" /> </a> | ||
| + | </div> | ||
| + | <div> | ||
| + | <a u=image href="http://www.nature.com/articles/nprot.2014.012" rel="nofollow"><img data-u="image" src="/data/images/pub_slideshow/natprot_moore2014.png" title="Moore, M.*, Zhang, C.*, Gantman, E.C., Mele, A., Darnell, J.C., Darnell, R.B. 2014. Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. Nat Protocols. 9:263-293." width="196" height="238" /> </a> | ||
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| − | + | ['''*''' co-first authors; '''†''' co-corresponding authors] | |
| − | + | ==2024== | |
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| − | + | =====Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences===== | |
| − | + | Xu, C.*, '''Bao, S.'''*, Chen, H., Jiang, T. †, '''Zhang, C.''' † | |
| + | In submission. | ||
| − | + | [http://biorxiv.org/cgi/content/short/2024.03.22.586363v1. preprint] [http://github.com/chaolinzhanglab/DeltaSplice software] | |
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| + | =====Lineage-specific splicing regulation reveals adaptation of MAPT function in the primate brain.===== | ||
| − | + | '''Recinos, Y.'''*, '''Bao, S.'''*, '''Wang, X.'''*, '''Phillips, B.L.''', '''Weyn-Vanhentenryck, S.M.''', Swanson, M.S., '''Zhang, C.''' | |
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| − | + | Cell Genomics, in press. | |
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| − | + | =====CRISPR/dCas13d-based deep screening of proximal and distal splicing-regulatory elements===== | |
| − | + | '''Recinos, Y.''', '''Ustianenko, D.''', '''Yeh, Y.T.''', '''Wang, X.''', '''Jacko, M.''', '''Yesantharao, L.V.''', '''Wu, Q.''', '''Zhang, C.''' | |
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| − | + | Nat Commun. in press [preprint: bioRxiv. https://doi.org/10.1101/2023.08.21.554109.] | |
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| − | + | ===== Structure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes===== | |
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| − | + | '''Feng,H.''', Lu, X.-J., '''Maji, S.''', Liu, L., '''Ustianenko, M.''', Rudnick, N., '''Zhang, C.''' | |
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| − | + | Nat Commun.15: 2279. https://doi.org/10.1038/s41467-024-46429-y. | |
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| − | + | [http://pubmed.ncbi.nlm.nih.gov/38480694/ PubMed] [https://link.springer.com/content/pdf/10.1038/s41467-024-46429-y.pdf PDF] [http://github.com/chaolinzhanglab/PxR3D software] | |
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| − | + | ||
| − | + | ==2023== | |
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| − | + | ===== Lineage tracing and single-cell profiling unravel coordinated bone marrow stromal remodeling and identify glial cells as a therapeutic target in myelofibrosis===== | |
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| − | + | Sarkaria, S., Zhou, J., '''Bao, S.''', Zhao, W., Fang, Y., Que, J., Bhagat, G., '''Zhang, C.''', Ding, L. | |
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| − | + | Cell Stem Cell, 30:832-850.e6. | |
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| − | + | [http://pubmed.ncbi.nlm.nih.gov/37267917/ PubMed] [http://www.cell.com/action/showPdf?pii=S1934-5909%23%00172-8 PDF] | |
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| − | + | ===== Multiomics analyses reveal DARS1-AS1/YBX1-controlled posttranscriptional circuits promoting glioblastoma tumorigenesis/radioresistance===== | |
| + | Zheng, C., Wei, Y., Zhang, Q., Sun, M., Wang, Y., Hou, J., Zhang, P., Lv, X., Su, D., Jiang, Y., Gumin, J., Sahni, N., Hu, B., Wang, W., Chen, X., McGrail, D.J., '''Zhang, C.''', Huang, S., Xu, H., Chen, J., Lang, F.F., Hu, J., Chen, Y. | ||
| − | + | Sci Adv. 2023 9:eadf3984. | |
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| − | + | [http://pubmed.ncbi.nlm.nih.gov/37540752/ PubMed] [http://www.science.org/doi/epdf/10.1126/sciadv.adf3984 PDF] | |
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| − | + | ===== Trans-cellular control of synapse properties by a cell type-specific splicing regulator===== | |
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| − | + | Traunmüller, L., Schulz, J., '''Feng, H.''', Furlanis, E., Gomez, A., Schreiner, D., Bischofberger, J., '''Zhang, C.''', Scheiffele, P. | |
| − | + | Cell Rep. 42: 112183. | |
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| − | + | [http://pubmed.ncbi.nlm.nih.gov/36862556/ PubMed] [http://www.cell.com/action/showPdf?pii=S2211-1247%2823%2900184-5 PDF] | |
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| − | + | ==2022== | |
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| − | + | ===== The germ cell-specific RNA binding protein RBM46 is essential for spermatogonial differentiation in mice===== | |
| − | Zhang C, | + | Peart, N. J., Johnson, T. A., Lee, S., Sears, M. J., Yang, F., Quesnel-Vallieres, M., '''Feng, H.''', '''Recinos, Y.''', Barash, Y., '''Zhang, C.''', Hermann, B. P., Wang, P. J., Geyer, C. B., Carstens, R. |
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| − | + | PLoS Genet. 18: e1010416. | |
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| − | + | [http://www.ncbi.nlm.nih.gov/pubmed/36129965 PubMed] [http://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1010416&type=printable PDF] | |
| − | = | + | ===== Endothelial Notch signaling directly regulates the small GTPase RND1 to facilitate Notch suppression of endothelial migration===== |
| + | Swaminathan, B., Youn, S.-W. Naiche, L.A., Du, J., Villa, S.R., Metz, J.B., '''Feng, H.''', '''Zhang, C.''', Kopan, R., Sims, P.A., Kitajewski, J.K. 2022. | ||
| + | Sci Rep 12:1655. doi: 10.1038/s41598-022-05666-1. | ||
| − | + | [http://www.ncbi.nlm.nih.gov/pubmed/35102202 PubMed] [http://www.nature.com/articles/s41598-022-05666-1.pdf PDF] | |
| − | + | ||
| − | + | ==2021== | |
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| + | ===== Vascular-derived SPARC and SerpinE1 regulate interneuron tangential migration and maturation===== | ||
| + | Genestine, M., Ambriz, D., Crabtree, G.W., Dummer, P., Molotkova, A., Quintero, M., Mela, A., Biswas, S., '''Feng, H.''', '''Zhang, C.''', Canoll, P., Hargus, G., Agalliu, D., Gogos, J.A., Au, E. | ||
| − | + | ''eLife''. 10:e56063. DOI: 10.7554/eLife.56063. | |
| − | + | ||
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| − | + | =====Gain of toxic function by long-term AAV9-mediated SMN overexpression in the sensory-motor circuit===== | |
| − | + | Alstyne, M.V., Tattoli1,I., Delestree,N., '''Recinos, Y.''', Workman, E., Shihabuddin, L.S., '''Zhang, C.''', Mentis, G.Z., Pellizzoni, L., 2021. | |
| − | + | ''Nat Neurosci''. https://doi.org/10.1038/s41593-021-00827-3. | |
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| − | + | ||
| − | |||
| − | |||
| − | |||
| − | + | =====Complexity and graded regulation of neuronal cell type-specific alternative splicing revealed by single-cell RNA sequencing===== | |
| − | + | '''Feng, H.''', '''Moakley, D.F.''', '''Chen, S.''', '''McKenzie, M.G.''', Menon, V., '''Zhang, C.''' 2021. | |
| − | + | ''Proc. Nat. Acad. Sci. USA.'' 118:e2013056118 | |
| − | + | ||
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| − | + | ||
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| − | + | ||
| − | + | ==2020== | |
| − | + | ||
| − | + | =====Alternative splicing at neuroligin site A regulates glycan interaction and synaptogenic activity===== | |
| − | Zhang, C. | + | Oku, S., '''Feng, H.''', Connor, S.A., Toledo, A., Zhang, P., Zhang, Y., Thoumine, O, '''Zhang, C.''', Craig, A.M. 2020. |
| − | + | ''eLife''. 9:e58668. | |
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| − | |||
| − | |||
| − | |||
| − | + | =====Proteome-scale analysis of phase-separated proteins in immunofluorescence images===== | |
| + | Yu, C., Shen, B., You, K., Huang, Q., Shi, M., Wu, C., Chen, Y., '''Zhang, C.''', Li, T. , 2020. | ||
| + | ''Brief Bioinform''. DOI: 10.1093/bib/bbaa187. | ||
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| − | |||
| − | |||
| − | + | =====Brain translation – a feather tips the scale===== | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | '''Ustianenko, D.''', '''McKenzie, M.G.''', '''Zhang, C.''', 2020. | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ''Mol Cell''. 77:1155-1156. (preview) | |
| − | + | ||
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| − | + | ||
| − | + | [http://www.ncbi.nlm.nih.gov/pubmed/32200794 PubMed] [http://reader.elsevier.com/reader/sd/pii/S1097276520301477?token=5965FF16D41E5360B7B19F6DA5F6EA5D757B31297A9F3F6E5EBF7C99148109E7897B9FC0E58E4D312E985A61A1315F08 PDF] | |
| − | + | ||
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| − | + | ||
| − | + | ==2019== | |
| − | + | ||
| − | + | ||
| − | + | ||
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| − | + | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| + | =====Modeling RNA-binding protein specificity in vivo by precisely registering protein-RNA crosslink sites===== | ||
| + | '''Feng, H.*''', '''Bao, S.*''', Rahman, M.,A., '''Weyn-Vanhentenryck, S.M.''', Khan, A., '''Wong, J.''', '''Shah, A.''', '''Flynn, E.D.''', Krainer, A.R., '''Zhang, C.''', 2019. | ||
| − | + | ''Mol Cell''. 74:1189-1204.E6. | |
| − | + | ||
| − | + | ||
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| − | + | [http://www.ncbi.nlm.nih.gov/pubmed/31226278 PubMed] [https://www.sciencedirect.com/science/article/pii/S1097276519300929/pdfft?md5=7015c1ebf368db775161e1c78c7439fb&pid=1-s2.0-S1097276519300929-main.pdf PDF] [http://zhanglab.c2b2.columbia.edu/index.php/MCross software/database] | |
| − | + | ||
| − | |||
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| − | |||
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| − | |||
| − | |||
| + | =====A role for sensory end organ‐derived signals in regulating muscle spindle proprioceptor phenotype===== | ||
| − | + | Wu, D., Schieren, I., '''Qian, Y.''', '''Zhang, C.''', Jessell, T.M., de Nooij, J.C., 2019. | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ''J Neurosci''. 39:4252-4267. | |
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| − | + | ||
| − | + | ||
| − | + | ||
| − | |||
| − | |||
| − | + | =====Stage-specific requirement for Mettl3-dependent m6A mRNA methylation during haematopoietic stem cell differentiation===== | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | Lee, H. '''Bao, S.''', '''Qian, Y.''', Geula, S., Leslie, J., '''Zhang, C.''', Hanna, J., Ding, L. , 2019. | |
| − | + | ||
| − | + | ''Nat Cell Biol''. 6:700-709. | |
| − | + | ||
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| − | + | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | + | =====The splicing code goes deep===== | |
| − | + | ||
| + | '''Bao, S.''', '''Moakley, D.,F.''', '''Zhang, C.''', 2019. | ||
| − | + | ''Cell'', 176:414-416 (preview). | |
| − | + | ||
| − | + | ||
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| − | + | [http://www.ncbi.nlm.nih.gov/pubmed/30682368 PubMed] [https://www.sciencedirect.com/science/article/pii/S0092867419300467/pdfft?md5=148547ab2365650c435f22377360d768&pid=1-s2.0-S0092867419300467-main.pdf PDF] | |
| − | </ | + | ==2018== |
| − | </ | + | |
| − | </html> | + | |
| + | =====DAZL regulates germ cell survival through a network of polyA-proximal mRNA interactions===== | ||
| + | |||
| + | Zagore, L.L., Sweet, T.J., Hannigan, M.M., ‘’‘Weyn-Vanhentenryck, S.M.’‘’, Jobava, R., Hatzoglou, M., '''Zhang, C.''', Licatalosi, D.D. 2018. | ||
| + | |||
| + | ''Cell Rep.'' 25: 1225-1240. | ||
| + | |||
| + | [http://www.ncbi.nlm.nih.gov/pubmed/30380414 PubMed] [http://www.cell.com/cell-reports/fulltext/S2211-1247(18)31575-4?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2211124718315754%3Fshowall%3Dtrue# PDF] | ||
| + | |||
| + | |||
| + | |||
| + | =====Special issue on RNA processing and regulation===== | ||
| + | |||
| + | Xiao, X.†, '''Zhang, C.'''† 2018. | ||
| + | |||
| + | ''Quant Biol'', '''6''':193-194. (Editorial) | ||
| + | |||
| + | [https://link.springer.com/content/pdf/10.1007%2Fs40484-018-0152-7.pdf PDF] [http://link.springer.com/journal/40484/6/3/page/1 Content of the special issue] | ||
| + | |||
| + | |||
| + | |||
| + | =====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. | ||
| + | |||
| + | ''Genome Biol'', '''19''':117. | ||
| + | |||
| + | [http://www.ncbi.nlm.nih.gov/pubmed/30111345 PubMed] [http://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-018-1493-2 PDF] | ||
| + | |||
| + | |||
| + | |||
| + | =====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'', '''71''':271-283.e5. (cover story) | ||
| + | |||
| + | [http://www.ncbi.nlm.nih.gov/pubmed/30029005 PubMed] [http://authors.elsevier.com/a/1XPn83vVUP60qL PDF] | ||
| + | |||
| + | [[File:LIN28_cover.jpg|link=https://authors.elsevier.com/a/1XPn83vVUP60qL|thumb]] | ||
| + | |||
| + | |||
| + | |||
| + | =====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'','''9''': 2189. | ||
| + | |||
| + | [http://www.ncbi.nlm.nih.gov/pubmed/29875359 PubMed] [https://www.nature.com/articles/s41467-018-04559-0.pdf PDF] [[Splicescope|software]] | ||
| + | |||
| + | |||
| + | |||
| + | =====Systematic reconstruction of autism biology from massive genetic mutation profiles===== | ||
| + | |||
| + | Luo,W., '''Zhang,C.''', Jiang,Y., Brouwer,C.R. 2018. | ||
| + | |||
| + | ''Science Advances'', <b>4</b>:e1701799. | ||
| + | |||
| + | [http://www.ncbi.nlm.nih.gov/pubmed/29651456 PubMed] [http://advances.sciencemag.org/content/4/4/e1701799.full.pdf PDF] | ||
| + | |||
| + | |||
| + | |||
| + | =====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'', <b>97</b>: 853-868.e6. | ||
| + | |||
| + | [http://www.ncbi.nlm.nih.gov/pubmed/29398366 PubMed] [http://www.sciencedirect.com/science/article/pii/S0896627318300230/pdfft?md5=ca3f1421ccd4f00eeb8fbf6d7891e4f1&pid=1-s2.0-S0896627318300230-main.pdf PDF] | ||
| + | |||
| + | -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'', <b>15</b>:213-220. | ||
| + | |||
| + | [http://www.ncbi.nlm.nih.gov/pubmed/?term=29431736 PubMed] [http://www.nature.com/articles/nmeth.4595.pdf PDF] | ||
| + | |||
| + | ==2017== | ||
| + | |||
| + | =====Microexons: discovery, regulation, and function===== | ||
| + | |||
| + | '''Ustianenko,D.''', '''Weyn-Vanhentenryck, S.M.''', '''Zhang, C.''' 2017. | ||
| + | |||
| + | ''WIRES RNA'', e1418. DOI: 10.1002/wrna.1418 (review) | ||
| + | |||
| + | [http://www.ncbi.nlm.nih.gov/pubmed/28188674 PubMed] | ||
| + | [http://onlinelibrary.wiley.com/store/10.1002/wrna.1418/asset/wrna1418.pdf?v=1&t=iz73mrnx&s=669917a4fea342b485dc0ebd178a9bf52c3f3a92 PDF] | ||
| + | |||
| + | |||
| + | |||
| + | =====A cell type-specific expression signature predicts haploinsufficient autism-susceptibility genes===== | ||
| + | |||
| + | '''Zhang,C.'''*,†, Shen,Y.*,† 2017. | ||
| + | |||
| + | ''Human Mutation'', <b>38</b>: 204-215. | ||
| + | |||
| + | [http://www.ncbi.nlm.nih.gov/pubmed/27860035?dopt=Abstract PubMed] | ||
| + | [http://onlinelibrary.wiley.com/doi/10.1002/humu.23147/epdf PDF] | ||
| + | [http://dx.doi.org/10.1101/058826 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''. <b>33</b>:566-567. DOI: 10.1093/bioinformatics/btw653. | ||
| + | |||
| + | [http://www.ncbi.nlm.nih.gov/pubmed/27797762?dopt=Abstract PubMed] | ||
| + | [https://academic.oup.com/bioinformatics/article-pdf/33/4/566/10408129/btw653.pdf PDF] | ||
| + | [http://zhanglab.c2b2.columbia.edu/index.php/CTK Software] | ||
| + | |||
| + | ==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. | ||
| + | |||
| + | [http://www.ncbi.nlm.nih.gov/pubmed/26965268?dopt=Abstract PubMed] | ||
| + | [http://download.springer.com/static/pdf/166/chp%253A10.1007%252F978-1-4939-3591-8_17.pdf?originUrl=http%3A%2F%2Flink.springer.com%2Fprotocol%2F10.1007%2F978-1-4939-3591-8_17&token2=exp=1458051088~acl=%2Fstatic%2Fpdf%2F166%2Fchp%25253A10.1007%25252F978-1-4939-3591-8_17.pdf%3ForiginUrl%3Dhttp%253A%252F%252Flink.springer.com%252Fprotocol%252F10.1007%252F978-1-4939-3591-8_17*~hmac=e07d1a73e2e58f24b94f4496e0651907558197416c86ebf75586aa553a4f216c PDF] | ||
| + | |||
| + | ==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., <b>Weyn-Vanhentenryck, S.M. </b>, <b>Zhang, C.</b>, Reid, T., Ranum, L.P.W., Day, J.W., Swanson, M.S. 2015. | ||
| + | |||
| + | ''Cell Rep.'' <b>12</b>:1159-1168. | ||
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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] | ||
| + | |||
| + | |||
| + | |||
| + | =====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. | ||
| + | |||
| + | ''Nat Comm.'' '''6''':7816. doi: 10.1038/ncomms8816. | ||
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| + | [http://www.ncbi.nlm.nih.gov/pubmed/26234653 PubMed] | ||
| + | [http://www.nature.com/ncomms/2015/150803/ncomms8816/pdf/ncomms8816.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.'' '''112''':3445-3450. | ||
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| + | [http://www.ncbi.nlm.nih.gov/pubmed/25737549 PubMed] | ||
| + | [http://www.pnas.org/content/early/2015/03/02/1502849112.full.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. | ||
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| + | [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. | ||
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| + | [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.'' '''6''':1139-1152. | ||
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| + | [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://www.sciencedirect.com/science/article/pii/S0092867411006556/pdfft?md5=26c91a5ff5f26d35dea3fb07bb6d1323&pid=1-s2.0-S0092867411006556-main.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.''', 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 07:34, 8 April 2024
Search Google Scholar (citations: 12,729; h-index: 40, i10-index: 49; as of Dec 22, 2022)
[* co-first authors; † co-corresponding authors]
2024
Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences
Xu, C.*, Bao, S.*, Chen, H., Jiang, T. †, Zhang, C. †
In submission.
Lineage-specific splicing regulation reveals adaptation of MAPT function in the primate brain.
Recinos, Y.*, Bao, S.*, Wang, X.*, Phillips, B.L., Weyn-Vanhentenryck, S.M., Swanson, M.S., Zhang, C.
Cell Genomics, in press.
CRISPR/dCas13d-based deep screening of proximal and distal splicing-regulatory elements
Recinos, Y., Ustianenko, D., Yeh, Y.T., Wang, X., Jacko, M., Yesantharao, L.V., Wu, Q., Zhang, C.
Nat Commun. in press [preprint: bioRxiv. https://doi.org/10.1101/2023.08.21.554109.]
Structure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes
Feng,H., Lu, X.-J., Maji, S., Liu, L., Ustianenko, M., Rudnick, N., Zhang, C.
Nat Commun.15: 2279. https://doi.org/10.1038/s41467-024-46429-y.
2023
Lineage tracing and single-cell profiling unravel coordinated bone marrow stromal remodeling and identify glial cells as a therapeutic target in myelofibrosis
Sarkaria, S., Zhou, J., Bao, S., Zhao, W., Fang, Y., Que, J., Bhagat, G., Zhang, C., Ding, L.
Cell Stem Cell, 30:832-850.e6.
Multiomics analyses reveal DARS1-AS1/YBX1-controlled posttranscriptional circuits promoting glioblastoma tumorigenesis/radioresistance
Zheng, C., Wei, Y., Zhang, Q., Sun, M., Wang, Y., Hou, J., Zhang, P., Lv, X., Su, D., Jiang, Y., Gumin, J., Sahni, N., Hu, B., Wang, W., Chen, X., McGrail, D.J., Zhang, C., Huang, S., Xu, H., Chen, J., Lang, F.F., Hu, J., Chen, Y.
Sci Adv. 2023 9:eadf3984.
Trans-cellular control of synapse properties by a cell type-specific splicing regulator
Traunmüller, L., Schulz, J., Feng, H., Furlanis, E., Gomez, A., Schreiner, D., Bischofberger, J., Zhang, C., Scheiffele, P.
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The germ cell-specific RNA binding protein RBM46 is essential for spermatogonial differentiation in mice
Peart, N. J., Johnson, T. A., Lee, S., Sears, M. J., Yang, F., Quesnel-Vallieres, M., Feng, H., Recinos, Y., Barash, Y., Zhang, C., Hermann, B. P., Wang, P. J., Geyer, C. B., Carstens, R.
PLoS Genet. 18: e1010416.
Endothelial Notch signaling directly regulates the small GTPase RND1 to facilitate Notch suppression of endothelial migration
Swaminathan, B., Youn, S.-W. Naiche, L.A., Du, J., Villa, S.R., Metz, J.B., Feng, H., Zhang, C., Kopan, R., Sims, P.A., Kitajewski, J.K. 2022.
Sci Rep 12:1655. doi: 10.1038/s41598-022-05666-1.
2021
Vascular-derived SPARC and SerpinE1 regulate interneuron tangential migration and maturation
Genestine, M., Ambriz, D., Crabtree, G.W., Dummer, P., Molotkova, A., Quintero, M., Mela, A., Biswas, S., Feng, H., Zhang, C., Canoll, P., Hargus, G., Agalliu, D., Gogos, J.A., Au, E.
eLife. 10:e56063. DOI: 10.7554/eLife.56063.
Gain of toxic function by long-term AAV9-mediated SMN overexpression in the sensory-motor circuit
Alstyne, M.V., Tattoli1,I., Delestree,N., Recinos, Y., Workman, E., Shihabuddin, L.S., Zhang, C., Mentis, G.Z., Pellizzoni, L., 2021.
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Complexity and graded regulation of neuronal cell type-specific alternative splicing revealed by single-cell RNA sequencing
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Alternative splicing at neuroligin site A regulates glycan interaction and synaptogenic activity
Oku, S., Feng, H., Connor, S.A., Toledo, A., Zhang, P., Zhang, Y., Thoumine, O, Zhang, C., Craig, A.M. 2020. eLife. 9:e58668. PubMed PDF
Proteome-scale analysis of phase-separated proteins in immunofluorescence images
Yu, C., Shen, B., You, K., Huang, Q., Shi, M., Wu, C., Chen, Y., Zhang, C., Li, T. , 2020.
Brief Bioinform. DOI: 10.1093/bib/bbaa187.
Brain translation – a feather tips the scale
Ustianenko, D., McKenzie, M.G., Zhang, C., 2020.
Mol Cell. 77:1155-1156. (preview)
2019
Modeling RNA-binding protein specificity in vivo by precisely registering protein-RNA crosslink sites
Feng, H.*, Bao, S.*, Rahman, M.,A., Weyn-Vanhentenryck, S.M., Khan, A., Wong, J., Shah, A., Flynn, E.D., Krainer, A.R., Zhang, C., 2019.
Mol Cell. 74:1189-1204.E6.
A role for sensory end organ‐derived signals in regulating muscle spindle proprioceptor phenotype
Wu, D., Schieren, I., Qian, Y., Zhang, C., Jessell, T.M., de Nooij, J.C., 2019.
J Neurosci. 39:4252-4267.
Stage-specific requirement for Mettl3-dependent m6A mRNA methylation during haematopoietic stem cell differentiation
Lee, H. Bao, S., Qian, Y., Geula, S., Leslie, J., Zhang, C., Hanna, J., Ding, L. , 2019.
Nat Cell Biol. 6:700-709.
The splicing code goes deep
Bao, S., Moakley, D.,F., Zhang, C., 2019.
Cell, 176:414-416 (preview).
2018
DAZL regulates germ cell survival through a network of polyA-proximal mRNA interactions
Zagore, L.L., Sweet, T.J., Hannigan, M.M., ‘’‘Weyn-Vanhentenryck, S.M.’‘’, Jobava, R., Hatzoglou, M., Zhang, C., Licatalosi, D.D. 2018.
Cell Rep. 25: 1225-1240.
Special issue on RNA processing and regulation
Xiao, X.†, Zhang, C.† 2018.
Quant Biol, 6:193-194. (Editorial)
PDF Content of the special issue
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.
Genome Biol, 19:117.
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, 71:271-283.e5. (cover story)
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,9: 2189.
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.
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.