Difference between revisions of "Publications"
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=====Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences===== | =====Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences===== | ||
| − | Xu, C.*, '''Bao, S.'''*, '''Wang, Y.''', | + | Xu, C.*, '''Bao, S.'''*, '''Wang, Y.''', Li, W., Chen, H., Shen, Y., Jiang, T. †, '''Zhang, C.''' † |
Genome Res. in press. | Genome Res. in press. | ||
[http://biorxiv.org/cgi/content/short/2024.03.22.586363v1. preprint] [http://github.com/chaolinzhanglab/DeltaSplice software] | [http://biorxiv.org/cgi/content/short/2024.03.22.586363v1. preprint] [http://github.com/chaolinzhanglab/DeltaSplice software] | ||
| − | |||
=====Lineage-specific splicing regulation reveals adaptation of MAPT function in the primate brain===== | =====Lineage-specific splicing regulation reveals adaptation of MAPT function in the primate brain===== | ||
Revision as of 09:34, 18 July 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
Oncogenic NOVA1 expression dysregulates alternative splicing in breast cancer
Moakley, D.F., Zhang, C.
In submission.
Reverse engineering neuron type-specific and type-orthogonal splicing-regulatory networks using single-cell transcriptomes
Moakley, D.F., Campbell, M., Anglada-Girotto, M., Feng, H., Califano, A., Au, E., Zhang, C.
In submission.
Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences
Xu, C.*, Bao, S.*, Wang, Y., Li, W., Chen, H., Shen, Y., Jiang, T. †, Zhang, C. †
Genome Res. in press.
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, https://doi.org/10.1016/j.xgen.2024.100563.
Preview: Aya, F. and J. Valcarcel (2024). Shaping human brain development and vulnerability through alternative splicing. Cell Genom 4: 100584.
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. 15:3839.
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.
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.
Cell Rep. 42: 112183.
2022
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.
Nat Neurosci. https://doi.org/10.1038/s41593-021-00827-3.
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
2020
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.