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...our contributions to science & academia

Journal Articles & Books

You, Y., Cuevas-Diaz Duran, R., Jiang L., Dong X., Zong S., Snyder M., Wu J. Q., An integrated global regulatory network of hematopoietic precursor cell self-renewal and differentiation, Integr. Biol., (2018), doi:10.1039/c8ib00059j. PMID: 29892750.
Dong, X., Cuevas-Diaz Duran, R., You, Y., Wu, J. Q. Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis. J. Vis. Exp. (134), e57547, doi:10.3791/57547 (2018). PMID: 29708547.
Exosomes Mediate Epithelium−Mesenchyme Crosstalk in Organ Development. Jiang, N., Xiang, L., He, L., Yang, G., Zheng, J., Wang, C., Zhang, Y., Wang, S., Zhou, Y., Sheu, T., Wu, J., Chen, K., Coelho, P.G., Tovar, N.M., Kim, S.H., Chen, M., Zhou, Y-H., and Mao, J. ACS Nano. 2017 Jul 27. doi: 10.1021/acsnano.7b01087. PMID: 28727410.
Cuevas-Diaz Duran R, Wei H, Wu JQ. Single-cell RNA-sequencing of the brain. Clinical and Translational Medicine. 2017;6:20. doi:10.1186/s40169-017-0150-9.
Cuevas-Diaz Duran, R., Yan, H., Zheng, Y., Huang, X., Grill, R., Kim, DH., Cao, Q., and Wu, JQ. The systematic analysis of coding and long non-coding RNAs in the sub-chronic and chronic stages of spinal cord injury, Scientific Reports. 2017, Jan. 20; 7:41008. doi: 10.1038/srep41008.
Cuevas-Diaz Duran, R., Menon, S., and Wu, J. (2016). The Analyses of Global Gene Expression and Transcription Factor Regulation. In Transcriptomics and Gene Regulation (pp. 1-35). Springer Netherlands.
Dong, X., Muppani, N. R., and Wu, J. (2016). Long Noncoding RNAs: Critical Regulators for Cell Lineage Commitment in the Central Nervous System. In Transcriptomics and Gene Regulation (pp. 73-97). Springer Netherlands.
Transcriptomics and Gene Regulation. Wu, J. Q. (ed.), Springer Netherlands. 2016
Dong, X., Chen, K., Cuevas-Diaz Duran, R., You, Y., Sloan, S. A., Zhang, Y., Cao, Q., Barres, B. A., and Wu, J. Q. Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination, Plos Genetics. 2015, 11(12): e1005669.
Dong, X., You, Y., and Wu, J.Q. (2015). Building an RNA-sequencing transcriptome of the nervous system. The Neuroscientist. PMID: 26463470
Yan, Q., Weyn-Vanhentenryck, S. M., Wu, J., Sloan, S., Zhang, Y., Chen, K., Wu, J. Q., Barres, B., Zhang, C. Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators. PNAS. Mar 17;112(11):3445-50, 2015
Chen, K., Dai X., and Wu, J.Q. Alternative splicing: An important mechanism in stem cell biology. World Journal of Stem Cells. 2015 January 26; 7(1): 1-10
Zhang, Y., Chen, K., Sloan, S., Bennett, M., Scholze, A., O'Keeffe, S., Phatnani, H., Guarnieri, P., Caneda, C., Ruderisch, N., Deng, S., Liddelow, S., Zhang, C., Daneman, R., Maniatis, T., Barres, B., Wu, J.Q. An RNA-Seq transcriptome and splicing database of neurons, glia and vascular cells of the cerebral cortex. J. Neurosci., 34(36): 11929-11947. PMID:25186741
Zong, S., Deng, S., Chen, K., and Wu, J.Q. Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis. J. Vis. Exp. (93), e52104, doi:10.3791/52104. PMID:25407807
Chen, K., Dong, X., and Wu, J.Q. The Application of single-cell sequencing in dynamic transcriptomes. Single Cell Sequencing. X. Wang (ed.), Single Cell Sequencing and Systems Immunology, Translational Bioinformatics 5. Springer Publisher Dordrecht 2015. 41-63
Chen, K., Deng, S., Lu, H., Zheng, Y., Yang, G., Kim, D., Cao, Q., and Wu, J.Q. (2013) RNA-Seq characterization of spinal cord injury transcriptome in acute/subacute phases: a resource for understanding the pathology at the systems level. Plos One. 8(8):e72567. PMC3739761
Wu, J. Q., Seay, M., Schulz, V., Hariharan, M., Tuck, D., Lian, J., Du, J., Shi, M., Ye, Z. J., Gerstein, M., Snyder, M., and Weissman, S. (2012). Tcf7 is a key regulator of the self-renewal and differentiation switch in a multipotential hematopoietic cell line. PLoS Genet 8(3): e1002565. PMC3297581
Wu, J. Q. (2011). Characterize mammalian transcriptome complexity. Deutschland, Germany: LAP LAMBERT Academic Publishing.
Wu, J. Q., Habegger, L., Noisa, P., Szekely, A., Qiu, C., Hutchison, S., Raha, D., Lin, H., Egholm, M., Weissman, S., Cui, W., Gerstein, M., and Snyder, M. (2010). Dynamic Transcriptomes during Neural Differentiation of Human Embryonic Stem Cells Revealed by Integrating Short, Long, and Paired-end Sequencing. PNAS. 107: 5254-5259.
The MGC Project Team. (2009). The Completion of the Mammalian Gene Collection. Genome Res 19:2324-2333
Wu, J. Q. and Snyder, M. (2008). RNA polymerase II promoter proximal stalling: Loading at the start line prepares genes for a sprint. Genome Biology. 9:220
Wu, J. Q., Du, J., Rozowsky, J. Zhang , Z., Weissman, S., Gerstein, M., Snyder, M. (2008). Systematic analysis of transcribed loci in selected ENCODE regions using RACE sequencing. Genome Biology. 9(1):R3
The ENCODE Project Consortium (2007). The ENCODE pilot project: identification and analysis of functional elements in 1% of the human genome. Nature. 447:799-816.
Wu, J. Q.*, Trinklein, N.D.* , Karaöz, U.*, Halees, A.*, Aldred, S.F., Collins, P.J., Zheng, D., Zhang , Z., Gerstein, M., Snyder, M., Myers, R.M., and Weng, Z. P. (2007). Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. Genome Res. 17:720-31.
Rozowsky, J. , Newburger, D. , Sayward, F. , Wu J. Q. , Jordan, G., Korbel, J., Nagalakshmi, U., Yang, J., Zheng, D., Guigo, R., Gingeras, T., Weissman, S., Miller, P., Snyder M. and Gerstein M. (2007). Analysis and Classification of Unannotated Transcription within the ENCODE Regions: Associating Transcription with Known and Novel Loci. Genome Res. 17:732-45.
Wu, J. Q. *, Tenney, A.*, Langton L, Klueh P, Quatrano R, Brent M. R. (2007). A tale of two templates: Automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices. Genome Res. 17 :212-218.
Rozowsky, J., Wu, J.Q., Lian, Z., Nagalakshmi, U., Korbel, J.O., Kapranov, P., Zheng, D., Dyke, S., Newburger, P., Miller, P., Gingeras, T.R., Weissman, S., Gerstein, M., and Snyder, M. (2006). Novel transcribed regions in the human genome. Cold Spring Harb Symp Quant Biol. 71:111-6.
Wu, J. Q., Garcia, A. M., Hulyk, S., Sneed, A., Kowis, A., Yuan, Y., Steffen, D., McPherson, J. D., Gunaratne, P. H., and Gibbs, R. A. (2004). Large scale RT-PCR recovery of full-length cDNA clones. BioTechniques. 36: 690-700.
Wu, J. Q., Shteynberg, D., Arumugam, M., Gibbs, R. A., and Brent, M. R.. (2004). Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing. Genome Res. 14: 665-671
Wu, J. Q. *, Dewey, C.*, Cawley, S., Alexandersson, M., Gibbs, R. A. and Pachter, L. (2004). Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat. GenomeRes. 14: 661-664
The MGC Project Team. (2004). The Status, Quality and Expansion of the NIH Full-length cDNA Project: The Mammalian Gene Collection (MGC).Genome Res. 14: 2121-2127
Rat Genome Sequencing Project Consortium. (2004). Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 428: 493 - 521
International Human Genome Sequencing Consortium. (2004). Finishing the euchromatic sequence of the human genome. Nature. 431: 931-45.
Zhang, Z., Burch, P. E., Cooney, A. J., Lanz R. B., Pereira, F. A., Wu, J. Q., Gibbs, R. A., Weinstock, G., and Wheeler, D. A. (2004). Genomic Analysis of the Nuclear Receptor Family: New Insights into Structure, Regulation, and Evolution from the Rat Genome. Genome Res. 14: 580-590.
Gunaratne, P. H., Wu, J. Q., Garcia, A. M., Hulyk, S., Worley, K., Margolin, J. F., and Gibbs, R. A. (2003). Concatenation cDNA sequencing for transcriptome analysis. C. R. Biologies 326: 971-977
Tzafrir, I., McElver, J. A., Liu, C. M., Yang, L. J., Wu, J. Q.,Martinez, A., Patton, D. A., Meinke, D. W. (2002). Diversity of TITAN Functions in Arabidopsis Seed Development. Plant Physiol 128: 38-51
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