The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases

 Jiaqian Wu, Ph.D

Jiaqian Wu, Ph.D

Assistant Professor
Department of Neurosurgery
Center for Stem Cell and Regenerative Medicine


Dr. Jiaqian Wu earned her doctorate from the laboratory of Dr. Richard Gibbs in Molecular and Human Genetics at Baylor College of Medicine in Houston, where her research focused on novel mammalian gene discovery and the characterization of transcriptome complexity. Her postdoctoral work in Dr. Michael Snyder’s laboratory at Yale and Stanford University focused on high-throughput analysis of gene expression, novel regulatory site discovery, transcription factor binding site identification, and regulatory networks of stem cell self-renewal and differentiation. Dr. Wu’s work has resulted in a number of high-impact publications. She also authored a book and a patent.  Dr. Wu received prestige Pathway to Independence (PI) Award (K99/R00) from the National Heart, Lung and Blood Institute and subsequently joined the department of Neurosurgery at the University of Texas Health Science Center at Houston as an Assistant Professor.

Wu laboratory combines stem cell biology and systems-based approaches involving functional genomics, bioinformatics and next-generation sequencing technologies to unravel gene transcription and regulatory mechanisms governing neural differentiation. Our goal is to identify key regulators during this process as therapeutic targets and develop safe treatment for spinal cord injury and neurological diseases. The other area of our research interest lies in the studies of the regulatory networks of hematopoietic precursor cell self-renewal and differentiation using multipotent EML (erythroid, myeloid, and lymphocytic) cell as a model system. We are using integrated genomic and proteomic approaches to globally identify key components that control the switch and  generate a novel and comprehensive view of the regulation of earl stages of hematopoietic precursor self-renewal and differentiation.

Selected Publications

  • 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. Genome Res. 14: 661-664 (*authors contribute equally to this work)
  • 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. *, 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. (*authors contribute equally to this work)
  • 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.*, 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. (*authors contribute equally to this work)
  • 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., 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
  • 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
  • The MGC Project Team. (2009). The Completion of the Mammalian Gene Collection. Genome Res. 19:2324-2333
  • 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.
  • Wu, J. Q. (2011). Characterize mammalian transcriptome complexity.  Deutschland, Germany: LAP LAMBERT Academic Publishing.
  •  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
  • 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
  • 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. (2014) 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., Wu, J. Q. (2014). 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 ImmunologyTranslational Bioinformatics 5. Springer Publisher Dordrecht 2015. 41-63
  • Yan, Q., Weyn-Vanhentenryck, S. M., Wu, J., Sloan, S., Zhang, Y., Chen, K.,Wu, J. Q., Barres, B., Zhang, C. (2015) Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators. PNAS. Mar 17;112(11):3445-50
  • Chen, K., Dai X., and Wu, J.Q. (2015) Alternative splicing: An important mechanism in stem cell biology. World Journal of Stem Cells. 7(1): 1-10. PMID: 25621101


“Nucleic Acid Molecules Encoding Proteins Essential for Plant Growth and Development and Uses Thereof”

International Application No. WO 03/074653

Filed: February 14, 2003 by SYNGENTA

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Wide Variety of Genetic Splicing Found in Embryonic Stem Cells

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