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Laboratory of Jia Qian Wu, Ph.D.

18 published peer-reviewed papers; eight are first author papers; one book

• 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.
• 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. Transcriptional Regulation Underlying the Mouse EML Hematopoietic Precursor Cell Self-renewal and Differentiation. Submitted.
• 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.
  (*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.*, 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., 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. Genome Res. 14: 661–664
  (*authors contribute equally to this work)
• 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

Patent

“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