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Education

• B.S., Biology, Beijing University, Beijing, China, 1992.
• M.S., Biochemistry, University of Tennessee, Memphis, 1995.
• M.S., Computer Science, University of Memphis, 1998.
• Ph.D., Computer Science, University of Memphis, 2001, Adviser: Giri Narasimhan
• Postdoc, Genetics, Harvard Medical School, 2003, Adviser: George Church

Publications

• Li* JB, Levanon* EY, Yoon J-K, Aach J, Xie B, LeProust E, Zhang K, Gao Y, Church GM (2009) Genome-wide Identification of Human RNA Editing Sites by Massively Parallel DNA Capturing and Sequencing. Science 324(5931):1210-3. * Equal Contribution
• Li* JB, Gao* Y, Aach* J, Zhang* K, Kryukov* GV, Xie B, Ahlford A, Yoon J-K, Rosenbaum AM, Zaranek AW, LeProust E, Sunyaev SR, Church GM (2009) Multiplex padlock capturing and sequencing reveal human hypermutable CpG variations. Genome Research, Published in Advance June 12, 2009, doi: 10.1101/gr.092213.109. * Equal Contribution
• Deng, J., Shoemaker, R., Xie, B., Gore, A., Leproust, E., Antosiewica-Bourget, J., Egli, D., Maherali, N., Park, I-H, Yu, J., Daley, G.Q., Eggan, K., Hochedlinger, K., Thomson, J., Wang, W., Gao*, Y., Zhang*, K. (2009) Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nature Biotechnology, Published online: 29 March 2009 | doi:10.1038/nbt.1530. * Co-corresponding Authors, Article
• Ball*, M.P., Li*, J.B., Gao, Y., Lee, J., LeProust, E. Park, I.H. Xie, B. Daley, G.Q. Church, G.M. (2009) Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nature Biotechnology, Published online: 29 March 2009 | doi:10. * Equal Contribution, Article
• Eaves, H. and Gao, Y. (2009) MOM: Maximal Oligo Mapping. Bioinformatics 2009; doi: 10.1093/bioinformatics/btp09.
• Valente*, A., Robert*, S., Buck, G. and Gao, Y. (2009) Functional Organization of the Yeast Proteome by a Novel Yeast Interactome Map. Proc Natl Acad Sci USA, published online before print January 23, 2009, doi:10.1073/pnas. 0808376106. * Equal Contribution.
• Chiu, R., Chan, A., Gao, Y., Lau, V., Zheng, W., Leung, T., Foo, C., Xie, B., Tsui, N., Lun, F., Zee, B., Lau., T., Cantor, C., Lo, Y.M. (2008) Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma. Proc Natl Acad Sci USA, Vol. 105, No. 51. (23 December 2008), pp. 20458-20463
• Porreca GJ, Zhang K, Li JB, Xie B, Austin D, Vassallo SL, Leproust EM, Peck BJ, Emig CJ, Dahl F, Gao Y., Church GM, Shendure J (2007) Multiplex Amplification of Large Sets of Human Exons. Nature Methods Published online: 14 October 2007 | doi:10.1038/nmeth1110
• Gao, Y., and Church, G. (2006). FLEXTMOTIF: A Generic Flexible Motif Discovery Algorithm for Unaligned Sequences. Submitted.
• Lin*, X., Gao*, Y., Shi, Y., and Church, G. (2006). The Sound of Silence: Biological Switches through Single Protein Multisite Modifications. * Equal Contribution. in revision.
• Gao, Y., and Church, G. (2005) Improving Molecular Cancer Classification through Sparse Non-Negative Matrix Factorization. Bioinformatics 21: 3970-3975.
• Narasimhan, G, Bu, C., Gao, Y., Wang, X, Xu, N, and Mathee, K. (2002) Mining Protein Sequences for Motifs. Journal of Computational Biology, 9(5):707-720.
• Floratos, A., Rigoutsos, I., Parida, L., and Gao, Y. (2001). DELPHI: A pattern-based method for detecting sequence similarity." IBM Journal of Research and Development, vol 45, Number 3/4, 455--474.
• Platt, D., Parida, L., Gao, Y. Floratos, A., and Rigoutsos, I. (2001). QSAR in Grossly Underdetermined Systems: Opportunities and Issues. IBM Journal of Research and Development, vol 45, Number 3/4, 533--544.
• Gao, Y., Rigoutsos, I., Floratos, A., Parida, L., and Narasimhan, G. (2000). Unsupervised Building and Exploitation of Composite Descriptors for Collections of Protein and Protein Fragments. IBM T. J. Watson Research Center Technical Report, 2000.
• Rigoutsos, I., Floratos, A., Parida, L., Gao, Y., and Platt, D. (2000). The Emergence of Pattern Discovery Techniques in Computational Biology." Metabolic Engineering. 2(3):159-177.
• Narasimhan, G., Gao, Y., Zheng, G., and Mathee, K. (2001). Pattern Discovery Applications in Bioinformatics,” Invited paper for the Proceedings of the Fourth International Conference on Information Technology, India, 2001.
• Parida, L., Rigoutsos, I., Floratos, A., Platt, D., and Gao, Y. (2000). Pattern Discovery on Character Sets and Real Valued Data: Linear Bound on Irredundant Motifs and an Efficient Polynomial Time Algorithm. In Proceedings 11th Annual ACM/SIAM Symposium on Discrete Algorithms (SODA '00). San Francisco, CA. January 2000.
• Rigoutsos, I., Floratos, A., Ouzounis, C., Gao, Y., and Parida, L. (1999). Dictionary Building Via Unsupervised Hierarchical Motif Discovery In The Sequence Space of Natural Proteins. Journal of Proteins: Structure, Function and Genetics, 37(2) ):264-77.
• Stolovitzky, G., Gao, Y., Floratos, A., and Rigoutsos, I. (1999). Tandem Repeat Detection using Pattern Discovery with Applications to the Identification of Yeast Satellites. IBM T. J. Watson Research Center Research Report, RC 21508. May 1999.
• Gao, Y., Garzon, M., Murphy, R., Rose, J., Deaton, R., Franceschetti, and Stevens. E. (1999). DNA Implementation of Nondeterminism. DIMACS Series in Discrete Mathematics and Theoretical Computer Sciences, vol. 48. 137-148.
• Rigoutsos, I., Gao, Y., Floratos, A., and Parida, L. (1999). Building Dictionaries Of 1D and 3D Motifs by Mining the Unaligned 1D Sequence of 17 Archaeal and Bacterial Genomes. In Proceedings Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB '99), 223-233, Heidelberg, Germany. August 1999.
• Floratos, A., Rigoutsos, I., Parida, L., Stolovitzky G., and Gao, Y. (1999). Sequence Homology Detection Through Large-Scale Pattern Discovery." In Proceedings Third Annual ACM International Conference on Computational Molecular Biology (RECOMB '99). Lyon, France. April 1999.
• Gao, Y., Mathee, K., Narasimhan, G., Wang, X. (1999). Detection of HTH Motifs via Data Mining. Proceedings of SPIRE’ 99 – String Processing and Information Retrieval, 63-72.
• Rigoutsos, I., Floratos, A., Ouzounis, C., and Gao, Y. (1998). From Motif Discovery To Functional Characterization and Structure Prediction: A Feasible Journey." In Proceedings Second Annual TIGR Conference on Computational Genomics. Reston, VA. November 1998.
• Gao, Y., Rigoutsos, I., Floratos, A., Parida, L., and Stolovitzky. (1998). Human Breast Cancer Gene 2 (BRCA2), A Function Analysis” IBM T. J. Watson Research Center Research Report, Bioinformatics/Data Mining, April 1998.
• Garzon, M, Gao, Y., Rose, J., Murphy, K., Deaton, R., Franceschetti and Stevens, E. (1998). In-Vitro Implementation of Finite-state Machines. In Proc. 2nd International Workshop on Implementing Automata WIA'97, Springer-Verlag LNCS 1436, 56-71.
• Rose, J., Gao, Y., Garzon, M., Deaton, R., Franceschetti, Murphy, K., and Stevens, E. (1997). Implementation of Finite-state Machines. In Proc. 2nd Genetic Programming Conference, Stanford, CA, Morgan-Kaufmann, 479-487.

Research Interests

• Computational biology, genome sequencing, algorithm design and analysis, data mining, computer and biological networks

Research Lab

• High Throughput Genomics