People

JHU biomedical engineering primary faculty

Yuan  Gao, PhD

Yuan Gao, PhD

Adjunct Associate Professor

Office: Rangos 344
Lab: Genetics, Epigenetics and Bioinformatics Laboratory
(410) 955-0805
ygao24@jhmi.edu

Education

Ph.D., Computer Science, University of Memphis, Memphis, 2001
M.S., Computer Science, University of Memphis, Memphis, 1998
M.S., Biochemistry , University of Tennessee, Memphis, 1995
B.A., Biology, Beijing University, Beijing, 1992

Research Interests

I am interested in understanding the genetic and epigenetic basis of brain function and neurological diseases — with a focus on schizophrenia, bipolar spectrum disorder and major depression. There is a growing reliance on high-throughput technologies that are increasingly changing the way we do basic and translational research. Next-generation sequencing is bringing the dream closer to the reality of transforming biology into quantitative information science. However, the need to sift through tremendous amounts of data — in order to make biological sense — has made it apparent that bioinformatics is becoming a new bottleneck. In my Genetics, Epigenetics and Bioinformatics Lab we develop new high-throughput technologies to study RNA splicing, RNA editing and DNA methylation in postmortem brain and mouse model. In addition, our development of algorithms and bioinformatics software has enabled us to analyze the very-large datasets generated from high-throughput experiments, especially those from our next-generation sequencing experiments.

Selected Publications

Gao, Y., and Church, G. (2005) Improving Molecular Cancer Classification through Sparse Non-Negative Matrix Factorization. Bioinformatics 21: 3970-3975.

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. PNAS, Vol. 105, No. 51. (23 December 2008), pp. 20458-2046.

Eaves, H.L. and Gao, Y. (2009) MOM: Maximum Oligonucleotide Mapping. Bioinformatics 25:969-70.

Valente*, A.X.C.N., Robert*, S.B., Buck, G.A. and Gao, Y. (2009) Functional Organization of the Yeast Proteome by a Novel Yeast Interactome Map. PNAS vol. 106 no. 5 1490-1495.

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, 27, 361 - 368 *Equal Contribution, Article, Cover Story

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, 27:353-60. *Co-corresponding Authors, Article, Cover Story

Nechaev, S., Fargo, D.C., Santos, G.D., Liu, L., Gao, Y. and Adelman K. (2010) Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II. Science, 2010 Jan 15;327(5963): 335-8

Gilchrist, D.A., Dos Santos, G., Fargo, D.C., Xie., Gao Y., Li, L., and Adelman, K. (2010). Pausing of RNA polymerase II disrupts DNA-encoded nucleosome organization to facilitate precise gene regulation. Cell. Volume 143, Issue 4, 12 November 2010, pp 540-551.

Guo, J., Ma, D., Mo, H., Ball, M.P., Jang, M.H., Bonaguidi, M.A., Balazer, J.A., Eaves, H.L., Xie, B., Ford, E., Zhang, K., Ming, G.L., Gao, Y.* & Song, H.* (2011) Neuronal activity modifies DNA methylation landscape in the adult brain. Nature Neuroscience 14, 1345-1351 *Co-corresponding Authors

Valente, A.X.C.N, Shin, J.H., Sarkar, A., Gao, Y. (2012) Rare coding SNP in DZIP1 gene associated with late-onset sporadic Parkinson's disease. Scientific Reports 2, Article number:256 doi:10.1038/srep00256

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