User:Alekseyenko av

Contact Information
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Scientific Interests

 * Biomathematics
 * Computational Bayesian analysis
 * MCMC sampling and inference
 * Inference using temporal and spatial stochastic models
 * Applications to biological data analysis
 * Bioinformatics methods in molecular biology and genetics
 * Combinatorial algorithms for biological data analysis

Education
September 2002 -- present, Ph.D. student in Biomathematics, University of California, Los Angeles, CA Advisor: Christopher J. Lee (Dept. of Chemistry and Biochemistry) Advisor: Marc Suchard (Dept. of Biomathematics) December 2003	M.Sc. in Biomathematics University of California, Los Angeles, CA August 2002, B.Sc. in Computer Science, Case Western Reserve University, Cleveland, OH

Experience
November 2002 -- present, Graduate Student Researcher, Molecular Biology Institute, Bioinformatics, Center for Computational Biology, University of California Los Angeles, Los Angeles, CA

May 2001 -- May 2002, Research Assistant, Department of Genetics, Case Western Reserve University, Cleveland, OH

2001 – 2002, Head Teaching Assistant, Department of Computer Science, Case Western Reserve University, Cleveland, OH

Awards
2006 -- pres	NIH SIB Graduate Fellowship, University of California, Los Angeles

2005 FASEB MARC Travel Fellowship

2003 -- 2005	NSF IGERT Graduate Fellowship, University of California, Los Angeles

2002 -- 2003	Biomathematics Fellowship, University of California, Los Angeles

2001 -- 2002	Senior Year Scholarship, Case Western Reserve Alumni Association

Publications

 * Alekseyenko AV., Kim N., Lee CJ, Global analysis of exon creation vs. loss, and the role of alternative splicing, in 17 vertebrate genomes, RNA 2007, 13:661-670. doi:10.1261/rna.325107.
 * Alekseyenko, AV and Lee, CJ, Nested Containment List (NCList): A new algorithm for accelerating interval query of genome alignment and * interval databases. Bioinformatics Advance Access published on January 18, 2007, DOI 10.1093/bioinformatics/btl647. (link)
 * Kim N, Alekseyenko AV, Roy M, Lee, CJ, The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species. Nucleic Acids Research 2007 Jan; 35 (Database issue):D93-8. Epub 2006 Nov 15. (link)
 * Resch, A., Xing, Y., Alekseyenko, A., Modrek, B., Lee, C. (2004) Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation, Nucl. Acids. Res. 32: 1261-1269. (link)

Conferences

 * Alekseyenko, AV. “A comparative genomics approach to distinguishing exon creation and loss shows increased exon creation associated with alternative splicing” (Elevated abstract, talk), ISMB. Detroit, MI, USA, 2005
 * Lee CJ, Alekseyenko AV. “Pygr: a python graph database framework for sequence analysis” (Software demonstration), ISMB. Detroit, MI, USA, 2005
 * Alekseyenko, AV., Suchard MA. “A stochastic model for creation and loss of sequence blocks” (Poster), RECOMB. Boston, MA, 2005