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Alexander V Alekseyenko
3854 Mentone Av #5
Culver City, CA 90232
e-mail:
shuriko@BoT-TaK.org
http://www.BoT-TaK.org
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Education:
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2008
| Ph.D. in Biomathematics
University of California, Los Angeles, CA
Advisor: Marc Suchard
(Dept. of Biomathematics)
Advisor: Christopher J. Lee
(Dept. of Chemistry and Biochemistry)
| | 2003 | M.Sc. in Biomathematics
University of California, Los Angeles, CA
| 2002
| B.Sc. in Computer Science
Case Western Reserve University, Cleveland, OH
Advisor: Cenk Sahinalp
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Research interests:
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- Bayesian statistics
- Markov chain Monte Carlo simulations
- Stochastic processes
- Statistical computing
- Statistical genetics and phylogenetics
- Multi-scale modeling in Biology
- Combinatorial and randomized algorithms
- Bioinformatics methods for molecular biology and genetics
- Evolutionary modeling
- High-throughput experimental data analysis
- Genomics and Proteomics
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Professional experience:
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2008 – present
| Postdoctoral Fellow,
EMBL outstation
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, CB10 1SD, U.K.
| 2002 – 2008
| Research Assistant,
Molecular Biology Institute,
Center for Genomics and Proteomics,
Center for Computational Biology,
University of California, Los Angeles, CA
| Summer 2002
| RnD executive project lead,
ZyxBio, LLC
11000 Cedar Ave.,
Cleveland, OH 44106 | | 2001 – 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 |
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Professional service:
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Bioinformatics Student Advisory Board, UCLA (member)
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Students mentored:
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| Qi Wang (Ph.D. student at UCLA) | | Lukasz Goldschmidt (Ph.D. student at UCLA) |
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Referee activity:
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Ad hoc reviewer for: Nucleic Acids Research, Trends in Genetics, PNAS
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Awards:
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| 2006 -- 2008 | NIH SIB Graduate Fellowship, University of California, Los Angeles |
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| | | 2005 | FASEB MARC Travel Fellowship |
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| | | 2003 -- 2005 | NSF IGERT Graduate Fellowship, University of California, Los Angeles |
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| | | 2002 -- 2003 | Biomathematics Fellowship, University of California, Los Angeles |
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| | | 2001 -- 2002 | Senior Year Scholarship, Case Western Reserve Alumni Association |
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Languages:
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English, Russian, Ukrainian
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Skills:
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- Statistical & Math packages: R/Splus, Mathematica, Matlab, SAS
- Bioinformatics software: clustal, blast, poa, genemine, biopython, bioperl, etc.
- Programming languages: C/C++, Java, perl, python, lisp, gnu development tools
- Web and Database: HTML/XML/XSL/CSS, php, web content management, MySQL, DBI
- OS and environments: Windows 95/NT/2000/XP, Mac OS X, UNIX/Linux, shell scripting
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Publications and talks:
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Refereed publications Alekseyenko AV., Lee CJ., Suchard MA. “Wagner and Dollo: a stochastic duet by composing two parsimonious solos”, Systematic Biology, 2008 (in press) 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. (link)
Alekseyenko, AV and Lee, CJ, Nested Containment List (NCList): A new algorithm for accelerating interval query of genome alignment and interval databases. Bioinformatics 2007 23(11):1386-1393; 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 35(Database issue):D93-D98; doi:10.1093/nar/gkl884
(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)
| Manuscripts in preparation - Alekseyenko, AV., Suchard, MA., and Goldman, N. “Phylogenetically inspired weighting for profile-HMMs in sequence class membership testing”
- Alekseyenko, AV. and Lange, KL. “An MM that regularly zeroes in on mixtures with controversial constituents: haplotype frequency estimation analyzing new generation sequencing data” (data analysis in progress).
- Sehl, M., Alekseyenko, AV. and Lange, KL. “Accurate Stochastic Simulation via the Step Anticipation τ -Leaping (SAL) Algorithm” (close to submission).
- Kim, N., Pan, C., Alekseynko, AV., and Lee, CJ. “Pygr: A Python graph framework for highly scalable comparative genomics and annotation database analysis”
- Lee, CJ*, Pan, C., Chen,L., and Alekseyenko, AV. “An Asymmetric Measure of
Functional Interactions between Mutations in Highly Polymorphic Sequences” (written 2007, to be re-submitted)
- Alekseyenko, AV., Lee, CJ. “VEEDB: Verterbrate Exon Evolution Database”
| Invited talks Alekseyenko, AV. “Evolution of alternatively spliced exons via bioinformatic, algorithmicand mathematical modeling techniques”, Scripps Research Institute, La Jolla, CA December 2007 Alekseyenko, AV. “Computational, comparative and stochastic modeling approaches to creation and loss of alternatively spliced exons”, NCBI, NIH, Bethesda, MD November 2007
| Contributed talks and posters
- Alekseyenko, AV. “Wagner and Dollo: A stochastic duet by composing two parsimonious solos, Bayesian Phylogeny Workshop, Budapest, Hungary”, June 2008
- Alekseyenko, AV., Lange, KL. "A method for estimation of HIV genotype frequencies in the course of drug treatment", HIV Research: The Next Generation conference, CHIPTS, UCLA, Los Angeles, CA, USA, 2008
- Alekseyenko, AV.
“Ordering properties of intervals: An enabling perspective for
cross-genome databases”, (Poster), Institute for Digital Research and
Education, UCLA November 2007
- Alekseyenko, AV. “Ordering properties of intervals: An enabling perspective for cross-genome databases”, (Poster), Workshop for Young Researchers in Mathematical Biology, Ohio State University, Columbus, OH March 2007
- Xing, Y., Alekseyenko, AV. and Lee, CJ. “How alternative splicing helped build the genome: exon creation, locally accelerated sequence evolution, and the production of new tissue-specific functions.”, The FASEB Journal. 20:A61 2006.
- Kim, N., Lee, CJ., Alekseyenko, AV., Parker, S. “Pygr: a Python Graph Database Framework for Bioinformatics”, (Software demonstration), ISMB, Fortaleza, Brazil August 2006
- Alekseyenko, AV. “A comparative genomics approach to distinguishing exon creation and loss shows increased exon creation associated with alternative splicing”, (Elevated abstract), ISMB. Detroit, MI June 2005
- Lee, CJ., Alekseyenko, AV., Parker, S. “Pygr: a python graph database framework for sequence analysis”, (Software demonstration), ISMB. Detroit, MI June 2005
- Alekseyenko, AV., Suchard MA. “A stochastic model for creation and loss of sequence blocks”, (Poster), RECOMB. Boston, MA May 2005
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