Alexander V Alekseyenko

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Alexander V Alekseyenko, D.Phil.

Associate Professor; Assoc Oper Dir BestPrac Interg Inform Consult Core
Department of Medicine (Clin Pharm Div)

Contact Info

227 E. 30th Street
Floor 7 Room 7-40
Translational Research Building
New York, NY 10016

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2002-2003 — University of California Los Angeles, Graduate Education
2003-2008 — University of California Los Angeles, Graduate Education
2008 — European Bioinformatics Institute, PostDoctoral Training
2009 — Stanford Universtiy, PostDoctoral Training

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Research Interests Dr Alekseyenko is a leading participant in the effort of CHIBI and NYU to harness next generation sequencing technologies for applications in medical and basic science research. His is the primary informatics faculty working in the area of understanding the microbiomic diversity present in the human body through utilization and development of evolutionary and ecological statistical models. Dr. Alekseyenko's training includes rigorous mathematical, computational and biological components, which puts him into a position to understand the problems of modern biomedical research from multiple perspectives and to speak the language of multiple disciplines. The synthesis of these disciplines during Dr. Alekseyenko?s graduate research yielded an extensive database of alternative splicing events and effective full-genome scale evolutionary models for splicing signaling. This research generated much interest in the community marked by invitations to give lectures at places such as NCBI, Scripps Research Institute, Universities of Oxford, Bristol and Bath. After receiving his Ph.D. in Biomathematics from University of California Los Angeles, Dr. Alekseyenko has continued to postdoctoral training first at EMBL -- European Bioinformatics Institute, Cambridge, UK and then at Stanford University Statistics Department. To date some notable contributions include: (a) development of highly efficient genome-scale databases for sequence annotation query; (b) derivation of a unifying framework multi-state stochastic Dollo for modeling evolutionary traits encompassing both reversible and irreversible changes; (c) development of accurate and fast methods for stochastic kinetic simulations; (d) sizable effort in open source scientific software projects, such as Bayesian Evolutionary Analysis by Sampling Trees (BEAST) and Python graph database framework (PyGr). Specific theoretical work currently underway includes: (a) models for sequencing errors in amplified datasets; (b) methods for de novo assembly of heterogeneous samples; (c) phylogenetic tree statistics for fast filtering of ?interesting? sequence sites.

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All data from NYU Health Sciences Library Faculty Bibliography — -


Altering the Intestinal Microbiota during a Critical Developmental Window Has Lasting Metabolic Consequences
Cox, Laura M; Yamanishi, Shingo; Sohn, Jiho; Alekseyenko, Alexander V; Leung, Jacqueline M; Cho, Ilseung; Kim, Sungheon G; Li, Huilin; Gao, Zhan; Mahana, Douglas; Zarate Rodriguez, Jorge G; Rogers, Arlin B; Robine, Nicolas; Loke, P'ng; Blaser, Martin J
2014 Aug;158(4):705-721, Cell
— id: 1132022, year: 2014, vol: 158, page: 705, stat: Journal Article,

The cutaneous microbiota in atopic dermatitis changes with topical corticosteroid and bleach bath treatment
Gonzalez, M. E.; Schaffer, J. V.; Orlow, S. J.; Gao, Z.; Li, H.; Alekseyenko, A. V.; Blaser, M. J.
2014 MAY;134 1 1:S109-S109, Journal of investigative dermatology
— id: 997122, year: 2014, vol: 134 1 1, page: S109, stat: Journal Article,

Correction: Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation
Segal, Leopoldo N; Alekseyenko, Alexander V; Clemente, Jose C; Kulkarni, Rohan; Wu, Benjamin; Gao, Zhan; Chen, Hao; Berger, Kenneth I; Goldring, Roberta M; Rom, William N; Blaser, Martin J; Weiden, Michael D
2014 ;2:21-21, Microbiome
— id: 1065932, year: 2014, vol: 2, page: 21, stat: Journal Article,

Enrichment of lung microbiome with supraglotic microbes is associated with increased pulmonary inflammation
Segal, Leopoldo N; Alekseyenko, Alexander; Clemente, Jose C; Berger, Kenneth; Goldring, Roberta; Rom, William N; Blaser, Martin J; Weiden, Michael D
2014 Jan;11 Suppl 1:S71-S71 S71, Annals of the American Thoracic Society
— id: 753802, year: 2014, vol: 11 Suppl 1, page: S71, stat: Journal Article,

Community differentiation of the cutaneous microbiota in psoriasis
Alekseyenko, Alexander V; Perez-Perez, Guillermo I; De Souza, Aieska; Strober, Bruce; Gao, Zhan; Bihan, Monika; Li, Kelvin; Methe, Barbara A; Blaser, Martin J
2013 ;1(1):31-31, Microbiome
— id: 760032, year: 2013, vol: 1, page: 31, stat: Journal Article,

Alekseyenko, Alexander; Brown, Stuart M
Next-generation DNA sequencing informatics Cold Spring Harbor, New York : Cold Spring Harbor Laboratory Press, 2013,
— id: 1432932, year: 2013, vol: , page: ?, stat: Chapter,

Phylogenetic analysis of glucosyltransferases and implications for the coevolution of mutans streptococci with their Mammalian hosts
Argimon, Silvia; Alekseyenko, Alexander V; Desalle, Rob; Caufield, Page W
2013 ;8(2):e56305-e56305 e56305, PLoS one
— id: 231392, year: 2013, vol: 8, page: e56305, stat: Journal Article,

Strategic applications of gene expression: from drug discovery/development to bedside
Bai, Jane P F; Alekseyenko, Alexander V; Statnikov, Alexander; Wang, I-Ming; Wong, Peggy H
2013 Apr;15(2):427-437, AAPS journal
— id: 470392, year: 2013, vol: 15, page: 427, stat: Journal Article,

The nonfermentable dietary fiber hydroxypropyl methylcellulose modulates intestinal microbiota
Cox, Laura M; Cho, Ilseung; Young, Scott A; Anderson, W H Kerr; Waters, Bartholomew J; Hung, Shao-Ching; Gao, Zhan; Mahana, Douglas; Bihan, Monika; Alekseyenko, Alexander V; Methe, Barbara A; Blaser, Martin J
2013 Feb;27(2):692-702, FASEB journal
— id: 242182, year: 2013, vol: 27, page: 692, stat: Journal Article,

Pilot study of oral microbiome and risk of pancreatic cancer
Lin, I-Hsin; Wu, Jing; Cohen, Steven M.; Chen, Calvin; Bryk, Darren; Marr, Mollie; Melis, Marcovalerio; Newman, Elliot; Pachter, H. Leon; Alekseyenko, Alexander V.; Hayes, Richard B.; Ahn, Jiyoung
2013 APR 15;73(8 1 1):-, Cancer research
— id: 853292, year: 2013, vol: 73, page: , stat: Journal Article,

Quantitation and composition of cutaneous microbiota in diabetic and nondiabetic men
Redel, Henry; Gao, Zhan; Li, Huilin; Alekseyenko, Alexander V; Zhou, Yanjiao; Perez-Perez, Guillermo I; Weinstock, George; Sodergren, Erica; Blaser, Martin J
2013 Apr;207(7):1105-1114, Journal of infectious diseases
— id: 264262, year: 2013, vol: 207, page: 1105, stat: Journal Article,

Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation
Segal, Leopoldo N; Alekseyenko, Alexander V; Clemente, Jose C; Kulkarni, Rohan; Wu, Benjamin; Chen, Hao; Berger, Kenneth I; Goldring, Roberta M; Rom, William N; Blaser, Martin J; Weiden, Michael D
2013 ;1(1):19-19, Microbiome
— id: 760012, year: 2013, vol: 1, page: 19, stat: Journal Article,

Comparative genomics of oral isolates of Streptococcus mutans by in silico genome subtraction does not reveal accessory DNA associated with severe early childhood caries
Silvia, Argimon; Kranti, Konganti; Hao, Chen; Alekseyenko, Alexander V; Stuart, Brown; Caufield, Page W
2013 Nov;:269-278, Infection, genetics & evolution
— id: 666462, year: 2013, vol: , page: 269, stat: Journal Article,

Microbiomic signatures of psoriasis: feasibility and methodology comparison
Statnikov, Alexander; Alekseyenko, Alexander V; Li, Zhiguo; Henaff, Mikael; Perez-Perez, Guillermo I; Blaser, Martin J; Aliferis, Constantin F
2013 Sep;3:2620-2620, Scientific reports
— id: 529142, year: 2013, vol: 3, page: 2620, stat: Journal Article,

A comprehensive evaluation of multicategory classification methods for microbiomic data
Statnikov, Alexander; Henaff, Mikael; Narendra, Varun; Konganti, Kranti; Li, Zhiguo; Yang, Liying; Pei, Zhiheng; Blaser, Martin J; Aliferis, Constantin F; Alekseyenko, Alexander V
2013 ;1(1):11-11, Microbiome
— id: 764032, year: 2013, vol: 1, page: 11, stat: Journal Article,

Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty
Baele, Guy; Lemey, Philippe; Bedford, Trevor; Rambaut, Andrew; Suchard, Marc A; Alekseyenko, Alexander V
2012 Sep;29(9):2157-2167, Molecular biology & evolution
— id: 177226, year: 2012, vol: 29, page: 2157, stat: Journal Article,

Mapping the origins and expansion of the Indo-European language family
Bouckaert, Remco; Lemey, Philippe; Dunn, Michael; Greenhill, Simon J; Alekseyenko, Alexander V; Drummond, Alexei J; Gray, Russell D; Suchard, Marc A; Atkinson, Quentin D
2012 Aug;337(6097):957-960, Science
— id: 177236, year: 2012, vol: 337, page: 957, stat: Journal Article,

Antibiotics in early life alter the murine colonic microbiome and adiposity
Cho, Ilseung; Yamanishi, Shingo; Cox, Laura; Methe, Barbara A; Zavadil, Jiri; Li, Kelvin; Gao, Zhan; Mahana, Douglas; Raju, Kartik; Teitler, Isabel; Li, Huilin; Alekseyenko, Alexander V; Blaser, Martin J
2012 Aug;488(7413):621-626, Nature
— id: 177150, year: 2012, vol: 488, page: 621, stat: Journal Article,

Diversity of 5S rRNA genes within individual prokaryotic genomes
Pei, Anna; Li, Hongru; Oberdorf, William E.; Alekseyenko, Alexander V.; Parsons, Tamasha; Yang, Liying; Gerz, Erika A.; Lee, Peng; Xiang, Charlie; Nossa, Carlos W.; Pei, Zhiheng
2012 OCT;335(1):11-18, FEMS microbiology letters
— id: 180171, year: 2012, vol: 335, page: 11, stat: Journal Article,

Diversity of 5S rRNA genes within individual prokaryotic genomes
Pei, Anna; Li, Hongru; Oberdorf, William E; Alekseyenko, Alexander V; Parsons, Tamasha; Yang, Liying; Gerz, Erika A; Lee, Peng; Xiang, Charlie; Nossa, Carlos W; Pei, Zhiheng
2012 Jul;:11-18, FEMS microbiology letters
— id: 175922, year: 2012, vol: , page: 11, stat: Journal Article,

Causal graph-based analysis of genome-wide association data in rheumatoid arthritis
Alekseyenko, Alexander V; Lytkin, Nikita I; Ai, Jizhou; Ding, Bo; Padyukov, Leonid; Aliferis, Constantin F; Statnikov, Alexander
2011 ;6:25-25, Biology direct
— id: 134450, year: 2011, vol: 6, page: 25, stat: Journal Article,

Trends and developments in bioinformatics in 2010: prospects and perspectives
Aliferis, C F; Alekseyenko, A V; Aphinyanaphongs, Y; Brown, S; Fenyo, D; Fu, L; Shen, S; Statnikov, A; Wang, J
2011 ;6(1):146-155, Yearbook of medical informatics
— id: 174460, year: 2011, vol: 6, page: 146, stat: Journal Article,

The RAG2 C terminus suppresses genomic instability and lymphomagenesis
Deriano, Ludovic; Chaumeil, Julie; Coussens, Marc; Multani, Asha; Chou, YiFan; Alekseyenko, Alexander V; Chang, Sandy; Skok, Jane A; Roth, David B
2011 Mar 3;471(7336):119-123, Nature
— id: 128877, year: 2011, vol: 471, page: 119, stat: Journal Article,

Simrank: Rapid and sensitive general-purpose k-mer search tool
DeSantis, Todd Z; Keller, Keith; Karaoz, Ulas; Alekseyenko, Alexander V; Singh, Navjeet N S; Brodie, Eoin L; Pei, Zhiheng; Andersen, Gary L; Larsen, Niels
2011 ;11:11-11, BMC ecology
— id: 177250, year: 2011, vol: 11, page: 11, stat: Journal Article,

Testing spatiotemporal hypothesis of bacterial evolution using methicillin-resistant Staphylococcus aureus ST239 genome-wide data within a bayesian framework
Gray, Rebecca R; Tatem, Andrew J; Johnson, Judith A; Alekseyenko, Alexander V; Pybus, Oliver G; Suchard, Marc A; Salemi, Marco
2011 May;28(5):1593-1603, Molecular biology & evolution
— id: 134253, year: 2011, vol: 28, page: 1593, stat: Journal Article,

Visualization and statistical comparisons of microbial communities using R packages on phylochip data
Holmes, Susan; Alekseyenko, Alexander; Timme, Alden; Nelson, Tyrrell; Pasricha, Pankaj Jay; Spormann, Alfred
2011 ;:142-153, Pacific symposium on biocomputing
— id: 120830, year: 2011, vol: , page: 142, stat: Journal Article,

PhyloChip microarray analysis reveals altered gastrointestinal microbial communities in a rat model of colonic hypersensitivity
Nelson TA; Holmes S; Alekseyenko AV; Shenoy M; Desantis T; Wu CH; Andersen GL; Winston J; Sonnenburg J; Pasricha PJ; Spormann A
2011 Feb;23(2):27-41, Neurogastroenterology & motility
— id: 120829, year: 2011, vol: 23, page: 27, stat: Journal Article,

Exploring the future of bioinformatics data sharing and mining with Pygr and Worldbase
Lee CJ; Alekseyenko AV; Brown CT
SciPy 2009 : proceedings of the 8th Python in Science Conference, Pasadena, CA, August 18-23, 2009 [S.l. : s.n., 2009],
— id: 5559, year: 2009, vol: , page: 62, stat: Chapter,

Accurate stochastic simulation via the step anticipation tau-leaping (SAL) algorithm
Sehl, Mary; Alekseyenko, Alexander V; Lange, Kenneth L
2009 Sep;16(9):1195-1208, Journal of computational biology
— id: 104108, year: 2009, vol: 16, page: 1195, stat: Journal Article,

Wagner and Dollo: a stochastic duet by composing two parsimonious solos
Alekseyenko, Alexander V; Lee, Christopher J; Suchard, Marc A
2008 Oct;57(5):772-784, Systematic biology
— id: 104067, year: 2008, vol: 57, page: 772, stat: Journal Article,

Global analysis of exon creation versus loss and the role of alternative splicing in 17 vertebrate genomes
Alekseyenko, Alexander V; Kim, Namshin; Lee, Christopher J
2007 May;13(5):661-670, RNA
— id: 104014, year: 2007, vol: 13, page: 661, stat: Journal Article,

Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases
Alekseyenko, Alexander V; Lee, Christopher J
2007 Jun 1;23(11):1386-1393, Bioinformatics
— id: 104008, year: 2007, vol: 23, page: 1386, stat: Journal Article,

The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species
Kim, Namshin; Alekseyenko, Alexander V; Roy, Meenakshi; Lee, Christopher
2007 Jan;35(Database issue):D93-D98, Nucleic acids research
— id: 104000, year: 2007, vol: 35, page: D93, stat: Journal Article,

Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation
Resch, Alissa; Xing, Yi; Alekseyenko, Alexander; Modrek, Barmak; Lee, Christopher
2004 ;32(4):1261-1269, Nucleic acids research
— id: 120828, year: 2004, vol: 32, page: 1261, stat: Journal Article,