Alexander V Alekseyenko

Biosketch / Results /

Alexander Alekseyenko

Adjunct Associate Professor, Department of Medicine
Assoc Oper Dir BestPrac Interg Inform Consult Core

Contact Info

Address
227 East 30th Street
New York, NY 10016

Alexander.Alekseyenko@nyumc.org

Research Interests

http://www.nyuinformatics.org/people/faculty/alexander-alekseyenko 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.

Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis
Gonzalez, Mercedes E; Schaffer, Julie V; Orlow, Seth J; Gao, Zhan; Li, Huilin; Alekseyenko, Alexander V; Blaser, Martin J. Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis. Journal of the American Academy of Dermatology. 2016 Sep;75(3):481-493.e8 (2219492)

Cigarette smoking and the oral microbiome in a large study of American adults
Wu, Jing; Peters, Brandilyn A; Dominianni, Christine; Zhang, Yilong; Pei, Zhiheng; Yang, Liying; Ma, Yingfei; Purdue, Mark P; Jacobs, Eric J; Gapstur, Susan M; Li, Huilin; Alekseyenko, Alexander V; Hayes, Richard B; Ahn, Jiyoung. Cigarette smoking and the oral microbiome in a large study of American adults. ISME journal. 2016 Mar 25;10(10):2435-2446 (2052252)

Plasma levels of interleukin-1 receptor antagonist (IL1Ra) predict radiographic progression of symptomatic knee osteoarthritis
Attur, M; Statnikov, A; Samuels, J; Li, Z; Alekseyenko, A V; Greenberg, J D; Krasnokutsky, S; Rybak, L; Lu, Q A; Todd, J; Zhou, H; Jordan, J M; Kraus, V B; Aliferis, C F; Abramson, S B. Plasma levels of interleukin-1 receptor antagonist (IL1Ra) predict radiographic progression of symptomatic knee osteoarthritis. Osteoarthritis & cartilage. 2015 Nov ;23(11):1915-1924 (1825412)

Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment
Nobel, Yael R; Cox, Laura M; Kirigin, Francis F; Bokulich, Nicholas A; Yamanishi, Shingo; Teitler, Isabel; Chung, Jennifer; Sohn, Jiho; Barber, Cecily M; Goldfarb, David S; Raju, Kartik; Abubucker, Sahar; Zhou, Yanjiao; Ruiz, Victoria E; Li, Huilin; Mitreva, Makedonka; Alekseyenko, Alexander V; Weinstock, George M; Sodergren, Erica; Blaser, Martin J. Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment. Nature communications. 2015 Jun 30;6:7486-7486 (1649312)

Metagenomics
Perez-Perez, Guillermo I; Blumenberg, Miroslav; Alekseyenko, Alexander. Metagenomics IN: Next-generation DNA sequencing informatics. Cold Spring Harbor, New York : Cold Spring Harbor Laboratory Press, 2015 2nd edition. p.309-324 (1681512)