Alexander V Alekseyenko

Alexander V Alekseyenko

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Alexander V Alekseyenko

Alexander V Alekseyenko

Publications by authors named "Alexander V Alekseyenko"

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42Publications

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MODIMA, a Method for Multivariate Omnibus Distance Mediation Analysis, Allows for Integration of Multivariate Exposure-Mediator-Response Relationships.

Genes (Basel) 2019 07 11;10(7). Epub 2019 Jul 11.

Program for Human Microbiome Research, Medical University of South Carolina, 135 Cannon Street MSC 200, Charleston, SC 29425, USA.

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http://dx.doi.org/10.3390/genes10070524DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6679421PMC
July 2019

Longitudinal changes during pregnancy in gut microbiota and methylmercury biomarkers, and reversal of microbe-exposure correlations.

Environ Res 2019 May 11;172:700-712. Epub 2019 Jan 11.

Division of Gastroenterology and Hepatology and Microbiome Core Facility, University of North Carolina, Chapel Hill, NC, USA.

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http://dx.doi.org/10.1016/j.envres.2019.01.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6675619PMC
May 2019

W -test: robust distance-based multivariate analysis of variance

Microbiome 2019 04 1;7(1):51. Epub 2019 Apr 1.

Program for Human Microbiome Research, Medical University of South Carolina, 135 Cannon Street MSC 200, Charleston, 29425, SC, USA.

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http://dx.doi.org/10.1186/s40168-019-0659-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6444669PMC
April 2019

Antibiotic Perturbation of Gut Microbiota Dysregulates Osteoimmune Cross Talk in Postpubertal Skeletal Development.

Am J Pathol 2019 Feb 16;189(2):370-390. Epub 2019 Jan 16.

Department of Oral Health Sciences, Medical University of South Carolina College of Dental Medicine, Charleston, South Carolina; Endocrinology Division, Department of Pediatrics, Medical University of South Carolina College of Medicine, Charleston, South Carolina. Electronic address:

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http://dx.doi.org/10.1016/j.ajpath.2018.10.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360355PMC
February 2019

Phylogenic inference using alignment-free methods for applications in microbial community surveys using 16s rRNA gene.

PLoS One 2017 14;12(11):e0187940. Epub 2017 Nov 14.

Department of Medicine, New York University School of Medicine, New York, NY, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0187940PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5685621PMC
December 2017

A general framework for association analysis of microbial communities on a taxonomic tree.

Bioinformatics 2017 05;33(9):1278-1285

Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw804DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408811PMC
May 2017

Multivariate Welch t-test on distances.

Bioinformatics 2016 12 11;32(23):3552-3558. Epub 2016 Aug 11.

Departments of Public Health Sciences and Oral Health Sciences, Program for Human Microbiome Research, The Biomedical Informatics Center Medical University of South Carolina, 135 Cannon Street, MSC 200, Charleston, SC 29466, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw524DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5181538PMC
December 2016

Effect of antibiotic pre-treatment and pathogen challenge on the intestinal microbiota in mice.

Gut Pathog 2016 18;8:60. Epub 2016 Nov 18.

Department of Medicine, New York University School of Medicine, New York, NY USA ; Department of Microbiology, New York University School of Medicine, New York, NY USA.

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http://dx.doi.org/10.1186/s13099-016-0143-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5116224PMC
November 2016

PERMANOVA-S: association test for microbial community composition that accommodates confounders and multiple distances.

Bioinformatics 2016 09 19;32(17):2618-25. Epub 2016 May 19.

Biomedical Informatics Center, Department of Public Health Sciences and Department of Oral Health Sciences, Medical University of South Carolina, Charleston, SC 29403, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw311DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5013911PMC
September 2016

Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment.

Nat Commun 2015 Jun 30;6:7486. Epub 2015 Jun 30.

1] Department of Medicine, New York University School of Medicine, New York, New York 10016, USA [2] Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA [3] New York Harbor Department of Veterans Affairs Medical Center, New York, New York 10010, USA.

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http://dx.doi.org/10.1038/ncomms8486DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4491183PMC
June 2015

Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences.

Cell 2014 Aug;158(4):705-721

Department of Microbiology, NYU Langone Medical Center, New York, NY 10016, USA; Department of Medicine, NYU Langone Medical Center, New York, NY 10016, USA; New York Harbor Department of Veterans Affairs Medical Center, New York, NY 10010, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.05.052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4134513PMC
August 2014

Microbiomic signatures of psoriasis: feasibility and methodology comparison.

Sci Rep 2013 ;3:2620

1] Center for Health Informatics and Bioinformatics (CHIBI), New York University Langone Medical Center, New York, New York [2] Department of Medicine, New York University School of Medicine, New York, New York.

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http://dx.doi.org/10.1038/srep02620DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965359PMC
June 2014

Comparative genomics of oral isolates of Streptococcus mutans by in silico genome subtraction does not reveal accessory DNA associated with severe early childhood caries.

Infect Genet Evol 2014 Jan 26;21:269-78. Epub 2013 Nov 26.

New York University College of Dentistry, Department of Cariology and Comprehensive Care, 345 East 24th St, New York, NY 10010, USA.

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http://dx.doi.org/10.1016/j.meegid.2013.11.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3940162PMC
January 2014

Community differentiation of the cutaneous microbiota in psoriasis.

Microbiome 2013 Dec 23;1(1):31. Epub 2013 Dec 23.

Center for Health Informatics and Bioinformatics, New York University School of Medicine, 227 E 30th Street, 7th Floor, #740, New York, NY 10016, USA.

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http://dx.doi.org/10.1186/2049-2618-1-31DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4177411PMC
December 2013

Phylogenetic analysis of glucosyltransferases and implications for the coevolution of mutans streptococci with their mammalian hosts.

PLoS One 2013 14;8(2):e56305. Epub 2013 Feb 14.

Department of Cariology and Comprehensive Care, New York University College of Dentistry, New York, New York, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0056305PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3572963PMC
August 2013

Quantitation and composition of cutaneous microbiota in diabetic and nondiabetic men.

J Infect Dis 2013 Apr 8;207(7):1105-14. Epub 2013 Jan 8.

Department of Medicine, New York University School of Medicine, New York, NY 10010, USA.

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http://dx.doi.org/10.1093/infdis/jit005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3583274PMC
April 2013

Strategic applications of gene expression: from drug discovery/development to bedside.

AAPS J 2013 Apr 15;15(2):427-37. Epub 2013 Jan 15.

Office of Clinical Pharmacology, Office of Translational Science, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.

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http://ccdlab.org/paper-pdfs/aaps_2013.pdf
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http://link.springer.com/10.1208/s12248-012-9447-1
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http://dx.doi.org/10.1208/s12248-012-9447-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3675744PMC
April 2013

A comprehensive evaluation of multicategory classification methods for microbiomic data.

Microbiome 2013 Apr 5;1(1):11. Epub 2013 Apr 5.

Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, 227 East 30th Street, New York, NY, USA.

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http://dx.doi.org/10.1186/2049-2618-1-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3960509PMC
April 2013

Causal graph-based analysis of genome-wide association data in rheumatoid arthritis.

Biol Direct 2011 May 18;6:25. Epub 2011 May 18.

Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, NY 10016, USA.

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http://biologydirect.biomedcentral.com/articles/10.1186/1745
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http://dx.doi.org/10.1186/1745-6150-6-25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3118953PMC
May 2011

The RAG2 C terminus suppresses genomic instability and lymphomagenesis.

Nature 2011 Mar;471(7336):119-23

Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.

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http://dx.doi.org/10.1038/nature09755DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174233PMC
March 2011

Accurate stochastic simulation via the step anticipation tau-leaping (SAL) algorithm.

J Comput Biol 2009 Sep;16(9):1195-208

Department of Biomathematics, David Geffen School of Medicine, University of California , Los Angeles, Los Angeles, California 90095-1766, USA.

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http://dx.doi.org/10.1089/cmb.2008.0249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3148118PMC
September 2009

Wagner and Dollo: a stochastic duet by composing two parsimonious solos.

Syst Biol 2008 Oct;57(5):772-84

Department of Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, California 90095, USA.

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http://dx.doi.org/10.1080/10635150802434394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4677801PMC
October 2008

Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases.

Bioinformatics 2007 Jun 18;23(11):1386-93. Epub 2007 Jan 18.

Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095-1570, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl647DOI Listing
June 2007

Global analysis of exon creation versus loss and the role of alternative splicing in 17 vertebrate genomes.

RNA 2007 May 16;13(5):661-70. Epub 2007 Mar 16.

Department of Biomathematics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, USA.

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http://dx.doi.org/10.1261/rna.325107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852814PMC
May 2007

The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.

Nucleic Acids Res 2007 Jan 15;35(Database issue):D93-8. Epub 2006 Nov 15.

Department of Chemistry and Biochemistry, Center for Computational Biology Institute for Genomics and Proteomics, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095-1570, USA.

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http://dx.doi.org/10.1093/nar/gkl884DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1669709PMC
January 2007