Keywords
Last Name
Institution

Alexander Vladimirovich Alekseyenko

Title
InstitutionMedical University of South Carolina
DepartmentPublic Health Sciences
AddressP.O. Box MSC 200
Cannon Place - 135 Cannon St.
Phone843-792-2043
vCardDownload vCard

    Collapse Biography 
    Collapse education and training
    University of California Los AngelesPhD06/2008Biomathematics

    Collapse Overview 
    Collapse keywords
    microbiome, multivariate analysis, panomics, data science

    Collapse ORNG Applications 
    Collapse Faculty Mentoring

    Collapse Research 
    Collapse research activities and funding
    R01LM012517     (ALEKSEYENKO, ALEXANDER V.)Jun 1, 2018 - Apr 30, 2022
    NIH
    Distance-based Panomic Analytics for Microbiome Data
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    List All   |   Timeline
    1. Zhang Y, Alekseyenko AV. Phylogenic inference using alignment-free methods for applications in microbial community surveys using 16s rRNA gene. PLoS One. 2017; 12(11):e0187940. PMID: 29136663.
      View in: PubMed
    2. Beiko T, Janech MG, Alekseyenko AV, Atkinson C, Coxson HO, Barth JL, Stephenson SE, Wilson CL, Schnapp LM, Barker A, Brantly M, Sandhaus RA, Silverman EK, Stoller JK, Trapnell B, Charlie S. Serum Proteins Associated with Emphysema Progression in Severe Alpha-1 Antitrypsin Deficiency. Chronic Obstr Pulm Dis. 2017 Jul 15; 4(3):204-216. PMID: 28848932.
      View in: PubMed
    3. Tang ZZ, Chen G, Alekseyenko AV, Li H. A general framework for association analysis of microbial communities on a taxonomic tree. Bioinformatics. 2017 May 01; 33(9):1278-1285. PMID: 28003264.
      View in: PubMed
    4. Iizumi T, Taniguchi T, Yamazaki W, Vilmen G, Alekseyenko AV, Gao Z, Perez Perez GI, Blaser MJ. Effect of antibiotic pre-treatment and pathogen challenge on the intestinal microbiota in mice. Gut Pathog. 2016; 8:60. PMID: 27891184.
      View in: PubMed
    5. Fan X, Alekseyenko AV, Wu J, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Abnet CC, Stolzenberg-Solomon R, Miller G, Ravel J, Hayes RB, Ahn J. Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study. Gut. 2018 01; 67(1):120-127. PMID: 27742762.
      View in: PubMed
    6. Gonzalez ME, Schaffer JV, Orlow SJ, Gao Z, Li H, Alekseyenko AV, Blaser MJ. Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis. J Am Acad Dermatol. 2016 Sep; 75(3):481-493.e8. PMID: 27543211; PMCID: PMC4992571 [Available on 09/01/17].
    7. Livanos AE, Greiner TU, Vangay P, Pathmasiri W, Stewart D, McRitchie S, Li H, Chung J, Sohn J, Kim S, Gao Z, Barber C, Kim J, Ng S, Rogers AB, Sumner S, Zhang XS, Cadwell K, Knights D, Alekseyenko A, Bäckhed F, Blaser MJ. Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice. Nat Microbiol. 2016 Aug 22; 1(11):16140. PMID: 27782139.
      View in: PubMed
    8. Alekseyenko AV. Multivariate Welch t-test on distances. Bioinformatics. 2016 12 01; 32(23):3552-3558. PMID: 27515741.
      View in: PubMed
    9. Tang ZZ, Chen G, Alekseyenko AV. PERMANOVA-S: association test for microbial community composition that accommodates confounders and multiple distances. Bioinformatics. 2016 09 01; 32(17):2618-25. PMID: 27197815; PMCID: PMC5013911.
    10. Wu J, Peters BA, Dominianni C, Zhang Y, Pei Z, Yang L, Ma Y, Purdue MP, Jacobs EJ, Gapstur SM, Li H, Alekseyenko AV, Hayes RB, Ahn J. Cigarette smoking and the oral microbiome in a large study of American adults. ISME J. 2016 10; 10(10):2435-46. PMID: 27015003.
      View in: PubMed
    11. Nobel YR, Cox LM, Kirigin FF, Bokulich NA, Yamanishi S, Teitler I, Chung J, Sohn J, Barber CM, Goldfarb DS, Raju K, Abubucker S, Zhou Y, Ruiz VE, Li H, Mitreva M, Alekseyenko AV, Weinstock GM, Sodergren E, Blaser MJ. Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment. Nat Commun. 2015 Jun 30; 6:7486. PMID: 26123276.
      View in: PubMed
    12. Cox LM, Yamanishi S, Sohn J, Alekseyenko AV, Leung JM, Cho I, Kim SG, Li H, Gao Z, Mahana D, Zárate Rodriguez JG, Rogers AB, Robine N, Loke P, Blaser MJ. Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences. Cell. 2014 Aug 14; 158(4):705-721. PMID: 25126780; PMCID: PMC4134513.
    13. Alekseyenko AV, Perez-Perez GI, De Souza A, Strober B, Gao Z, Bihan M, Li K, Methé BA, Blaser MJ. Community differentiation of the cutaneous microbiota in psoriasis. Microbiome. 2013 Dec 23; 1(1):31. PMID: 24451201; PMCID: PMC4177411.
    14. Argimón S, Konganti K, Chen H, Alekseyenko AV, Brown S, Caufield PW. 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; 21:269-78. PMID: 24291226; PMCID: PMC3940162.
    15. Statnikov A, Henaff M, Narendra V, Konganti K, Li Z, Yang L, Pei Z, Blaser MJ, Aliferis CF, Alekseyenko AV. A comprehensive evaluation of multicategory classification methods for microbiomic data. Microbiome. 2013 Apr 05; 1(1):11. PMID: 24456583; PMCID: PMC3960509.
    16. Argimón S, Alekseyenko AV, DeSalle R, Caufield PW. Phylogenetic analysis of glucosyltransferases and implications for the coevolution of mutans streptococci with their mammalian hosts. PLoS One. 2013; 8(2):e56305. PMID: 23457545; PMCID: PMC3572963.
    17. Bai JP, Alekseyenko AV, Statnikov A, Wang IM, Wong PH. Strategic applications of gene expression: from drug discovery/development to bedside. AAPS J. 2013 Apr; 15(2):427-37. PMID: 23319288; PMCID: PMC3675744.
    18. Statnikov A, Alekseyenko AV, Li Z, Henaff M, Perez-Perez GI, Blaser MJ, Aliferis CF. Microbiomic signatures of psoriasis: feasibility and methodology comparison. Sci Rep. 2013; 3:2620. PMID: 24018484; PMCID: PMC3965359.
    19. Cho I, Yamanishi S, Cox L, Methé BA, Zavadil J, Li K, Gao Z, Mahana D, Raju K, Teitler I, Li H, Alekseyenko AV, Blaser MJ. Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature. 2012 Aug 30; 488(7413):621-6. PMID: 22914093; PMCID: PMC3553221.
    20. Bouckaert R, Lemey P, Dunn M, Greenhill SJ, Alekseyenko AV, Drummond AJ, Gray RD, Suchard MA, Atkinson QD. Mapping the origins and expansion of the Indo-European language family. Science. 2012 Aug 24; 337(6097):957-60. PMID: 22923579; PMCID: PMC4112997.
    21. Pei A, Li H, Oberdorf WE, Alekseyenko AV, Parsons T, Yang L, Gerz EA, Lee P, Xiang C, Nossa CW, Pei Z. Diversity of 5S rRNA genes within individual prokaryotic genomes. FEMS Microbiol Lett. 2012 Oct; 335(1):11-8. PMID: 22765222; PMCID: PMC3439594.
    22. Baele G, Lemey P, Bedford T, Rambaut A, Suchard MA, Alekseyenko AV. Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Mol Biol Evol. 2012 Sep; 29(9):2157-67. PMID: 22403239; PMCID: PMC3424409.
    23. Alekseyenko AV, Lytkin NI, Ai J, Ding B, Padyukov L, Aliferis CF, Statnikov A. Causal graph-based analysis of genome-wide association data in rheumatoid arthritis. Biol Direct. 2011 May 18; 6:25. PMID: 21592391; PMCID: PMC3118953.
    24. DeSantis TZ, Keller K, Karaoz U, Alekseyenko AV, Singh NN, Brodie EL, Pei Z, Andersen GL, Larsen N. Simrank: Rapid and sensitive general-purpose k-mer search tool. BMC Ecol. 2011 Apr 27; 11:11. PMID: 21524302; PMCID: PMC3097142.
    25. Deriano L, Chaumeil J, Coussens M, Multani A, Chou Y, Alekseyenko AV, Chang S, Skok JA, Roth DB. The RAG2 C terminus suppresses genomic instability and lymphomagenesis. Nature. 2011 Mar 03; 471(7336):119-23. PMID: 21368836; PMCID: PMC3174233.
    26. Holmes S, Alekseyenko A, Timme A, Nelson T, Pasricha PJ, Spormann A. Visualization and statistical comparisons of microbial communities using R packages on Phylochip data. Pac Symp Biocomput. 2011; 142-53. PMID: 21121042; PMCID: PMC3347925.
    27. Gray RR, Tatem AJ, Johnson JA, Alekseyenko AV, Pybus OG, Suchard MA, Salemi M. Testing spatiotemporal hypothesis of bacterial evolution using methicillin-resistant Staphylococcus aureus ST239 genome-wide data within a bayesian framework. Mol Biol Evol. 2011 May; 28(5):1593-603. PMID: 21112962; PMCID: PMC3115679.
    28. Sehl M, Alekseyenko AV, Lange KL. Accurate stochastic simulation via the step anticipation tau-leaping (SAL) algorithm. J Comput Biol. 2009 Sep; 16(9):1195-208. PMID: 19772431; PMCID: PMC3148118.
    29. Alekseyenko AV, Lee CJ, Suchard MA. Wagner and Dollo: a stochastic duet by composing two parsimonious solos. Syst Biol. 2008 Oct; 57(5):772-84. PMID: 18853363; PMCID: PMC4677801.
    30. Alekseyenko AV, Kim N, Lee CJ. Global analysis of exon creation versus loss and the role of alternative splicing in 17 vertebrate genomes. RNA. 2007 May; 13(5):661-70. PMID: 17369312; PMCID: PMC1852814.
    31. Alekseyenko AV, Lee CJ. Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases. Bioinformatics. 2007 Jun 01; 23(11):1386-93. PMID: 17234640.
      View in: PubMed
    32. Kim N, Alekseyenko AV, Roy M, Lee C. The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species. Nucleic Acids Res. 2007 Jan; 35(Database issue):D93-8. PMID: 17108355; PMCID: PMC1669709.
    33. Resch A, Xing Y, Alekseyenko A, Modrek B, Lee C. Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation. Nucleic Acids Res. 2004; 32(4):1261-9. PMID: 14982953; PMCID: PMC390276.
    Alekseyenko's Networks
    Click the "See All" links for more information and interactive visualizations!
    Concepts Expand Description
    _
    Co-Authors Expand Description
    _
    Similar People Expand Description
    _
    Same Department Expand Description
    Physical Neighbors Expand Description
    _