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Alexander Vladimirovich Alekseyenko

Title
InstitutionMedical University of South Carolina
DepartmentPublic Health Sciences
Phone843-792-2043
ORCID ORCID Icon0000-0002-5748-2085 Additional info
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    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 
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    Collapse Research 
    Collapse research activities and funding
    U54CA210962     (FORD, MARVELLA ELIZABETH)Sep 21, 2017 - Aug 31, 2022
    NIH
    South Carolina Cancer Disparities Research Center (SC CADRE)
    Role: Co-Investigator

    P50AR070591     (BUYON, JILL P)Sep 22, 2017 - Aug 31, 2022
    NIH
    Translational Center of Molecular Profiling in Preclinical and Established Lupus (COMPEL)
    Role: Co-Investigator

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

    R21TR002513     (ALEKSEYENKO, ALEXANDER V.)Aug 15, 2018 - May 31, 2020
    NIH
    Increasing Access to Clinical Microbiome Specimens via a Living µbiome Bank
    Role: Principal Investigator

    U01DE027637     (CORBY, PATRICIA M)Sep 15, 2018 - Aug 31, 2023
    NIH
    ARMOR Trial
    Role: Co-Investigator

    R01HS026491     (CATCHPOLE, KEN)Sep 30, 2018 - Jul 31, 2023
    NIH
    Human Factors and Systems Integration in High Technology Surgery (HF-SIgHTS)
    Role: Co-Investigator

    R01CA226086     (BARON, JOHN ANTHONY)Apr 9, 2019 - Mar 31, 2024
    NIH
    The immune contexture of colorectal adenomas and serrated polyps
    Role: Co-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.
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    1. Sierra MA, Li Q, Pushalkar S, Paul B, Sandoval TA, Kamer AR, Corby P, Guo Y, Ruff RR, Alekseyenko AV, Li X, Saxena D. The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community. Genes (Basel). 2020 Aug 03; 11(8). PMID: 32756341.
      View in: PubMed
    2. Sutherland VL, McQueen CA, Mendrick D, Gulezian D, Cerniglia C, Foley S, Forry S, Khare S, Liang X, Manautou JE, Tweedie D, Young H, Alekseyenko AV, Burns F, Dietert R, Wilson A, Chen C. The Gut Microbiome and Xenobiotics: Identifying Knowledge Gaps. Toxicol Sci. 2020 Jul 01; 176(1):1-10. PMID: 32658296.
      View in: PubMed
    3. Wallace K, Li H, Brazeal JG, Lewin DN, Sun S, Ba A, Paulos CM, Rachidi S, Li Z, Alekseyenko AV. Platelet and hemoglobin count at diagnosis are associated with survival in African American and Caucasian patients with colorectal cancer. Cancer Epidemiol. 2020 Jun 07; 67:101746. PMID: 32521488.
      View in: PubMed
    4. He Y, Wang H, Zheng J, Beiting DP, Masci AM, Yu H, Liu K, Wu J, Curtis JL, Smith B, Alekseyenko AV, Obeid JS. OHMI: the ontology of host-microbiome interactions. J Biomed Semantics. 2019 12 30; 10(1):25. PMID: 31888755.
      View in: PubMed
    5. Lobach I, Kim I, Alekseyenko A, Lobach S, Zhang L. A Simple Approximation to Bias in Gene-Environment Interaction Estimates When a Case Might Not Be the Case. Front Genet. 2019; 10:886. PMID: 31681402.
      View in: PubMed
    6. Silverman GJ, Azzouz DF, Alekseyenko AV. Systemic Lupus Erythematosus and dysbiosis in the microbiome: cause or effect or both? Curr Opin Immunol. 2019 Dec; 61:80-85. PMID: 31590039.
      View in: PubMed
    7. Ogunrinde E, Zhou Z, Luo Z, Alekseyenko A, Li QZ, Macedo D, Kamen DL, Oates JC, Gilkeson GS, Jiang W. A Link Between Plasma Microbial Translocation, Microbiome, and Autoantibody Development in First-Degree Relatives of Systemic Lupus Erythematosus Patients. Arthritis Rheumatol. 2019 11; 71(11):1858-1868. PMID: 31106972.
      View in: PubMed
    8. Hamidi B, Wallace K, Alekseyenko AV. 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). PMID: 31336807.
      View in: PubMed
    9. Hamidi B, Wallace K, Vasu C, Alekseyenko AV. W*d -test: robust distance-based multivariate analysis of variance Microbiome. 2019 04 01; 7(1):51. PMID: 30935409.
      View in: PubMed
    10. Lobach I, Kim I, Alekseyenko A, Lobach S, Zhang L. A simple approximation to bias in the genetic effect estimates when multiple disease states share a clinical diagnosis. Genet Epidemiol. 2019 07; 43(5):522-531. PMID: 30888715.
      View in: PubMed
    11. Azzouz D, Omarbekova A, Heguy A, Schwudke D, Gisch N, Rovin BH, Caricchio R, Buyon JP, Alekseyenko AV, Silverman GJ. Lupus nephritis is linked to disease-activity associated expansions and immunity to a gut commensal. Ann Rheum Dis. 2019 Jul; 78(7):947-956. PMID: 30782585.
      View in: PubMed
    12. Luo Z, Li M, Wu Y, Meng Z, Martin L, Zhang L, Ogunrinde E, Zhou Z, Qin S, Wan Z, Westerink MAJ, Warth S, Liu H, Jin P, Stroncek D, Li QZ, Wang E, Wu X, Heath SL, Li Z, Alekseyenko AV, Jiang W. Systemic translocation of Staphylococcus drives autoantibody production in HIV disease. Microbiome. 2019 02 14; 7(1):25. PMID: 30764863.
      View in: PubMed
    13. Hathaway-Schrader JD, Steinkamp HM, Chavez MB, Poulides NA, Kirkpatrick JE, Chew ME, Huang E, Alekseyenko AV, Aguirre JI, Novince CM. Antibiotic Perturbation of Gut Microbiota Dysregulates Osteoimmune Cross Talk in Postpubertal Skeletal Development. Am J Pathol. 2019 02; 189(2):370-390. PMID: 30660331.
      View in: PubMed
    14. Rothenberg SE, Wagner CL, Hamidi B, Alekseyenko AV, Andrea Azcarate-Peril M. Longitudinal changes during pregnancy in gut microbiota and methylmercury biomarkers, and reversal of microbe-exposure correlations. Environ Res. 2019 05; 172:700-712. PMID: 30903970.
      View in: PubMed
    15. Lobach I, Sampson J, Lobach S, Alekseyenko A, Piryatinska A, He T, Zhang L. A simple approximation to the bias of gene-environment interactions in case-control studies with silent disease. Genet Epidemiol. 2019 04; 43(3):292-299. PMID: 30623487.
      View in: PubMed
    16. Landeros A, Stutz T, Keys KL, Alekseyenko A, Sinsheimer JS, Lange K, Sehl ME. BioSimulator.jl: Stochastic simulation in Julia. Comput Methods Programs Biomed. 2018 Dec; 167:23-35. PMID: 30501857.
      View in: PubMed
    17. Xu W, Luo Z, Alekseyenko AV, Martin L, Wan Z, Ling B, Qin Z, Heath SL, Maas K, Cong X, Jiang W. Distinct systemic microbiome and microbial translocation are associated with plasma level of anti-CD4 autoantibody in HIV infection. Sci Rep. 2018 08 27; 8(1):12863. PMID: 30150778.
      View in: PubMed
    18. Lobach I, Sampson J, Alekseyenko A, Lobach S, Zhang L. Case-control studies of gene-environment interactions. When a case might not be the case. PLoS One. 2018; 13(8):e0201140. PMID: 30133451.
      View in: PubMed
    19. Wallace K, Lewin DN, Sun S, Spiceland CM, Rockey DC, Alekseyenko AV, Wu JD, Baron JA, Alberg AJ, Hill EG. Tumor-Infiltrating Lymphocytes and Colorectal Cancer Survival in African American and Caucasian Patients. Cancer Epidemiol Biomarkers Prev. 2018 07; 27(7):755-761. PMID: 29769214.
      View in: PubMed
    20. Fan X, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Freedman ND, Alekseyenko AV, Wu J, Yang L, Pei Z, Hayes RB, Ahn J. Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults. Microbiome. 2018 04 24; 6(1):59. PMID: 29685174.
      View in: PubMed
    21. Steinkamp HM, Hathaway-Schrader JD, Chavez MB, Aartun JD, Zhang L, Jensen T, Shojaee Bakhtiari A, Helke KL, Stumpo DJ, Alekseyenko AV, Novince CM, Blackshear PJ, Kirkwood KL. Tristetraprolin Is Required for Alveolar Bone Homeostasis. J Dent Res. 2018 07; 97(8):946-953. PMID: 29514008.
      View in: PubMed
    22. 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
    23. Van Dyke TE, Diaz PI, Moutsopoulos N, Alekseyenko AV, Ioannidou E. Task Force on Design and Analysis in Oral Health Research: Host-Microbiome Interactions in Dysbiosis. JDR Clin Trans Res. 2018 Jan; 3(1):6-9. PMID: 29276775.
      View in: PubMed
    24. 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
    25. Tang ZZ, Chen G, Alekseyenko AV, Li H. A general framework for association analysis of microbial communities on a taxonomic tree. Bioinformatics. 2017 05 01; 33(9):1278-1285. PMID: 28003264.
      View in: PubMed
    26. 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
    27. 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
    28. 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.
      View in: PubMed
    29. 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
    30. Alekseyenko AV. Multivariate Welch t-test on distances. Bioinformatics. 2016 12 01; 32(23):3552-3558. PMID: 27515741.
      View in: PubMed
    31. 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.
      View in: PubMed
    32. 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
    33. Attur M, Statnikov A, Samuels J, Li Z, Alekseyenko AV, Greenberg JD, Krasnokutsky S, Rybak L, Lu QA, Todd J, Zhou H, Jordan JM, Kraus VB, Aliferis CF, Abramson SB. Plasma levels of interleukin-1 receptor antagonist (IL1Ra) predict radiographic progression of symptomatic knee osteoarthritis. Osteoarthritis Cartilage. 2015 Nov; 23(11):1915-24. PMID: 26521737.
      View in: PubMed
    34. 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
    35. 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.
      View in: PubMed
    36. 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.
      View in: PubMed
    37. 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.
      View in: PubMed
    38. Segal LN, Alekseyenko AV, Clemente JC, Kulkarni R, Wu B, Gao Z, Chen H, Berger KI, Goldring RM, Rom WN, Blaser MJ, Weiden MD. Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation. Microbiome. 2013 Jul 01; 1(1):19. PMID: 24450871.
      View in: PubMed
    39. 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.
      View in: PubMed
    40. 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.
      View in: PubMed
    41. 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.
      View in: PubMed
    42. Redel H, Gao Z, Li H, Alekseyenko AV, Zhou Y, Perez-Perez GI, Weinstock G, Sodergren E, Blaser MJ. Quantitation and composition of cutaneous microbiota in diabetic and nondiabetic men. J Infect Dis. 2013 Apr; 207(7):1105-14. PMID: 23300163.
      View in: PubMed
    43. 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.
      View in: PubMed
    44. Cox LM, Cho I, Young SA, Anderson WH, Waters BJ, Hung SC, Gao Z, Mahana D, Bihan M, Alekseyenko AV, Methé BA, Blaser MJ. The nonfermentable dietary fiber hydroxypropyl methylcellulose modulates intestinal microbiota. FASEB J. 2013 Feb; 27(2):692-702. PMID: 23154883.
      View in: PubMed
    45. 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.
      View in: PubMed
    46. 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.
      View in: PubMed
    47. 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.
      View in: PubMed
    48. 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.
      View in: PubMed
    49. 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.
      View in: PubMed
    50. 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.
      View in: PubMed
    51. 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.
      View in: PubMed
    52. 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.
      View in: PubMed
    53. Aliferis CF, Alekseyenko AV, Aphinyanaphongs Y, Brown S, Fenyo D, Fu L, Shen S, Statnikov A, Wang J. Trends and developments in bioinformatics in 2010: prospects and perspectives. Yearb Med Inform. 2011; 6:146-55. PMID: 21938341.
      View in: PubMed
    54. Nelson TA, Holmes S, Alekseyenko AV, Shenoy M, Desantis T, Wu CH, Andersen GL, Winston J, Sonnenburg J, Pasricha PJ, Spormann A. PhyloChip microarray analysis reveals altered gastrointestinal microbial communities in a rat model of colonic hypersensitivity. Neurogastroenterol Motil. 2011 Feb; 23(2):169-77, e41-2. PMID: 21129126.
      View in: PubMed
    55. 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.
      View in: PubMed
    56. 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.
      View in: PubMed
    57. 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.
      View in: PubMed
    58. 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.
      View in: PubMed
    59. 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
    60. 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.
      View in: PubMed
    61. 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.
      View in: PubMed
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