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

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    R01CA226086     (BARON, JOHN ANTHONY)Apr 9, 2019 - Mar 31, 2024
    NIH
    The immune contexture of colorectal adenomas and serrated polyps
    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
    U01DE027637     (CORBY, PATRICIA M)Sep 15, 2018 - Aug 31, 2023
    NIH
    ARMOR Trial
    Role: Co-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
    R01LM012517     (ALEKSEYENKO, ALEXANDER V.)Jun 1, 2018 - Apr 30, 2022
    NIH
    Distance-based Panomic Analytics for Microbiome Data
    Role: Principal 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
    U54CA210962     (FORD, MARVELLA ELIZABETH)Sep 21, 2017 - Aug 31, 2022
    NIH
    South Carolina Cancer Disparities Research Center (SC CADRE)
    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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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Carson MD, Warner AJ, Geiser VL, Hathaway-Schrader JD, Alekseyenko AV, Marshall J, Westwater C, Novince CM. Prolonged Antibiotic Exposure during Adolescence Dysregulates Liver Metabolism and Promotes Adiposity in Mice. Am J Pathol. 2023 Mar 10. PMID: 36906264.
      Citations:    Fields:    
    2. Hamidi B, Flume PA, Simpson KN, Alekseyenko AV. Not all phenotypes are created equal: covariates of success in e-phenotype specification. J Am Med Inform Assoc. 2023 01 18; 30(2):213-221. PMID: 36069977; PMCID: PMC9846689.
      Citations: 1     Fields:    
    3. Del Gaizo J, Obeid JS, Catchpole KR, Alekseyenko AV, Del Gaizo J, Obeid JS, Catchpole KR, Alekseyenko AV. Red Flag/Blue Flag visualization of a common CNN for text classification. JAMIA Open. 2023 Apr; 6(1):ooac112. PMID: 36660449; PMCID: PMC9841396.
      Citations:    
    4. Carson MD, Warner AJ, Hathaway-Schrader JD, Geiser VL, Kim J, Gerasco JE, Hill WD, Lemasters JJ, Alekseyenko AV, Wu Y, Yao H, Aguirre JI, Westwater C, Novince CM, Carson MD, Warner AJ, Hathaway-Schrader JD, Geiser VL, Kim J, Gerasco JE, Hill WD, Lemasters JJ, Alekseyenko AV, Wu Y, Yao H, Aguirre JI, Westwater C, Novince CM. Minocycline-induced disruption of the intestinal FXR/FGF15 axis impairs osteogenesis in mice. JCI Insight. 2023 01 10; 8(1). PMID: 36413391; PMCID: PMC9870091.
      Citations: 1     Fields:    Translation:Animals
    5. Alfred M, Del Gaizo J, Kanji F, Lawton S, Caron A, Nemeth LS, Alekseyenko AV, Shouhed D, Savage S, Anger JT, Catchpole K, Cohen T. A better way: training for direct observations in healthcare. BMJ Qual Saf. 2022 10; 31(10):744-753. PMID: 35985812.
      Citations:    Fields:    Translation:Humans
    6. Meystre SM, Heider PM, Kim Y, Davis M, Obeid J, Madory J, Alekseyenko AV, Meystre SM, Heider PM, Kim Y, Davis M, Obeid J, Madory J, Alekseyenko AV. Natural language processing enabling COVID-19 predictive analytics to support data-driven patient advising and pooled testing. J Am Med Inform Assoc. 2021 12 28; 29(1):12-21. PMID: 34415311; PMCID: PMC8714262.
      Citations:    
    7. Ritchie JB, Welch BM, Allen CG, Frey LJ, Morrison H, Schiffman JD, Alekseyenko AV, Dean B, Hughes Halbert C, Bellcross C, Ritchie JB, Welch BM, Allen CG, Frey LJ, Morrison H, Schiffman JD, Alekseyenko AV, Dean B, Hughes Halbert C, Bellcross C. Comparison of a Cancer Family History Collection and Risk Assessment Tool - ItRunsInMyFamily - with Risk Assessment by Health-Care Professionals. Public Health Genomics. 2021 Dec 06; 1-9. PMID: 34872100; PMCID: PMC9167897.
      Citations:    
    8. Swanson BA, Carson MD, Hathaway-Schrader JD, Warner AJ, Kirkpatrick JE, Corker A, Alekseyenko AV, Westwater C, Aguirre JI, Novince CM, Swanson BA, Carson MD, Hathaway-Schrader JD, Warner AJ, Kirkpatrick JE, Corker A, Alekseyenko AV, Westwater C, Aguirre JI, Novince CM. Antimicrobial-induced oral dysbiosis exacerbates naturally occurring alveolar bone loss. FASEB J. 2021 11; 35(11):e22015. PMID: 34699641; PMCID: PMC8732259.
      Citations:    
    9. Wallace K, El Nahas GJ, Bookhout C, Thaxton JE, Lewin DN, Nikolaishvili-Feinberg N, Cohen SM, Brazeal JG, Hill EG, Wu JD, Baron JA, Alekseyenko AV, Wallace K, El Nahas GJ, Bookhout C, Thaxton JE, Lewin DN, Nikolaishvili-Feinberg N, Cohen SM, Brazeal JG, Hill EG, Wu JD, Baron JA, Alekseyenko AV. Immune Responses Vary in Preinvasive Colorectal Lesions by Tumor Location and Histology. Cancer Prev Res (Phila). 2021 09; 14(9):885-892. PMID: 34341013; PMCID: PMC8811707.
      Citations:    
    10. De Maio N, Alekseyenko AV, Coleman-Smith WJ, Pardi F, Suchard MA, Tamuri AU, Truszkowski J, Goldman N, De Maio N, Alekseyenko AV, Coleman-Smith WJ, Pardi F, Suchard MA, Tamuri AU, Truszkowski J, Goldman N. A phylogenetic approach for weighting genetic sequences. BMC Bioinformatics. 2021 May 28; 22(1):285. PMID: 34049487; PMCID: PMC8164272.
      Citations:    
    11. Wallace K, Nahhas GJ, Bookhout C, Lewin DN, Paulos CM, Nikolaishvili-Feinberg N, Cohen SM, Guglietta S, Bakhtiari A, Camp ER, Hill EG, Baron JA, Wu JD, Alekseyenko AV, Wallace K, Nahhas GJ, Bookhout C, Lewin DN, Paulos CM, Nikolaishvili-Feinberg N, Cohen SM, Guglietta S, Bakhtiari A, Camp ER, Hill EG, Baron JA, Wu JD, Alekseyenko AV. Preinvasive Colorectal Lesions of African Americans Display an Immunosuppressive Signature Compared to Caucasian Americans. Front Oncol. 2021; 11:659036. PMID: 33987094; PMCID: PMC8112239.
      Citations:    
    12. Pécot T, Alekseyenko A, Wallace K, P?cot T, Alekseyenko A, Wallace K. A deep learning segmentation strategy that minimizes the amount of manually annotated images. F1000Res. 2021; 10:256. PMID: 35136569; PMCID: PMC8787559.
      Citations:    
    13. Del Gaizo J, Catchpole KR, Alekseyenko AV, Del Gaizo J, Catchpole KR, Alekseyenko AV. Research and Exploratory Analysis Driven-Time-data Visualization (read-tv) software. JAMIA Open. 2021 Jan; 4(1):ooab007. PMID: 33709063; PMCID: PMC7935610.
      Citations:    
    14. Alfred MC, Cohen TN, Cohen KA, Kanji FF, Choi E, Del Gaizo J, Nemeth LS, Alekseyenko AV, Shouhed D, Savage SJ, Anger JT, Catchpole K, Alfred MC, Cohen TN, Cohen KA, Kanji FF, Choi E, Del Gaizo J, Nemeth LS, Alekseyenko AV, Shouhed D, Savage SJ, Anger JT, Catchpole K. Using Flow Disruptions to Examine System Safety in Robotic-Assisted Surgery: Protocol for a Stepped Wedge Crossover Design. JMIR Res Protoc. 2021 Feb 09; 10(2):e25284. PMID: 33560239; PMCID: PMC7902184.
      Citations:    
    15. Sofi MH, Wu Y, Ticer T, Schutt S, Bastian D, Choi HJ, Tian L, Mealer C, Liu C, Westwater C, Armeson KE, Alekseyenko AV, Yu XZ, Sofi MH, Wu Y, Ticer T, Schutt S, Bastian D, Choi HJ, Tian L, Mealer C, Liu C, Westwater C, Armeson KE, Alekseyenko AV, Yu XZ. A single strain of Bacteroides fragilis protects gut integrity and reduces GVHD. JCI Insight. 2021 02 08; 6(3). PMID: 33554953; PMCID: PMC7934839.
      Citations:    
    16. Castillo EJ, Messer JG, Abraham AM, Jiron JM, Alekseyenko AV, Israel R, Thomas S, Gonzalez-Perez GM, Croft S, Gohel A, Bhattacharyya I, Yarrow JF, Novince CM, Kimmel DB, Aguirre JI, Castillo EJ, Messer JG, Abraham AM, Jiron JM, Alekseyenko AV, Israel R, Thomas S, Gonzalez-Perez GM, Croft S, Gohel A, Bhattacharyya I, Yarrow JF, Novince CM, Kimmel DB, Aguirre JI. Preventing or controlling periodontitis reduces the occurrence of osteonecrosis of the jaw (ONJ) in rice rats (Oryzomys palustris). Bone. 2021 04; 145:115866. PMID: 33515777; PMCID: PMC8265021.
      Citations:    
    17. Alekseyenko AV, Hamidi B, Faith TD, Crandall KA, Powers JG, Metts CL, Madory JE, Carroll SL, Obeid JS, Lenert LA, Alekseyenko AV, Hamidi B, Faith TD, Crandall KA, Powers JG, Metts CL, Madory JE, Carroll SL, Obeid JS, Lenert LA. Each patient is a research biorepository: informatics-enabled research on surplus clinical specimens via the living BioBank. J Am Med Inform Assoc. 2021 01 15; 28(1):138-143. PMID: 33166379; PMCID: PMC7810447.
      Citations:    
    18. Arbizu RA, Collins D, Wilson RC, Alekseyenko AV, Arbizu RA, Collins D, Wilson RC, Alekseyenko AV. Evidence for Differentiation of Colon Tissue Microbiota in Patients with and without Postoperative Hirschsprung's Associated Enterocolitis: A Pilot Study. Pediatr Gastroenterol Hepatol Nutr. 2021 Jan; 24(1):30-37. PMID: 33505891; PMCID: PMC7813566.
      Citations:    
    19. Luo Z, Alekseyenko AV, Ogunrinde E, Li M, Li QZ, Huang L, Tsao BP, Kamen DL, Oates JC, Li Z, Gilkeson GS, Jiang W, Luo Z, Alekseyenko AV, Ogunrinde E, Li M, Li QZ, Huang L, Tsao BP, Kamen DL, Oates JC, Li Z, Gilkeson GS, Jiang W. Rigorous Plasma Microbiome Analysis Method Enables Disease Association Discovery in Clinic. Front Microbiol. 2020; 11:613268. PMID: 33488555; PMCID: PMC7820181.
      Citations:    
    20. Sierra MA, Li Q, Pushalkar S, Paul B, Sandoval TA, Kamer AR, Corby P, Guo Y, Ruff RR, Alekseyenko AV, Li X, Saxena D, 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 08 03; 11(8). PMID: 32756341; PMCID: PMC7465726.
      Citations:    
    21. 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, 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 07 01; 176(1):1-10. PMID: 32658296; PMCID: PMC7850111.
      Citations:    
    22. Wallace K, Li H, Brazeal JG, Lewin DN, Sun S, Ba A, Paulos CM, Rachidi S, Li Z, Alekseyenko AV, 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 08; 67:101746. PMID: 32521488; PMCID: PMC7548121.
      Citations:    
    23. He Y, Wang H, Zheng J, Beiting DP, Masci AM, Yu H, Liu K, Wu J, Curtis JL, Smith B, Alekseyenko AV, Obeid JS, 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; PMCID: PMC6937947.
      Citations:    
    24. Lobach I, Kim I, Alekseyenko A, Lobach S, Zhang L, 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; PMCID: PMC6812609.
      Citations:    
    25. Silverman GJ, Azzouz DF, Alekseyenko AV, Silverman GJ, Azzouz DF, Alekseyenko AV. Systemic Lupus Erythematosus and dysbiosis in the microbiome: cause or effect or both? Curr Opin Immunol. 2019 12; 61:80-85. PMID: 31590039; PMCID: PMC6901743.
      Citations:    
    26. Orr RK, Hoehn JL, Col NF, 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; PMCID: PMC6817371.
      Citations:    
    27. Hamidi B, Wallace K, Alekseyenko AV, 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; PMCID: PMC6679421.
      Citations:    
    28. Hamidi B, Wallace K, Vasu C, Alekseyenko AV, 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; PMCID: PMC6444669.
      Citations:    
    29. Lobach I, Kim I, Alekseyenko A, Lobach S, Zhang L, 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; PMCID: PMC6559860.
      Citations:    
    30. Azzouz D, Omarbekova A, Heguy A, Schwudke D, Gisch N, Rovin BH, Caricchio R, Buyon JP, Alekseyenko AV, Silverman GJ, 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 07; 78(7):947-956. PMID: 30782585; PMCID: PMC6585303.
      Citations:    
    31. 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, 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; PMCID: PMC6376754.
      Citations:    
    32. Hathaway-Schrader JD, Steinkamp HM, Chavez MB, Poulides NA, Kirkpatrick JE, Chew ME, Huang E, Alekseyenko AV, Aguirre JI, Novince CM, 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; PMCID: PMC6360355.
      Citations:    
    33. Rothenberg SE, Wagner CL, Hamidi B, Alekseyenko AV, Andrea Azcarate-Peril M, 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; PMCID: PMC6675619.
      Citations:    
    34. Lobach I, Sampson J, Lobach S, Alekseyenko A, Piryatinska A, He T, Zhang L, 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; PMCID: PMC6416064.
      Citations:    
    35. Landeros A, Stutz T, Keys KL, Alekseyenko A, Sinsheimer JS, Lange K, Sehl ME, 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; PMCID: PMC6388686.
      Citations:    
    36. Xu W, Luo Z, Alekseyenko AV, Martin L, Wan Z, Ling B, Qin Z, Heath SL, Maas K, Cong X, Jiang W, 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; PMCID: PMC6110826.
      Citations:    
    37. Lobach I, Sampson J, Alekseyenko A, Lobach S, Zhang L, 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; PMCID: PMC6104951.
      Citations:    
    38. Wallace K, Lewin DN, Sun S, Spiceland CM, Rockey DC, Alekseyenko AV, Wu JD, Baron JA, Alberg AJ, Hill EG, 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; PMCID: PMC6449046.
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    39. Fan X, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Freedman ND, Alekseyenko AV, Wu J, Yang L, Pei Z, Hayes RB, Ahn J, 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; PMCID: PMC5914044.
      Citations:    
    40. 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, 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; PMCID: PMC6661319.
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    41. Zhang Y, Alekseyenko AV, 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; PMCID: PMC5685621.
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    42. Van Dyke TE, Diaz PI, Moutsopoulos N, Alekseyenko AV, Ioannidou E, 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; PMCID: PMC5734462.
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    43. 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, 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; PMCID: PMC5556912.
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    44. Tang ZZ, Chen G, Alekseyenko AV, Li H, 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; PMCID: PMC5408811.
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    45. Iizumi T, Taniguchi T, Yamazaki W, Vilmen G, Alekseyenko AV, Gao Z, Perez Perez GI, Blaser MJ, 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; PMCID: PMC5116224.
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    46. 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, 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; PMCID: PMC5607064.
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    47. Gonzalez ME, Schaffer JV, Orlow SJ, Gao Z, Li H, Alekseyenko AV, Blaser MJ, 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.
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    48. 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, 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, B?ckhed 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; PMCID: PMC5808443.
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    49. Alekseyenko AV, Alekseyenko AV. Multivariate Welch t-test on distances. Bioinformatics. 2016 12 01; 32(23):3552-3558. PMID: 27515741; PMCID: PMC5181538.
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    50. Tang ZZ, Chen G, Alekseyenko AV, 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.
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    51. 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, 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; PMCID: PMC5030690.
      Citations:    
    52. 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, 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; PMCID: PMC4630783.
      Citations:    
    53. 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, 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; PMCID: PMC4491183.
      Citations:    
    54. 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, Cox LM, Yamanishi S, Sohn J, Alekseyenko AV, Leung JM, Cho I, Kim SG, Li H, Gao Z, Mahana D, Z?rate 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.
      Citations:    
    55. Alekseyenko AV, Perez-Perez GI, De Souza A, Strober B, Gao Z, Bihan M, Li K, Methé BA, Blaser MJ, Alekseyenko AV, Perez-Perez GI, De Souza A, Strober B, Gao Z, Bihan M, Li K, Meth? BA, Blaser MJ. Community differentiation of the cutaneous microbiota in psoriasis. Microbiome. 2013 Dec 23; 1(1):31. PMID: 24451201; PMCID: PMC4177411.
      Citations:    
    56. Argimón S, Konganti K, Chen H, Alekseyenko AV, Brown S, Caufield PW, Argim?n 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.
      Citations:    
    57. Segal LN, Alekseyenko AV, Clemente JC, Kulkarni R, Wu B, Gao Z, Chen H, Berger KI, Goldring RM, Rom WN, Blaser MJ, Weiden MD, 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; PMCID: PMC3971609.
      Citations:    
    58. Statnikov A, Henaff M, Narendra V, Konganti K, Li Z, Yang L, Pei Z, Blaser MJ, Aliferis CF, Alekseyenko AV, 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.
      Citations:    
    59. Argimón S, Alekseyenko AV, DeSalle R, Caufield PW, Argim?n 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.
      Citations:    
    60. Bai JP, Alekseyenko AV, Statnikov A, Wang IM, Wong PH, 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.
      Citations:    
    61. Orr RK, Hoehn JL, Col NF, 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; PMCID: PMC3583274.
      Citations:    
    62. Statnikov A, Alekseyenko AV, Li Z, Henaff M, Perez-Perez GI, Blaser MJ, Aliferis CF, 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.
      Citations:    
    63. Cox LM, Cho I, Young SA, Anderson WH, Waters BJ, Hung SC, Gao Z, Mahana D, Bihan M, Alekseyenko AV, Methé BA, Blaser MJ, Cox LM, Cho I, Young SA, Anderson WH, Waters BJ, Hung SC, Gao Z, Mahana D, Bihan M, Alekseyenko AV, Meth? BA, Blaser MJ. The nonfermentable dietary fiber hydroxypropyl methylcellulose modulates intestinal microbiota. FASEB J. 2013 Feb; 27(2):692-702. PMID: 23154883; PMCID: PMC3545536.
      Citations:    
    64. 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, Cho I, Yamanishi S, Cox L, Meth? 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.
      Citations:    
    65. Bouckaert R, Lemey P, Dunn M, Greenhill SJ, Alekseyenko AV, Drummond AJ, Gray RD, Suchard MA, Atkinson QD, 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.
      Citations:    
    66. Pei A, Li H, Oberdorf WE, Alekseyenko AV, Parsons T, Yang L, Gerz EA, Lee P, Xiang C, Nossa CW, Pei Z, 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.
      Citations:    
    67. Baele G, Lemey P, Bedford T, Rambaut A, Suchard MA, Alekseyenko AV, 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.
      Citations:    
    68. Alekseyenko AV, Lytkin NI, Ai J, Ding B, Padyukov L, Aliferis CF, Statnikov A, 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.
      Citations:    
    69. DeSantis TZ, Keller K, Karaoz U, Alekseyenko AV, Singh NN, Brodie EL, Pei Z, Andersen GL, Larsen N, 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.
      Citations:    
    70. Deriano L, Chaumeil J, Coussens M, Multani A, Chou Y, Alekseyenko AV, Chang S, Skok JA, Roth DB, 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.
      Citations:    
    71. Holmes S, Alekseyenko A, Timme A, Nelson T, Pasricha PJ, Spormann A, 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.
      Citations:    
    72. Aliferis CF, Alekseyenko AV, Aphinyanaphongs Y, Brown S, Fenyo D, Fu L, Shen S, Statnikov A, Wang J, 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.
      Citations:    
    73. Nelson TA, Holmes S, Alekseyenko AV, Shenoy M, Desantis T, Wu CH, Andersen GL, Winston J, Sonnenburg J, Pasricha PJ, Spormann A, 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; PMCID: PMC3353725.
      Citations:    
    74. Gray RR, Tatem AJ, Johnson JA, Alekseyenko AV, Pybus OG, Suchard MA, Salemi M, 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.
      Citations:    
    75. Sehl M, Alekseyenko AV, Lange KL, 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.
      Citations:    
    76. Alekseyenko AV, Lee CJ, Suchard MA, 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.
      Citations:    
    77. Alekseyenko AV, Kim N, Lee CJ, 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.
      Citations:    
    78. Alekseyenko AV, Lee CJ, 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.
      Citations:    
    79. Kim N, Alekseyenko AV, Roy M, Lee C, 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.
      Citations:    
    80. Orr RK, Hoehn JL, Col NF, 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.
      Citations: 47     Fields:    Translation:HumansAnimalsCells
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