Alexander Alekseyenko

Ritchie JB., Welch BM., Allen CG., Frey LJ., Morrison H., Schiffman JD., Alekseyenko, AV., Dean BC., Hughes-Halbert C., Bellcross C. "Comparison of a Cancer Family History Collection and Risk Assessment Tool - ItRunsInMyFamily - with Risk Assessment by Healthcare Professionals" Public Health Genomics 2021 in press.

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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 Test- ing", Journal of the American Medical Informatics Association, 2021;, ocab186, https://doi.org/10.1093/jamia/ocab186

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Brazeal JG, Alekseyenko, AV., Li, H., Fugal, M., Kirchoff, K., Marsh, C., Lewin DN, Wu J, Obeid J, Wallace, K."Assessing Quality and Agreement of Structured Data in Automatic versus Manual Abstraction of the Electronic Health Record for a Clinical Epidemiology Study" Research Methods in Medicine & Health Sciences 2021 - in press 75. De Maio, N., Alekseyenko, AV., Coleman-Smith, WJ., Pardi, F., Suchard, MA., Tamuri, AU., Truszkowski, J., Goldman, N. "Phylogenetic Novelty Scores: a new Approach for Weighting Genetic Sequences". BMC Bioinformatics. 2021 May 28;22(1):285. doi: 10.1186/s12859-021-04183-8.

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2021 Apr 27;11:659036. doi: 10.3389/fonc.2021.659036. eCollection 2021. PMID: 33987094

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Wallace, K., Nahas, G., Bookhout, C., Thaxton, J., Lewin, D., Nikolaishvili-Feinberg, N., Cohen, S., Brazeal, J. G., Hill, E. Wu, J., Baron, J., and Alekseyenko, AV."Immune responses vary in preinvasive colorectal lesions by tumor location and histology" Cancer Prev Res (Phila). 2021 Aug 2. doi: 10.1158/1940-6207.CAPR- 20-0592. Online ahead of print. PMID: 34341013.

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Hanief Sofi M, Wu Y, Ticer T, Schutt S, Bastian D, Choi HJ, Tian L, Mealer C, Liu C, Westwater C, Alek- seyenko, AV., and Yu XZ "A Single Strain of Bacteroides fragilis Protects Gut Integrity and Reduces GVHD" JCI Insight 2021 - in press.

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Alfred M, Cohen T, Cohen K, Kanji F, Choi E, Del Gaizo J, Nemeth LS, Alekseyenko, AV., Shouhed D, Savage S, Anger J, 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 9;10(2):e25284. doi: 10.2196/25284.

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Del Gaizo J., Catchpole KR., Alekseyenko, AV."Research and Exploratory Analysis Driven - Time-data Visualization (read-tv) Software". JAMIA Open. 2021 Mar 1;4(1):ooab007. doi: 10.1093/jamiaopen/ooab007. eCollection 2021 Jan. PMID: 33709063

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Castillo EJ, Messer JG, Abraham AM, Jiron JM, Alekseyenko, AV., Israel R., Thomas S, Gonzalez-Perez GM, Croft S, Bhattacharyya 4, Yarrow JF, Novince C2, Kimmel D1, Aguirre JI "Preventing or Controlling Periodontitis Reduces the Occurrence of Osteonecrosis of the Jaw (ONJ) in Rice Rats (Oryzomys palustris)" Bone. 2021 Apr;145:115866. doi: 10.1016/j.bone.2021.115866. Epub 2021 Jan 27. PMID: 33515777

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Arbizu, RA., Collins, D., 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. doi: 10.5223/pghn.2021.24.1.30. Epub 2021 Jan 8. PMID: 33505891

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Luo, Z., Alekseyenko, AV., Ogunrinde, E., Li M., Li Q-Z., 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. 2021 Jan 8;11:613268. doi: 10.3389/fmicb.2020.613268. eCollection 2020. PMID: 33488555

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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". JAMIA. Volume 28, Issue 1, January 2021, Pages 138-143, doi: 10.1093/jamia/ocaa236.

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Sierra, MA., Li, Q., Pushalkar, S., Paul, B., Sandoval, TA., Kamer, A., Corby, P., Guo, Y., Ruff, RR., Alekseyenko, AV., Li, X., Saxena, D. "The influences of bioinformatics tools and reference databases in analyzing human saliva microbial community". Genes. 2020 Aug 3;11(8):878. doi: 10.3390/genes11080878.

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Wallace, K., Li., H., J. Brazeal, JG., Lewin, DN., Sun, S., Ba, A., Paulos, CM., Rachidi, S., Li, Z., Alek- seyenko, AV."Platelet and hemoglobin count at diagnosis are associated with survival in African American and Caucasian patients with colorectal cancer". Cancer Epidemiol. 2020 Aug;67:101746. doi: 10.1016/j.canep.2020.101746. Epub 2020 Jun 7. PMID: 32521488

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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 1;176(1):1- 10. doi: 10.1093/toxsci/kfaa060. PMID: 32658296

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Preprints 2. Nicola De Maio, Alekseyenko, AV., William J. Coleman-Smith, Fabio Pardi, Marc A. Suchard, Asif U. Tamuri, Jakub Truszkowski, Nick Goldman. "Phylogenetic Novelty Scores: a New Approach for Weighting Genetic Sequences". 2020. https://www.biorxiv.org/content/10.1101/2020.12.03.410100v1

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He, Y., Wang, H., Zheng, J., Beiting, DP., Masci, AM., Yu, H., Liu, K., Wu, J., Curtis, JL., Smith, B., Alek- seyenko, AV., Obeid, JS. "OHMI: The Ontology of Host-Microbiome Interactions." Journal of Biomedical Semantics. 2019 Dec 30;10(1):25. doi: 10.1186/s13326-019-0217-1. PMID: 31888755

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Lobach, I., Kim, I., Alekseyenko, AV., Lobach, S., Zhang, L. "A Simple Approximation to Bias in Gene - Environment Interaction Estimates When a Case Might Not Be the Case." Frontiers in Genetics. 2019, 10, A866. doi: 10.3389/fgene.2019.00886

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Silverman, G.J., Azzouz, DF. and Alekseyenko, AV."Systemic Lupus Erythematosus and dysbiosis in the microbiome: cause or effect or both?" Current Opinion in Immunology 2019, 61:80-85.

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Genes (Basel). 2019 Jul 11;10(7). pii: E524. doi: 10.3390/genes10070524.

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Ogunrinde, E., Zhou, Z., Luo, Z., Alekseyenko, AV., Li, QZ., 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 May 20. doi: 10.1002/art.40935.

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Lobach, I., Kim, I., Alekseyenko, AV., 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 Jul;43(5):522- 531. doi: 10.1002/gepi.22201.

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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., Alekseyenko, AV., Jiang, W. "Systemic translocation of Staphylococcus drives autoantibody production in human with HIV disease and in mice". Microbiome. 2019 Feb 14;7(1):25. doi: 10.1186/s40168-019-0646-1.

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Hamidi, B.; Wallace, K.; Vasu, C.; Alekseyenko, AV."Wd(cid:63)-test: Robust Distance-Based Multivariate Anal- ysis of Variance". Microbiome. 2019 Apr 1;7(1):51. doi: 10.1186/s40168-019-0659-9.

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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 corre- lations." Environ Res. 2019 May;172:700-712. doi: 10.1016/j.envres.2019.01.014.

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Azzouz, DF., Omarbekova, A., Heguy, A., Schwudke, D., Gisch, N., Rovin, BH., Caricchio, R., Buyon, JP., Alekseyenko, AV.and 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. doi: 10.1136/annrheumdis-2018- 214856.

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Genet Epidemiol. 2019 Apr;43(3):292-299. doi: 10.1002/gepi.22186.

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Hathaway-Schrader, J., Steinkamp, H., Chavez, M., Poulides, N., Huang, E., Alekseyenko, AV., Novince, C. "Antibiotic-Perturbation of Gut Microbiota Dysregulates Osteoimmune Crosstalk in Post-Pubertal Skeletal Development". Am J Pathol. 2019 Feb;189(2):370-390. doi: 10.1016/j.a jpath.2018.10.017.

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Alfonso Landeros, Timothy Stutz, Kevin Keys, Alekseyenko, AV., Janet S. Sinsheimer, Kenneth Lange, Mary Sehl "BioSimulator.jl: Stochastic simulation in Julia", Computer Methods and Programs in Biomedicine, 2018, ISSN 0169-2607, doi.org/10.1016/j.cmpb.2018.09.009.

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Lobach I., Sampson J., Alekseyenko, AV., 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. https://doi.org/10.1371/journal.pone.0201140

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Wanli Xu, Zhenwu Luo, Alekseyenko, AV., Lisa Martin, Zhuang Wan, Binhua Ling, Zhiqiang Qin, Tongwen Ou, Sonya Heath, Kendra Maas, Xiaomei Cong, Wei Jiang "Distinct systemic microbiome and microbial translocation are associated with plasma level of anti-CD4 autoantibody in HIV infection". Nature Scientific Reports. 2018 Aug 27;8(1):12863. doi: 10.1038/s41598-018-31116-y.

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Xiaozhou Fan; Brandilyn A Peters; Eric J Jacobs; Susan M Gapstur; Mark P Purdue; Neal D Freedman; Alekseyenko, AV.; Jing Wu; Liying Yang; Zhiheng Pei; Richard B Hayes; Jiyoung Ahn "Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults". Microbiome 2018 6:59 https://doi.org/10.1186/s40168-018-0448-x 46. Steinkamp, HM., Hathaway-Schrader, JD, Chavez MB, Aartun JD1, Zhang L, Jensen T, Sho jaee Bakhtiari A, Helke K, Stumpo DJ, Alekseyenko, AV., Novince CM, Blackshear PJ, Kirkwood KL. "Tristetraprolin is Required for Alveolar Bone Homeostasis" Journal of Dental Research. 2018 Mar 1:22034518756889. doi: 10.1177/0022034518756889

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Kristin Wallace, David N Lewin, Shaoli Sun, Clayton Spiceland, Don Rockey, Alekseyenko, AV., Jennifer Wu, John A. Baron, Anthony J. Alberg, and Elizabeth G. Hill "Tumor Infiltrating Lymphocytes and Col- orectal Cancer Survival in African American and Caucasian Patients", Cancer Epidemiology, Biomarkers and Prevention. DOI: 10.1158/1055-9965.EPI-17-0870 Published July 2018

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Bakhtiari, A.S., Wallace, K., Lewin, D., Sun, S., Wu, J. and Alekseyenko, AV."Causal networks of immune cells defined by multivariate gene expression signatures", 4th Workshop on Data Mining for Medical Informatics: Causal Inference for Health Data Analytics. 2017.

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Van Dyke, T.E *, Diaz, P.I.*, Moutsopoulos, N.*, Alekseyenko, AV.* and Ioannidou, E. "Task Force on Design and Analysis in Oral Health Research: Host-Microbiome Interactions in Dysbiosis", JDR Clinical & Translational Research, 2017. * Contributed equally.

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Zhang, Y. and Alekseyenko, AV."Phylogenic Inference using Alignment-Free Methods for Applications in Microbial Community Surveys using 16s rRNA Gene", PLoS ONE November 14, 2017 https://doi.org/10.1371/journal.pone.0187940.

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Sho jaee Bakhtiari A, Bogatkevich G.S. and Alekseyenko, AV.Identification of predictive cytokine biomarkers of scleroderma via local causal neighborhood methods [version 1]. F1000Research 2017, 6:1875

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Beiko, T., Janech, M., Alekseyenko, AV., Atkinson, C., Coxson, H., Barth, J., Stephenson, S., Wilson, C., Schnapp, L., Barker, A., Brantly, M., Sandhaus, R., Silverman, E., Stoller, J., Trapnell, B., Strange, C. "Serum Proteins Associated with Emphysema Progression in Severe Alpha-1 Antitrypsin Deficiency". Journal of COPD foundation. 2017 Jul 15;4(3):204-216. doi: 10.15326/jcopdf.4.3.2016.0180

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Tang, ZZ., Chen, G., Alekseyenko, AV., Li, H. "A general framework for association analysis of microbial communities on a taxonomic tree." 2017: btw804. doi: 10.1093/bioinformatics/btw804 PMID: 28003264.

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Iizumi, T., Taniguchi, T., Yamazaki, W., Vilmen, G., Alekseyenko, AV., Gao, Z., Perez-Perez, G., Blaser, MJ."Effect of antibiotic pre-treatment and pathogen challenge on the intestinal microbiota in mice" Gut Pathogens. 2016 Nov 18;8:60. eCollection 2016.

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Fan, X., Alekseyenko, AV., Wu, K., 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. 2016 - in press.

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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., Knights, D., Alekseyenko, AV., Ba ---ackhed, F., Blaser, MJ. "Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice", Nature Microbiology. 2016 Aug 22. 1(11): 16140. doi:10.1038/nmicrobiol.2016.140

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Alekseyenko, AV."Multivariate Welch t-test on distances." Bioinformatics. 2016 Aug 11.

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Tang, ZZ., Chen, G., Alekseyenko, AV."PERMANOVA-S: Association test for microbial community com- position that accommodates confounders and multiple distances." Bioinformatics. 2016 May 19.

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Gonzalez, ME., Schaffer, JV., Orlow, SJ., Gao, Z., Li, H., Alekseyenko, AV., Blaser, MJ. "Cutaneous microbiome effects of fluticasone proprionate cream and adjunctive bleach baths in childhood atopic dermatitis." Journal of the American Academy of Dermatology, 2016 75(3) 481-493.

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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. doi:10.1038/ismej.2016.37. PMID: 27015003.

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Ray, B., Alekseyenko, AV., Ma, S., Statnikov, AR., Aliferis, CF. "Evaluation and Ensembling of Methods for Reverse Engineering of Brain Connectivity from Imaging Data" 2016. http://arxiv.org/abs/1603.04906

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Osteoarthritis and Cartilage. 2015 Nov; 23(11): 1915-24. doi: 10.1016/j.joca.2015.08.006. PMID: 26521737.

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Nobel, YR., Cox, LM., Kirigin, FF., Bokulich, NA., Yamanishi, S., Teitler, I., Chung, J., Sohn, J., Barber, C., Goldfarb, DS., Ra ju, 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 an- tibiotic treatment" Nature Communications, 2015 Jun 30;6:7486. doi: 10.1038/ncomms8486. PMID: 26123276.

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Perez-Perez, G.I.; Blumenberg, M.; Alekseyenko, AV."Metagenomics" IN: "Next-generation DNA sequencing informatics", Cold Spring Harbor, New York : Cold Spring Harbor Laboratory Press, 2015 p.309-324

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Cox, LM., Yamanishi, S., Sohn, J. Alekseyenko, AV., Leung, JM., Cho, I., Kim, S., Li, H., Gao, Z., Mahana, D., Z ---arate Rodriguez, JG., Rogers, AB., Robine, N., Loke, P., Blaser, MJ. "Altering the intestinal microbiota during a critical developmental1 window has lasting metabolic consequences." Cell. 2014 Aug 14;158(4):705 - 21. doi: 10.1016/j.cell.2014.05.052. PMID: 25126780.

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Argim ---on, 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." Infection, Genetics and Evolution Volume 21, January 2014, Pages 269 - 278. doi: 10.1016/j.meegid.2013.11.003. Epub 2013 Nov 26. PMID: 24291226. PMCID: PMC3940162.

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Alekseyenko, AV., Perez-Perez, GI., D'Souza, A., Strober, B., Gao, Z., Bihan, M., Li, K., Meth ---e, B., Blaser, MJ., "Community differentiation of the cutaneous microbiota in psoriasis." Microbiome 2013 Dec 23;1(1):31. doi: 10.1186/2049-2618-1-31. PMID: 24451201. PMCID: PMC4177411.

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Statnikov, A., Alekseyenko, AV., Li, Z., Henaff, M., Perez-Perez, GI., Blaser, MJ., Aliferis, CF. "Microbiomic Signatures of Psoriasis: Feasibility and Methodology Comparison." Scientific Reports 2013, 3:2620. doi: 0.1038/srep02620

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Segal, LN., Alekseyenko, AV., Clemente, JC., Kulkarni, R., Wu, B., 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, 1:19. doi:10.1186/2049-2618-1-19. PMID: 24450871.

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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 microbiomicdata." Microbiome 2013 Apr 5;1(1):11. doi: 10.1186/2049-2618-1-11 . PMID: 24456583. PMCID: PMC3960509.

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Bai, JP., Alekseyenko, AV., Statnikov, A., Wang, IM., Wong, PH. "Strategic Applications of Gene Expres- sion: From Drug Discovery/Development to Bedside." AAPS J. 2013 Apr;15(2):427-37. doi:10.1208/s12248-012-9447-1. PMID: 23319288

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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 non-diabetic men." J Infect Dis. 2013 Apr;207(7):1105-14. doi: 10.1093/infdis/jit005. PMID: 23300163

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Cox, LM., Cho, I., Young, SA., Anderson, W. H. K., Waters, BJ., Hung, SC., Gao, Z., Mahana, D., Bihan, M., Alekseyenko, AV., Meth ---e, BA., Blaser, MJ. "The nonfermentable dietary fiber hydroxypropyl methylcellu- lose modulates intestinal microbiota." FASEB J. 2013 Feb;27(2):692-702. doi: 10.1096/fj.12-219477. PMID: 23154883

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Alekseyenko, AV.and Stuart Brown, "Metagenomics". In Brown, SM. "Next-generation DNA Sequencing Informatics" (Chapter 11), Cold Spring Harbor Laboratory Press, New York: 2013.

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Bouckaert, R., Lemey, P., Dunn, M., Greenhill, SJ., Alekseyenko, AV., Drummond, AJ., Gray, R. D., Suchard, MA., Atkinson, QD. "Mapping the origins and expansion of the Indo-European language family." Science. 2012 Aug 24;337(6097):957-60. doi: 10.1126/science.1219669. PMID: 22923579

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Cho, I., Meth ---e, BA., Nondorf, L., Li, K., Alekseyenko, AV., Blaser, MJ. "Subtherapeutic antibiotics al- ter the colonic microbiome and early life adiposity in mice". Nature. 2012 Aug 30;488(7413):621-6. doi: 10.1038/nature11400. PMID: 22914093

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Pei, A., Li, H., Oberdorf, WE., Alekseyenko, AV., Parsons, T., Yang, L., Gerz, EA., Lee, P., Nossa, CW., Pei, Z. "Diversity of 5S rRNA genes within individual prokaryotic genomes". FEMS Microbiol Lett. 2012

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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. doi: 10.1093/molbev/mss084. PMID: 22403239

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Henaff M, Konganti K, Narendra V, Alekseyenko, AV."Application and comparison of SVMs and other methods for multicategory classification in microbiomics". In Statnikov A, Aliferis CF, Hardin DP, Guyon I. "A Gentle Introduction to Support Vector Machines in Biomedicine, Volume 2: Case Studies & Benchmarks" (Chapter 6), World Scientific Publishing, Singapore: 2012.

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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(1):146-55. PMID: 21938341

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DeSantis, TZ., Keller, K., Karaoz, U., Alekseyenko, AV., Singh, NNS., Brodie, E., Pei, Z., Andersen, GL., Larsen, N. "Simrank: Rapid and sensitive general-purpose k-mer search tool". BMC Ecol. 2011 Apr 27;11:11. doi: 10.1186/1472-6785-11-11. PMID: 21524302

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Alekseyenko, AV., Lytkin, NI., Ai, J., Padyukov, L., Aliferis, CF., Statnikov, A. "Causal Graph-Based Predictive Modelling of Rheumatoid Arthritis from Genome-Wide Association Data". Biology Direct 2011

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Deriano, L., Chaumeil, J., Multani, A., Chou Y., Alekseyenko, AV., Chang, S., Skok, JA. and Roth, DB. "The RAG2 C-terminus suppresses genomic instability and lymphomagenesis in developing lymphocytes" Nature, 2011 Mar 3;471(7336):119-23. PMID: 21368836

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Gray, RR., Tatem, AJ., Johnson, JA., Alekseyenko, AV., Pybus, OG., Suchard, MA., Salemi, M. "Bayesian phylogenetics of bacterial genomes: inferring the pandemic spread of Methicillin resistant Staphylococcus aureus ST239".Mol Biol Evol. 2011 May;28(5):1593-603. Epub 2010 Nov 26. PMID: 21112962

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Nelson, TA., Holmes S., Alekseyenko, AV., Shenoy, M., DeSantis, T., Wu, C., Anderson, GL., Sonnenburg, J., Pasricha, PJ. and Spormann, A. "PhyloChip MicroArray Analysis Reveals Altered Gastrointestinal Microbial Communities in a Rat Model of Colonic Hypersensitivity". Neurogastroenterology and Motility 2011 Feb; 23(2):169-77, e41-2. doi: 10.1111/j.1365-2982.2010.01637.x. Epub 2010 Dec 3. PMID: 21129126

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Blaser, M. , Meth ---e, B., Strober, B. , Perez Perez, G., Brown, S., and Alekseyenko, AV."Evaluation of the cutaneous microbiome in psoriasis." Available from Nature Precedings (2010)

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Sehl, M., Alekseyenko, AV. and Lange, KL. "Accurate Stochastic Simulation via the Step Anticipation --- -Leaping (SAL) Algorithm". Journal of Computational Biology, 2009, Vol. 16, No. 9: 1195-1208; doi: 10.1089/cmb.2008.0249. PMID: 19772431

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Lee, CJ., Alekseyenko, AV., Brown, CT. "Exploring the future of bioinformatics data sharing and mining with Pygr and Worldbase" in Proceedings of the 8th Python in Science conference (SciPy 2009), G Varoquaux, S van der Walt, J Millman (Eds.), pp. 62-67.

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Thesis Alekseyenko, AV. "Computational, Comparative and Stochastic Modeling Approaches to Evolution of Alterna- tively Spliced Exons," University of California Los Angeles, Los Angeles, CA, USA. 2008. Mathematics Sub ject Classification: 62 - Statistics.

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Alekseyenko, AV., Lee, CJ., Suchard, MA. "Wagner and Dollo: a stochastic duet by composing two parsi- monious solos". Systematic Biology 2008 57(5): 772 - 784; doi: 10.1080/10635150802434394. PMID: 18853363

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Alekseyenko, AV., Lee, CJ. "Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases." Bioinformatics 2007 23: 1386 - 1393; doi:10.1093/bioinformatics/btl647. PMID: 17234640

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Alekseyenko, AV., Kim, N., Lee, CJ, "Global analysis of exon creation vs. loss, and the role of alternative splicing, in 17 vertebrate genomes." RNA 2007, 13:661 - 670. doi:10.1261/rna.325107 PMID: 17369312

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Kim N, Alekseyenko, AV., Roy, M., Lee, CJ., "The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species." Nucl. Acids Res. 2007 Jan; 35 (Database issue): D93 - 8. Epub 2006 Nov 15. doi: 10.1093/nar/gkl884 PMID: 17108355

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2004, 32: 1261 - 1269. doi: 10.1093/nar/gkh284 PMID: 14982953

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Online ahead of print. PMID: 34415311

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Alekseyenko, A.V. Page 10 of 25

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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.

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Alekseyenko, A.V. Page 11 of 25

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Bashir Hamidi; Kristin Wallace and Alekseyenko, AV."MODIMA, a Method for Multivariate Omnibus Dis- tance Mediation Analysis, Allows for Integration of Multivariate Exposure-Mediator-Response Relationships".

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Lobach, I., Sampson, J., Neuhaus, J., Lobach, S., Alekseyenko, AV., Pryatinska, A., He, T., Zhang, L. "A simple approximation to the bias of gene-environment interaction in case/control studies with silent disease".

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Alekseyenko, A.V. Page 12 of 25

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Alekseyenko, A.V. Page 13 of 25

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Attur, M., Statnikov, AR., Samuels, J., Li, Z., Alekseyenko, AV., Greenberg, JD., Krasnokutsky, S., Rybak, L., Lu, QA., Todd, J., Jordan, JM., Kraus, VB., Aliferis, CF., Abramson, SB."Plasma levels of interleukin-1 receptor antagonist (IL1Ra) predict radiographic progression of symptomatic knee osteoarthritis (SKOA)".

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Alekseyenko, A.V. Page 14 of 25

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Agimo'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.

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Alekseyenko, A.V. Page 15 of 25

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Holmes, S.,Alekseyenko, AV., Timme, A., Nelson, T., Pasricha, PJ., Spormann, A. "Visualization and statistical comparisons of Microbial Communities using R packages on PhyloChip data." Pac Symp Biocomput.

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Resch, A., Xing, Y.,Alekseyenko, AV., Modrek, B., Lee, C. "Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation." Nucl. Acids Res.

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Alekseyenko, A.V. Page 16 of 25

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