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Items: 41

1.

Distinct systemic microbiome and microbial translocation are associated with plasma level of anti-CD4 autoantibody in HIV infection.

Xu W, Luo Z, Alekseyenko AV, Martin L, Wan Z, Ling B, Qin Z, Heath SL, Maas K, Cong X, Jiang W.

Sci Rep. 2018 Aug 27;8(1):12863. doi: 10.1038/s41598-018-31116-y.

2.

Tumor-Infiltrating Lymphocytes and Colorectal Cancer Survival in African American and Caucasian Patients.

Wallace K, Lewin DN, Sun S, Spiceland CM, Rockey DC, Alekseyenko AV, Wu JD, Baron JA, Alberg AJ, Hill EG.

Cancer Epidemiol Biomarkers Prev. 2018 Jul;27(7):755-761. doi: 10.1158/1055-9965.EPI-17-0870. Epub 2018 May 16.

PMID:
29769214
3.

Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults.

Fan X, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Freedman ND, Alekseyenko AV, Wu J, Yang L, Pei Z, Hayes RB, Ahn J.

Microbiome. 2018 Apr 24;6(1):59. doi: 10.1186/s40168-018-0448-x.

4.

Tristetraprolin Is Required for Alveolar Bone Homeostasis.

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.

J Dent Res. 2018 Jul;97(8):946-953. doi: 10.1177/0022034518756889. Epub 2018 Mar 7.

PMID:
29514008
5.

Task Force on Design and Analysis in Oral Health Research: Host-Microbiome Interactions in Dysbiosis.

Van Dyke TE, Diaz PI, Moutsopoulos N, Alekseyenko AV, Ioannidou E.

JDR Clin Trans Res. 2018 Jan;3(1):6-9. doi: 10.1177/2380084417728488. Epub 2017 Aug 17.

6.

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

Zhang Y, Alekseyenko AV.

PLoS One. 2017 Nov 14;12(11):e0187940. doi: 10.1371/journal.pone.0187940. eCollection 2017.

7.

Serum Proteins Associated with Emphysema Progression in Severe Alpha-1 Antitrypsin Deficiency.

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.

Chronic Obstr Pulm Dis. 2017 Jul 15;4(3):204-216. doi: 10.15326/jcopdf.4.3.2016.0180.

8.

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

Tang ZZ, Chen G, Alekseyenko AV, Li H.

Bioinformatics. 2017 May 1;33(9):1278-1285. doi: 10.1093/bioinformatics/btw804.

9.

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

Iizumi T, Taniguchi T, Yamazaki W, Vilmen G, Alekseyenko AV, Gao Z, Perez Perez GI, Blaser MJ.

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

10.

Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study.

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.

Gut. 2018 Jan;67(1):120-127. doi: 10.1136/gutjnl-2016-312580. Epub 2016 Oct 14.

PMID:
27742762
11.

Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis.

Gonzalez ME, Schaffer JV, Orlow SJ, Gao Z, Li H, Alekseyenko AV, Blaser MJ.

J Am Acad Dermatol. 2016 Sep;75(3):481-493.e8. doi: 10.1016/j.jaad.2016.04.066.

12.

Multivariate Welch t-test on distances.

Alekseyenko AV.

Bioinformatics. 2016 Dec 1;32(23):3552-3558. Epub 2016 Aug 11.

13.

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

Tang ZZ, Chen G, Alekseyenko AV.

Bioinformatics. 2016 Sep 1;32(17):2618-25. doi: 10.1093/bioinformatics/btw311. Epub 2016 May 19.

14.

Cigarette smoking and the oral microbiome in a large study of American adults.

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.

ISME J. 2016 Oct;10(10):2435-46. doi: 10.1038/ismej.2016.37. Epub 2016 Mar 25.

15.

Plasma levels of interleukin-1 receptor antagonist (IL1Ra) predict radiographic progression of symptomatic knee osteoarthritis.

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.

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

16.

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

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.

Nat Commun. 2015 Jun 30;6:7486. doi: 10.1038/ncomms8486.

17.

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

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.

Cell. 2014 Aug 14;158(4):705-721. doi: 10.1016/j.cell.2014.05.052.

18.

A comprehensive evaluation of multicategory classification methods for microbiomic data.

Statnikov A, Henaff M, Narendra V, Konganti K, Li Z, Yang L, Pei Z, Blaser MJ, Aliferis CF, Alekseyenko AV.

Microbiome. 2013 Apr 5;1(1):11. doi: 10.1186/2049-2618-1-11.

19.

Community differentiation of the cutaneous microbiota in psoriasis.

Alekseyenko AV, Perez-Perez GI, De Souza A, Strober B, Gao Z, Bihan M, Li K, Methé BA, Blaser MJ.

Microbiome. 2013 Dec 23;1(1):31. doi: 10.1186/2049-2618-1-31.

20.

Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation.

Segal LN, Alekseyenko AV, Clemente JC, Kulkarni R, Wu B, Gao Z, Chen H, Berger KI, Goldring RM, Rom WN, Blaser MJ, Weiden MD.

Microbiome. 2013 Jul 1;1(1):19. doi: 10.1186/2049-2618-1-19. Erratum in: Microbiome. 2014;2:21. Gao, Zhan [added].

21.

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

Argimón S, Konganti K, Chen H, Alekseyenko AV, Brown S, Caufield PW.

Infect Genet Evol. 2014 Jan;21:269-78. doi: 10.1016/j.meegid.2013.11.003. Epub 2013 Nov 26.

22.

Microbiomic signatures of psoriasis: feasibility and methodology comparison.

Statnikov A, Alekseyenko AV, Li Z, Henaff M, Perez-Perez GI, Blaser MJ, Aliferis CF.

Sci Rep. 2013;3:2620. doi: 10.1038/srep02620.

23.

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

Argimón S, Alekseyenko AV, DeSalle R, Caufield PW.

PLoS One. 2013;8(2):e56305. doi: 10.1371/journal.pone.0056305. Epub 2013 Feb 14.

24.

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

Bai JP, Alekseyenko AV, Statnikov A, Wang IM, Wong PH.

AAPS J. 2013 Apr;15(2):427-37. doi: 10.1208/s12248-012-9447-1. Epub 2013 Jan 15. Review.

25.

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

Redel H, Gao Z, Li H, Alekseyenko AV, Zhou Y, Perez-Perez GI, Weinstock G, Sodergren E, Blaser MJ.

J Infect Dis. 2013 Apr;207(7):1105-14. doi: 10.1093/infdis/jit005. Epub 2013 Jan 8.

26.

The nonfermentable dietary fiber hydroxypropyl methylcellulose modulates intestinal microbiota.

Cox LM, Cho I, Young SA, Anderson WH, Waters BJ, Hung SC, Gao Z, Mahana D, Bihan M, Alekseyenko AV, Methé BA, Blaser MJ.

FASEB J. 2013 Feb;27(2):692-702. doi: 10.1096/fj.12-219477. Epub 2012 Nov 14.

27.

Mapping the origins and expansion of the Indo-European language family.

Bouckaert R, Lemey P, Dunn M, Greenhill SJ, Alekseyenko AV, Drummond AJ, Gray RD, Suchard MA, Atkinson QD.

Science. 2012 Aug 24;337(6097):957-60. doi: 10.1126/science.1219669. Erratum in: Science. 2013 Dec 20;342(6165):1446.

28.

Antibiotics in early life alter the murine colonic microbiome and adiposity.

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.

Nature. 2012 Aug 30;488(7413):621-6. doi: 10.1038/nature11400.

29.

Diversity of 5S rRNA genes within individual prokaryotic genomes.

Pei A, Li H, Oberdorf WE, Alekseyenko AV, Parsons T, Yang L, Gerz EA, Lee P, Xiang C, Nossa CW, Pei Z.

FEMS Microbiol Lett. 2012 Oct;335(1):11-8. doi: 10.1111/j.1574-6968.2012.02632.x. Epub 2012 Aug 2.

30.

Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty.

Baele G, Lemey P, Bedford T, Rambaut A, Suchard MA, Alekseyenko AV.

Mol Biol Evol. 2012 Sep;29(9):2157-67. doi: 10.1093/molbev/mss084. Epub 2012 Mar 7.

31.

Trends and developments in bioinformatics in 2010: prospects and perspectives.

Aliferis CF, Alekseyenko AV, Aphinyanaphongs Y, Brown S, Fenyo D, Fu L, Shen S, Statnikov A, Wang J.

Yearb Med Inform. 2011;6:146-55. Review.

PMID:
21938341
32.

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

Alekseyenko AV, Lytkin NI, Ai J, Ding B, Padyukov L, Aliferis CF, Statnikov A.

Biol Direct. 2011 May 18;6:25. doi: 10.1186/1745-6150-6-25.

33.

Simrank: Rapid and sensitive general-purpose k-mer search tool.

DeSantis TZ, Keller K, Karaoz U, Alekseyenko AV, Singh NN, Brodie EL, Pei Z, Andersen GL, Larsen N.

BMC Ecol. 2011 Apr 27;11:11. doi: 10.1186/1472-6785-11-11.

34.

The RAG2 C terminus suppresses genomic instability and lymphomagenesis.

Deriano L, Chaumeil J, Coussens M, Multani A, Chou Y, Alekseyenko AV, Chang S, Skok JA, Roth DB.

Nature. 2011 Mar 3;471(7336):119-23. doi: 10.1038/nature09755.

35.

PhyloChip microarray analysis reveals altered gastrointestinal microbial communities in a rat model of colonic hypersensitivity.

Nelson TA, Holmes S, Alekseyenko AV, Shenoy M, Desantis T, Wu CH, Andersen GL, Winston J, Sonnenburg J, Pasricha PJ, Spormann A.

Neurogastroenterol Motil. 2011 Feb;23(2):169-77, e41-2. doi: 10.1111/j.1365-2982.2010.01637.x. Epub 2010 Dec 3.

36.

Testing spatiotemporal hypothesis of bacterial evolution using methicillin-resistant Staphylococcus aureus ST239 genome-wide data within a bayesian framework.

Gray RR, Tatem AJ, Johnson JA, Alekseyenko AV, Pybus OG, Suchard MA, Salemi M.

Mol Biol Evol. 2011 May;28(5):1593-603. doi: 10.1093/molbev/msq319. Epub 2010 Nov 26.

37.

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

Sehl M, Alekseyenko AV, Lange KL.

J Comput Biol. 2009 Sep;16(9):1195-208. doi: 10.1089/cmb.2008.0249.

38.

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

Alekseyenko AV, Lee CJ, Suchard MA.

Syst Biol. 2008 Oct;57(5):772-84. doi: 10.1080/10635150802434394.

39.
40.

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

Alekseyenko AV, Lee CJ.

Bioinformatics. 2007 Jun 1;23(11):1386-93. Epub 2007 Jan 18.

PMID:
17234640
41.

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

Kim N, Alekseyenko AV, Roy M, Lee C.

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

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