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Items: 1 to 50 of 55

1.

Intestinal IL-17R Signaling Constrains IL-18-Driven Liver Inflammation by the Regulation of Microbiome-Derived Products.

Castillo-Dela Cruz P, Wanek AG, Kumar P, An X, Elsegeiny W, Horne W, Fitch A, Burr AHP, Gopalakrishna KP, Chen K, Methé BA, Canna SW, Hand TW, Kolls JK.

Cell Rep. 2019 Nov 19;29(8):2270-2283.e7. doi: 10.1016/j.celrep.2019.10.042.

2.

Effects of rifaximin on circulating aged neutrophils in sickle cell disease.

Dutta D, Methe BA, Morris A, Lim SH.

Am J Hematol. 2019 Jun;94(6):E175-E176. doi: 10.1002/ajh.25467. Epub 2019 Apr 3. No abstract available.

PMID:
30900765
3.

Invasive non-typhoidal Salmonella in sickle cell disease in Africa: is increased gut permeability the missing link?

Lim SH, Methé BA, Knoll BM, Morris A, Obaro SK.

J Transl Med. 2018 Aug 30;16(1):239. doi: 10.1186/s12967-018-1622-4.

4.

The administration of intranasal live attenuated influenza vaccine induces changes in the nasal microbiota and nasal epithelium gene expression profiles.

Tarabichi Y, Li K, Hu S, Nguyen C, Wang X, Elashoff D, Saira K, Frank B, Bihan M, Ghedin E, Methé BA, Deng JC.

Microbiome. 2015 Dec 15;3:74. doi: 10.1186/s40168-015-0133-2.

5.

DEEP BIOSPHERE. Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor.

Inagaki F, Hinrichs KU, Kubo Y, Bowles MW, Heuer VB, Hong WL, Hoshino T, Ijiri A, Imachi H, Ito M, Kaneko M, Lever MA, Lin YS, Methé BA, Morita S, Morono Y, Tanikawa W, Bihan M, Bowden SA, Elvert M, Glombitza C, Gross D, Harrington GJ, Hori T, Li K, Limmer D, Liu CH, Murayama M, Ohkouchi N, Ono S, Park YS, Phillips SC, Prieto-Mollar X, Purkey M, Riedinger N, Sanada Y, Sauvage J, Snyder G, Susilawati R, Takano Y, Tasumi E, Terada T, Tomaru H, Trembath-Reichert E, Wang DT, Yamada Y.

Science. 2015 Jul 24;349(6246):420-4. doi: 10.1126/science.aaa6882. Epub 2015 Jul 23.

6.

Rationale and Design of the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis Study. Alpha-1 Protocol.

Strange C, Senior RM, Sciurba F, O'Neal S, Morris A, Wisniewski SR, Bowler R, Hochheiser HS, Becich MJ, Zhang Y, Leader JK, Methé BA, Kaminski N, Sandhaus RA; GRADS Alpha-1 Study Group.

Ann Am Thorac Soc. 2015 Oct;12(10):1551-60. doi: 10.1513/AnnalsATS.201503-143OC.

7.

NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly.

McCorrison JM, Venepally P, Singh I, Fouts DE, Lasken RS, Methé BA.

BMC Bioinformatics. 2014 Nov 19;15:357. doi: 10.1186/s12859-014-0357-3.

8.

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.

9.

Microbiology in the 'omics era: from the study of single cells to communities and beyond.

Methé BA, Lasa I.

Curr Opin Microbiol. 2013 Oct;16(5):602-4. doi: 10.1016/j.mib.2013.10.002. Epub 2013 Oct 17. No abstract available.

PMID:
24139987
10.

Analyses of the stability and core taxonomic memberships of the human microbiome.

Li K, Bihan M, Methé BA.

PLoS One. 2013 May 6;8(5):e63139. doi: 10.1371/journal.pone.0063139. Print 2013.

11.

A Bayesian model for pooling gene expression studies that incorporates co-regulation information.

Conlon EM, Postier BL, Methé BA, Nevin KP, Lovley DR.

PLoS One. 2012;7(12):e52137. doi: 10.1371/journal.pone.0052137. Epub 2012 Dec 28.

12.

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.

13.

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.

14.

The Human Microbiome Project: a community resource for the healthy human microbiome.

Gevers D, Knight R, Petrosino JF, Huang K, McGuire AL, Birren BW, Nelson KE, White O, Methé BA, Huttenhower C.

PLoS Biol. 2012;10(8):e1001377. doi: 10.1371/journal.pbio.1001377. Epub 2012 Aug 14. No abstract available.

15.

Complete genome sequences of Mycoplasma leachii strain PG50T and the pathogenic Mycoplasma mycoides subsp. mycoides small colony biotype strain Gladysdale.

Wise KS, Calcutt MJ, Foecking MF, Madupu R, DeBoy RT, Röske K, Hvinden ML, Martin TR, Durkin AS, Glass JI, Methé BA.

J Bacteriol. 2012 Aug;194(16):4448-9. doi: 10.1128/JB.00761-12.

16.

Analyses of the microbial diversity across the human microbiome.

Li K, Bihan M, Yooseph S, Methé BA.

PLoS One. 2012;7(6):e32118. doi: 10.1371/journal.pone.0032118. Epub 2012 Jun 13.

17.

A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP).

Goll J, Thiagarajan M, Abubucker S, Huttenhower C, Yooseph S, Methé BA.

PLoS One. 2012;7(6):e29044. doi: 10.1371/journal.pone.0029044. Epub 2012 Jun 13.

18.

Comparative genome analysis of 19 Ureaplasma urealyticum and Ureaplasma parvum strains.

Paralanov V, Lu J, Duffy LB, Crabb DM, Shrivastava S, Methé BA, Inman J, Yooseph S, Xiao L, Cassell GH, Waites KB, Glass JI.

BMC Microbiol. 2012 May 30;12:88. doi: 10.1186/1471-2180-12-88.

19.

HIV-1 and bacterial pneumonia in the era of antiretroviral therapy.

Segal LN, Methé BA, Nolan A, Hoshino Y, Rom WN, Dawson R, Bateman E, Weiden MD.

Proc Am Thorac Soc. 2011 Jun;8(3):282-7. doi: 10.1513/pats.201006-044WR. Review.

20.

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PS, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, DeSantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, San Gil I, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Methé BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spo A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Glöckner FO.

Nat Biotechnol. 2011 May;29(5):415-20. doi: 10.1038/nbt.1823.

21.

Complete genome sequence of Mycoplasma bovis type strain PG45 (ATCC 25523).

Wise KS, Calcutt MJ, Foecking MF, Röske K, Madupu R, Methé BA.

Infect Immun. 2011 Feb;79(2):982-3. doi: 10.1128/IAI.00726-10. Epub 2010 Dec 6.

22.

Genome sequence of the deltaproteobacterial strain NaphS2 and analysis of differential gene expression during anaerobic growth on naphthalene.

DiDonato RJ Jr, Young ND, Butler JE, Chin KJ, Hixson KK, Mouser P, Lipton MS, DeBoy R, Methé BA.

PLoS One. 2010 Nov 19;5(11):e14072. doi: 10.1371/journal.pone.0014072.

23.

METAREP: JCVI metagenomics reports--an open source tool for high-performance comparative metagenomics.

Goll J, Rusch DB, Tanenbaum DM, Thiagarajan M, Li K, Methé BA, Yooseph S.

Bioinformatics. 2010 Oct 15;26(20):2631-2. doi: 10.1093/bioinformatics/btq455. Epub 2010 Aug 26.

24.

ANDES: Statistical tools for the ANalyses of DEep Sequencing.

Li K, Venter E, Yooseph S, Stockwell TB, Eckerle LD, Denison MR, Spiro DJ, Methé BA.

BMC Res Notes. 2010 Jul 15;3:199. doi: 10.1186/1756-0500-3-199.

25.

De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.

Nagarajan H, Butler JE, Klimes A, Qiu Y, Zengler K, Ward J, Young ND, Methé BA, Palsson BØ, Lovley DR, Barrett CL.

PLoS One. 2010 Jun 8;5(6):e10922. doi: 10.1371/journal.pone.0010922.

26.

Genome enablement of the notothenioidei: genome size estimates from 11 species and BAC libraries from 2 representative taxa.

Detrich HW, Stuart A, Schoenborn M, Parker SK, Methé BA, Amemiya CT.

J Exp Zool B Mol Dev Evol. 2010 Jul 15;314(5):369-81. doi: 10.1002/jez.b.21341.

27.

Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens.

Risso C, Sun J, Zhuang K, Mahadevan R, DeBoy R, Ismail W, Shrivastava S, Huot H, Kothari S, Daugherty S, Bui O, Schilling CH, Lovley DR, Methé BA.

BMC Genomics. 2009 Sep 22;10:447. doi: 10.1186/1471-2164-10-447.

28.

Characterization of the intestinal microbiota of two Antarctic notothenioid fish species.

Ward NL, Steven B, Penn K, Methé BA, Detrich WH 3rd.

Extremophiles. 2009 Jul;13(4):679-85. doi: 10.1007/s00792-009-0252-4. Epub 2009 May 27.

PMID:
19472032
29.

Anode biofilm transcriptomics reveals outer surface components essential for high density current production in Geobacter sulfurreducens fuel cells.

Nevin KP, Kim BC, Glaven RH, Johnson JP, Woodard TL, Methé BA, Didonato RJ, Covalla SF, Franks AE, Liu A, Lovley DR.

PLoS One. 2009 May 20;4(5):e5628. doi: 10.1371/journal.pone.0005628.

30.

Molecular characterization of newly identified IS3, IS4 and IS30 insertion sequence-like elements in Mycoplasma bovis and their possible roles in genome plasticity.

Lysnyansky I, Calcutt MJ, Ben-Barak I, Ron Y, Levisohn S, Methé BA, Yogev D.

FEMS Microbiol Lett. 2009 May;294(2):172-82. doi: 10.1111/j.1574-6968.2009.01562.x.

31.

Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure.

Coyne RS, Thiagarajan M, Jones KM, Wortman JR, Tallon LJ, Haas BJ, Cassidy-Hanley DM, Wiley EA, Smith JJ, Collins K, Lee SR, Couvillion MT, Liu Y, Garg J, Pearlman RE, Hamilton EP, Orias E, Eisen JA, Methé BA.

BMC Genomics. 2008 Nov 26;9:562. doi: 10.1186/1471-2164-9-562.

32.

Highly conserved genes in Geobacter species with expression patterns indicative of acetate limitation.

Risso C, Methé BA, Elifantz H, Holmes DE, Lovley DR.

Microbiology. 2008 Sep;154(Pt 9):2589-99. doi: 10.1099/mic.0.2008/017244-0.

PMID:
18757793
33.

Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice.

Fouts DE, Tyler HL, DeBoy RT, Daugherty S, Ren Q, Badger JH, Durkin AS, Huot H, Shrivastava S, Kothari S, Dodson RJ, Mohamoud Y, Khouri H, Roesch LF, Krogfelt KA, Struve C, Triplett EW, Methé BA.

PLoS Genet. 2008 Jul 25;4(7):e1000141. doi: 10.1371/journal.pgen.1000141.

34.

Antarctic genomics.

Clark MS, Clarke A, Cockell CS, Convey P, Detrich HW 3rd, Fraser KP, Johnston IA, Methe BA, Murray AE, Peck LS, Römisch K, Rogers AD.

Comp Funct Genomics. 2004;5(3):230-8. doi: 10.1002/cfg.398.

35.

Characterizing regulation of metabolism in Geobacter sulfurreducens through genome-wide expression data and sequence analysis.

Mahadevan R, Yan B, Postier B, Nevin KP, Woodard TL, O'Neil R, Coppi MV, Methé BA, Krushkal J.

OMICS. 2008 Mar;12(1):33-59. doi: 10.1089/omi.2007.0043.

PMID:
18266557
36.

PilR, a transcriptional regulator for pilin and other genes required for Fe(III) reduction in Geobacter sulfurreducens.

Juárez K, Kim BC, Nevin K, Olvera L, Reguera G, Lovley DR, Methé BA.

J Mol Microbiol Biotechnol. 2009;16(3-4):146-58. doi: 10.1159/000115849. Epub 2008 Feb 4.

PMID:
18253022
37.

Involvement of Geobacter sulfurreducens SfrAB in acetate metabolism rather than intracellular, respiration-linked Fe(III) citrate reduction.

Coppi MV, O'neil RA, Leang C, Kaufmann F, Methé BA, Nevin KP, Woodard TL, Liu A, Lovley DR.

Microbiology. 2007 Oct;153(Pt 10):3572-85.

PMID:
17906154
38.

Benefits of in-situ synthesized microarrays for analysis of gene expression in understudied microorganisms.

Postier B, Didonato R Jr, Nevin KP, Liu A, Frank B, Lovley D, Methe BA.

J Microbiol Methods. 2008 Jul;74(1):26-32. Epub 2007 Jul 17.

PMID:
17720265
39.

Microbial environmental genomics.

Nelson KE, Methé BA, Kowalchuk GA.

Microb Ecol. 2007 Apr;53(3):367-8. No abstract available.

PMID:
17415611
40.

Genome-wide expression profiling in Geobacter sulfurreducens: identification of Fur and RpoS transcription regulatory sites in a relGsu mutant.

Krushkal J, Yan B, DiDonato LN, Puljic M, Nevin KP, Woodard TL, Adkins RM, Methé BA, Lovley DR.

Funct Integr Genomics. 2007 Jul;7(3):229-55. Epub 2007 Apr 4.

PMID:
17406915
41.

Environmental microbial ecology in an "omics" era: summary report of MicroEnGen-II (Shanghai, June 12-15, 2006).

Nelson K, Methé BA, Kowalchuk GA.

Microb Ecol. 2007 Apr;53(3):369-70. No abstract available.

PMID:
17404786
42.

Role of RelGsu in stress response and Fe(III) reduction in Geobacter sulfurreducens.

DiDonato LN, Sullivan SA, Methé BA, Nevin KP, England R, Lovley DR.

J Bacteriol. 2006 Dec;188(24):8469-78. Epub 2006 Oct 13.

43.

Computational prediction of RpoS and RpoD regulatory sites in Geobacter sulfurreducens using sequence and gene expression information.

Yan B, Núñez C, Ueki T, Esteve-Núñez A, Puljic M, Adkins RM, Methé BA, Lovley DR, Krushkal J.

Gene. 2006 Dec 15;384:73-95. Epub 2006 Jul 20.

PMID:
17014972
44.

Microarray and genetic analysis of electron transfer to electrodes in Geobacter sulfurreducens.

Holmes DE, Chaudhuri SK, Nevin KP, Mehta T, Methé BA, Liu A, Ward JE, Woodard TL, Webster J, Lovley DR.

Environ Microbiol. 2006 Oct;8(10):1805-15.

PMID:
16958761
45.

DNA microarray and proteomic analyses of the RpoS regulon in Geobacter sulfurreducens.

Núñez C, Esteve-Núñez A, Giometti C, Tollaksen S, Khare T, Lin W, Lovley DR, Methé BA.

J Bacteriol. 2006 Apr;188(8):2792-800.

46.

Adaptation to disruption of the electron transfer pathway for Fe(III) reduction in Geobacter sulfurreducens.

Leang C, Adams LA, Chin KJ, Nevin KP, Methé BA, Webster J, Sharma ML, Lovley DR.

J Bacteriol. 2005 Sep;187(17):5918-26.

47.

The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses.

Methé BA, Nelson KE, Deming JW, Momen B, Melamud E, Zhang X, Moult J, Madupu R, Nelson WC, Dodson RJ, Brinkac LM, Daugherty SC, Durkin AS, DeBoy RT, Kolonay JF, Sullivan SA, Zhou L, Davidsen TM, Wu M, Huston AL, Lewis M, Weaver B, Weidman JF, Khouri H, Utterback TR, Feldblyum TV, Fraser CM.

Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):10913-8. Epub 2005 Jul 25.

48.

DNA microarray analysis of nitrogen fixation and Fe(III) reduction in Geobacter sulfurreducens.

Methé BA, Webster J, Nevin K, Butler J, Lovley DR.

Appl Environ Microbiol. 2005 May;71(5):2530-8.

49.

Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes.

Seshadri R, Adrian L, Fouts DE, Eisen JA, Phillippy AM, Methe BA, Ward NL, Nelson WC, Deboy RT, Khouri HM, Kolonay JF, Dodson RJ, Daugherty SC, Brinkac LM, Sullivan SA, Madupu R, Nelson KE, Kang KH, Impraim M, Tran K, Robinson JM, Forberger HA, Fraser CM, Zinder SH, Heidelberg JF.

Science. 2005 Jan 7;307(5706):105-8.

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