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Items: 47

1.

Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes.

Douglas GM, Langille MGI.

Genome Biol Evol. 2019 Aug 26. pii: evz184. doi: 10.1093/gbe/evz184. [Epub ahead of print]

PMID:
31504488
2.

Metagenomic Functional Shifts to Plant Induced Environmental Changes.

Yurgel SN, Nearing JT, Douglas GM, Langille MGI.

Front Microbiol. 2019 Jul 26;10:1682. doi: 10.3389/fmicb.2019.01682. eCollection 2019.

3.

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG.

Nat Biotechnol. 2019 Sep;37(9):1091. doi: 10.1038/s41587-019-0252-6.

PMID:
31399723
4.

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG.

Nat Biotechnol. 2019 Aug;37(8):852-857. doi: 10.1038/s41587-019-0209-9. No abstract available. Erratum in: Nat Biotechnol. 2019 Sep;37(9):1091.

PMID:
31341288
5.

Drivers of Regional Bacterial Community Structure and Diversity in the Northwest Atlantic Ocean.

Zorz J, Willis C, Comeau AM, Langille MGI, Johnson CL, Li WKW, LaRoche J.

Front Microbiol. 2019 Feb 21;10:281. doi: 10.3389/fmicb.2019.00281. eCollection 2019.

6.

Infectious Complications Are Associated With Alterations in the Gut Microbiome in Pediatric Patients With Acute Lymphoblastic Leukemia.

Nearing JT, Connors J, Whitehouse S, Van Limbergen J, Macdonald T, Kulkarni K, Langille MGI.

Front Cell Infect Microbiol. 2019 Feb 19;9:28. doi: 10.3389/fcimb.2019.00028. eCollection 2019.

7.

Enhancement of the gut barrier integrity by a microbial metabolite through the Nrf2 pathway.

Singh R, Chandrashekharappa S, Bodduluri SR, Baby BV, Hegde B, Kotla NG, Hiwale AA, Saiyed T, Patel P, Vijay-Kumar M, Langille MGI, Douglas GM, Cheng X, Rouchka EC, Waigel SJ, Dryden GW, Alatassi H, Zhang HG, Haribabu B, Vemula PK, Jala VR.

Nat Commun. 2019 Jan 9;10(1):89. doi: 10.1038/s41467-018-07859-7.

8.

Predicting the Functional Potential of the Microbiome from Marker Genes Using PICRUSt.

Douglas GM, Beiko RG, Langille MGI.

Methods Mol Biol. 2018;1849:169-177. doi: 10.1007/978-1-4939-8728-3_11.

PMID:
30298254
9.

Processing a 16S rRNA Sequencing Dataset with the Microbiome Helper Workflow.

Douglas GM, Comeau AM, Langille MGI.

Methods Mol Biol. 2018;1849:131-141. doi: 10.1007/978-1-4939-8728-3_9.

PMID:
30298252
10.

The Phosphate Binder Ferric Citrate Alters the Gut Microbiome in Rats with Chronic Kidney Disease.

Lau WL, Vaziri ND, Nunes ACF, Comeau AM, Langille MGI, England W, Khazaeli M, Suematsu Y, Phan J, Whiteson K.

J Pharmacol Exp Ther. 2018 Dec;367(3):452-460. doi: 10.1124/jpet.118.251389. Epub 2018 Oct 4.

11.

The impact of chemerin or chemokine-like receptor 1 loss on the mouse gut microbiome.

Dranse HJ, Zheng A, Comeau AM, Langille MGI, Zabel BA, Sinal CJ.

PeerJ. 2018 Sep 12;6:e5494. doi: 10.7717/peerj.5494. eCollection 2018.

12.

Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches.

Nearing JT, Douglas GM, Comeau AM, Langille MGI.

PeerJ. 2018 Aug 8;6:e5364. doi: 10.7717/peerj.5364. eCollection 2018.

13.

Differences in adiposity and diet quality among individuals with inflammatory bowel disease in Eastern Canada.

DeClercq V, Langille MGI, Van Limbergen J.

PLoS One. 2018 Jul 19;13(7):e0200580. doi: 10.1371/journal.pone.0200580. eCollection 2018.

14.

Dissecting Community Structure in Wild Blueberry Root and Soil Microbiome.

Yurgel SN, Douglas GM, Dusault A, Percival D, Langille MGI.

Front Microbiol. 2018 Jun 6;9:1187. doi: 10.3389/fmicb.2018.01187. eCollection 2018.

15.

Exploring Linkages between Taxonomic and Functional Profiles of the Human Microbiome.

Langille MGI.

mSystems. 2018 Mar 27;3(2). pii: e00163-17. doi: 10.1128/mSystems.00163-17. eCollection 2018 Mar-Apr.

16.

Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn's disease.

Douglas GM, Hansen R, Jones CMA, Dunn KA, Comeau AM, Bielawski JP, Tayler R, El-Omar EM, Russell RK, Hold GL, Langille MGI, Van Limbergen J.

Microbiome. 2018 Jan 15;6(1):13. doi: 10.1186/s40168-018-0398-3.

17.

"Available upon request": not good enough for microbiome data!

Langille MGI, Ravel J, Fricke WF.

Microbiome. 2018 Jan 10;6(1):8. doi: 10.1186/s40168-017-0394-z. No abstract available.

18.

Taxonomic differences of gut microbiomes drive cellulolytic enzymatic potential within hind-gut fermenting mammals.

Finlayson-Trick ECL, Getz LJ, Slaine PD, Thornbury M, Lamoureux E, Cook J, Langille MGI, Murray LE, McCormick C, Rohde JR, Cheng Z.

PLoS One. 2017 Dec 27;12(12):e0189404. doi: 10.1371/journal.pone.0189404. eCollection 2017.

19.

Moderate Exercise Has Limited but Distinguishable Effects on the Mouse Microbiome.

Lamoureux EV, Grandy SA, Langille MGI.

mSystems. 2017 Aug 22;2(4). pii: e00006-17. doi: 10.1128/mSystems.00006-17. eCollection 2017 Jul-Aug.

20.

The Impact of Exclusive Enteral Nutrition (EEN) on the Gut Microbiome in Crohn's Disease: A Review.

MacLellan A, Moore-Connors J, Grant S, Cahill L, Langille MGI, Van Limbergen J.

Nutrients. 2017 May 1;9(5). pii: E0447. doi: 10.3390/nu9050447. Review.

21.

Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research.

Comeau AM, Douglas GM, Langille MG.

mSystems. 2017 Jan 3;2(1). pii: e00127-16. doi: 10.1128/mSystems.00127-16. eCollection 2017 Jan-Feb.

22.

Discovery of an expanded set of avian leucosis subgroup E proviruses in chickens using Vermillion, a novel sequence capture and analysis pipeline.

Rutherford K, Meehan CJ, Langille MG, Tyack SG, McKay JC, McLean NL, Benkel K, Beiko RG, Benkel B.

Poult Sci. 2016 Oct 19. pii: pew404. [Epub ahead of print] No abstract available.

PMID:
27765872
23.

Genomic Analysis of a Serotype 5 Streptococcus pneumoniae Outbreak in British Columbia, Canada, 2005-2009.

Miller RR, Langille MG, Montoya V, Crisan A, Stefanovic A, Martin I, Hoang L, Patrick DM, Romney M, Tyrrell G, Jones SJ, Brinkman FS, Tang P.

Can J Infect Dis Med Microbiol. 2016;2016:5381871. doi: 10.1155/2016/5381871. Epub 2016 Apr 14.

24.

Discovery of an expanded set of avian leukosis subroup E proviruses in chickens using Vermillion, a novel sequence capture and analysis pipeline.

Rutherford K, Meehan CJ, Langille MG, Tyack SG, McKay JC, McLean NL, Benkel K, Beiko RG, Benkel B.

Poult Sci. 2016 Oct 1;95(10):2250-8. doi: 10.3382/ps/pew194. Epub 2016 Jun 27. Erratum in: Poult Sci. 2016 Oct 19;:.

PMID:
27354549
25.

Frailty and the Microbiome.

Meehan CJ, Langille MG, Beiko RG.

Interdiscip Top Gerontol Geriatr. 2015;41:54-65. doi: 10.1159/000381162. Epub 2015 Jul 17. Review.

PMID:
26301979
26.

GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications.

Laird MR, Langille MG, Brinkman FS.

Bioinformatics. 2015 Oct 15;31(20):3348-9. doi: 10.1093/bioinformatics/btv376. Epub 2015 Jun 20.

27.

IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis.

Dhillon BK, Laird MR, Shay JA, Winsor GL, Lo R, Nizam F, Pereira SK, Waglechner N, McArthur AG, Langille MG, Brinkman FS.

Nucleic Acids Res. 2015 Jul 1;43(W1):W104-8. doi: 10.1093/nar/gkv401. Epub 2015 Apr 27.

28.

Fecal microbes, short chain fatty acids, and colorectal cancer across racial/ethnic groups.

Hester CM, Jala VR, Langille MG, Umar S, Greiner KA, Haribabu B.

World J Gastroenterol. 2015 Mar 7;21(9):2759-69. doi: 10.3748/wjg.v21.i9.2759.

29.

Microbial shifts in the aging mouse gut.

Langille MG, Meehan CJ, Koenig JE, Dhanani AS, Rose RA, Howlett SE, Beiko RG.

Microbiome. 2014 Dec 5;2(1):50. doi: 10.1186/s40168-014-0050-9. eCollection 2014.

30.

Which is more important for classifying microbial communities: who's there or what they can do?

Xu Z, Malmer D, Langille MG, Way SF, Knight R.

ISME J. 2014 Dec;8(12):2357-9. doi: 10.1038/ismej.2014.157. Epub 2014 Aug 29. No abstract available.

31.

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.

Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C.

Nat Biotechnol. 2013 Sep;31(9):814-21. doi: 10.1038/nbt.2676. Epub 2013 Aug 25.

32.

GenGIS 2: geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework.

Parks DH, Mankowski T, Zangooei S, Porter MS, Armanini DG, Baird DJ, Langille MG, Beiko RG.

PLoS One. 2013 Jul 29;8(7):e69885. doi: 10.1371/journal.pone.0069885. Print 2013.

33.

Interactions in the microbiome: communities of organisms and communities of genes.

Boon E, Meehan CJ, Whidden C, Wong DH, Langille MG, Beiko RG.

FEMS Microbiol Rev. 2014 Jan;38(1):90-118. doi: 10.1111/1574-6976.12035. Epub 2013 Aug 28. Review.

34.

IslandViewer update: Improved genomic island discovery and visualization.

Dhillon BK, Chiu TA, Laird MR, Langille MG, Brinkman FS.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W129-32. doi: 10.1093/nar/gkt394. Epub 2013 May 15.

35.

Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource.

Sharpton TJ, Jospin G, Wu D, Langille MG, Pollard KS, Eisen JA.

BMC Bioinformatics. 2012 Oct 13;13:264. doi: 10.1186/1471-2105-13-264.

36.

Functional biogeography of ocean microbes revealed through non-negative matrix factorization.

Jiang X, Langille MG, Neches RY, Elliot M, Levin SA, Eisen JA, Weitz JS, Dushoff J.

PLoS One. 2012;7(9):e43866. doi: 10.1371/journal.pone.0043866. Epub 2012 Sep 18.

37.

Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux.

Lynch EA, Langille MG, Darling A, Wilbanks EG, Haltiner C, Shao KS, Starr MO, Teiling C, Harkins TT, Edwards RA, Eisen JA, Facciotti MT.

PLoS One. 2012;7(7):e41389. doi: 10.1371/journal.pone.0041389. Epub 2012 Jul 24.

38.

MicrobeDB: a locally maintainable database of microbial genomic sequences.

Langille MG, Laird MR, Hsiao WW, Chiu TA, Eisen JA, Brinkman FS.

Bioinformatics. 2012 Jul 15;28(14):1947-8. doi: 10.1093/bioinformatics/bts273. Epub 2012 May 9.

39.

Human microbiome: a genetic bazaar for microbes?

Langille MG, Meehan CJ, Beiko RG.

Curr Biol. 2012 Jan 10;22(1):R20-2. doi: 10.1016/j.cub.2011.11.023. Review.

40.

BioTorrents: a file sharing service for scientific data.

Langille MG, Eisen JA.

PLoS One. 2010 Apr 14;5(4):e10071. doi: 10.1371/journal.pone.0010071.

41.

Detecting genomic islands using bioinformatics approaches.

Langille MG, Hsiao WW, Brinkman FS.

Nat Rev Microbiol. 2010 May;8(5):373-82. doi: 10.1038/nrmicro2350. Review.

PMID:
20395967
42.

The association of virulence factors with genomic islands.

Ho Sui SJ, Fedynak A, Hsiao WW, Langille MG, Brinkman FS.

PLoS One. 2009 Dec 1;4(12):e8094. doi: 10.1371/journal.pone.0008094.

43.

IslandViewer: an integrated interface for computational identification and visualization of genomic islands.

Langille MG, Brinkman FS.

Bioinformatics. 2009 Mar 1;25(5):664-5. doi: 10.1093/bioinformatics/btp030. Epub 2009 Jan 16.

44.

Bioinformatic detection of horizontally transferred DNA in bacterial genomes.

Langille MG, Brinkman FS.

F1000 Biol Rep. 2009 Mar 24;1:25. doi: 10.3410/B1-25.

45.

Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa.

Winstanley C, Langille MG, Fothergill JL, Kukavica-Ibrulj I, Paradis-Bleau C, Sanschagrin F, Thomson NR, Winsor GL, Quail MA, Lennard N, Bignell A, Clarke L, Seeger K, Saunders D, Harris D, Parkhill J, Hancock RE, Brinkman FS, Levesque RC.

Genome Res. 2009 Jan;19(1):12-23. doi: 10.1101/gr.086082.108. Epub 2008 Dec 1.

46.

Evaluation of genomic island predictors using a comparative genomics approach.

Langille MG, Hsiao WW, Brinkman FS.

BMC Bioinformatics. 2008 Aug 5;9:329. doi: 10.1186/1471-2105-9-329.

47.

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