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Items: 1 to 50 of 52

1.

Fecal source identification using random forest.

Roguet A, Eren AM, Newton RJ, McLellan SL.

Microbiome. 2018 Oct 18;6(1):185. doi: 10.1186/s40168-018-0568-3.

2.

New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes.

Kroeger ME, Delmont TO, Eren AM, Meyer KM, Guo J, Khan K, Rodrigues JLM, Bohannan BJM, Tringe SG, Borges CD, Tiedje JM, Tsai SM, Nüsslein K.

Front Microbiol. 2018 Jul 23;9:1635. doi: 10.3389/fmicb.2018.01635. eCollection 2018.

3.

Author Correction: Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes.

Delmont TO, Quince C, Shaiber A, Esen ÖC, Lee ST, Rappé MS, McLellan SL, Lücker S, Eren AM.

Nat Microbiol. 2018 Aug;3(8):963. doi: 10.1038/s41564-018-0209-4.

PMID:
30042441
4.

Minimizing confounders and increasing data quality in murine models for studies of the gut microbiome.

Miyoshi J, Leone V, Nobutani K, Musch MW, Martinez-Guryn K, Wang Y, Miyoshi S, Bobe AM, Eren AM, Chang EB.

PeerJ. 2018 Jul 12;6:e5166. doi: 10.7717/peerj.5166. eCollection 2018.

5.

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2018 Jul 6;36(7):660. doi: 10.1038/nbt0718-660a. No abstract available.

PMID:
29979671
6.

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes.

Delmont TO, Quince C, Shaiber A, Esen ÖC, Lee ST, Rappé MS, McLellan SL, Lücker S, Eren AM.

Nat Microbiol. 2018 Jul;3(7):804-813. doi: 10.1038/s41564-018-0176-9. Epub 2018 Jun 11. Erratum in: Nat Microbiol. 2018 Aug;3(8):963.

PMID:
29891866
7.

Gut microbes contribute to variation in solid organ transplant outcomes in mice.

McIntosh CM, Chen L, Shaiber A, Eren AM, Alegre ML.

Microbiome. 2018 May 25;6(1):96. doi: 10.1186/s40168-018-0474-8.

8.

Vaginal microbiome in early pregnancy and subsequent risk of spontaneous preterm birth: a case-control study.

Tabatabaei N, Eren AM, Barreiro LB, Yotova V, Dumaine A, Allard C, Fraser WD.

BJOG. 2018 May 23. doi: 10.1111/1471-0528.15299. [Epub ahead of print]

PMID:
29791775
9.

Microbial signals drive pre-leukaemic myeloproliferation in a Tet2-deficient host.

Meisel M, Hinterleitner R, Pacis A, Chen L, Earley ZM, Mayassi T, Pierre JF, Ernest JD, Galipeau HJ, Thuille N, Bouziat R, Buscarlet M, Ringus DL, Wang Y, Li Y, Dinh V, Kim SM, McDonald BD, Zurenski MA, Musch MW, Furtado GC, Lira SA, Baier G, Chang EB, Eren AM, Weber CR, Busque L, Godley LA, Verdú EF, Barreiro LB, Jabri B.

Nature. 2018 May;557(7706):580-584. doi: 10.1038/s41586-018-0125-z. Epub 2018 May 16.

10.

Linking pangenomes and metagenomes: the Prochlorococcus metapangenome.

Delmont TO, Eren AM.

PeerJ. 2018 Jan 25;6:e4320. doi: 10.7717/peerj.4320. eCollection 2018.

11.

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2018 Feb 6;36(2):196. doi: 10.1038/nbt0218-196a. No abstract available.

12.

Complete Genome Sequence of Hyperthermophilic Archaeon Thermococcus sp. EXT12c, Isolated from the East Pacific Rise 9°N.

Courtine D, Alain K, Georges M, Bienvenu N, Morrison HG, Eren AM, Maignien L.

Genome Announc. 2017 Dec 14;5(50). pii: e01385-17. doi: 10.1128/genomeA.01385-17.

13.

Simulations predict microbial responses in the environment? This environment disagrees retrospectively.

Delmont TO, Eren AM.

Proc Natl Acad Sci U S A. 2017 Oct 24;114(43):E8947-E8949. doi: 10.1073/pnas.1712186114. Epub 2017 Oct 10. No abstract available.

14.

Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents.

Anderson RE, Reveillaud J, Reddington E, Delmont TO, Eren AM, McDermott JM, Seewald JS, Huber JA.

Nat Commun. 2017 Oct 24;8(1):1114. doi: 10.1038/s41467-017-01228-6.

15.

Recurrent patterns of microdiversity in a temperate coastal marine environment.

Chafee M, Fernàndez-Guerra A, Buttigieg PL, Gerdts G, Eren AM, Teeling H, Amann RI.

ISME J. 2018 Jan;12(1):237-252. doi: 10.1038/ismej.2017.165. Epub 2017 Oct 24.

16.

DESMAN: a new tool for de novo extraction of strains from metagenomes.

Quince C, Delmont TO, Raguideau S, Alneberg J, Darling AE, Collins G, Eren AM.

Genome Biol. 2017 Sep 21;18(1):181. doi: 10.1186/s13059-017-1309-9.

17.

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2017 Aug 8;35(8):725-731. doi: 10.1038/nbt.3893.

PMID:
28787424
18.

Peripartum Antibiotics Promote Gut Dysbiosis, Loss of Immune Tolerance, and Inflammatory Bowel Disease in Genetically Prone Offspring.

Miyoshi J, Bobe AM, Miyoshi S, Huang Y, Hubert N, Delmont TO, Eren AM, Leone V, Chang EB.

Cell Rep. 2017 Jul 11;20(2):491-504. doi: 10.1016/j.celrep.2017.06.060.

19.

Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics.

Lee STM, Kahn SA, Delmont TO, Shaiber A, Esen ÖC, Hubert NA, Morrison HG, Antonopoulos DA, Rubin DT, Eren AM.

Microbiome. 2017 May 4;5(1):50. doi: 10.1186/s40168-017-0270-x.

20.

A Few Pseudomonas Oligotypes Dominate in the Meat and Dairy Processing Environment.

Stellato G, Utter DR, Voorhis A, De Angelis M, Eren AM, Ercolini D.

Front Microbiol. 2017 Mar 2;8:264. doi: 10.3389/fmicb.2017.00264. eCollection 2017.

21.

Early Transcriptomic Changes in the Ileal Pouch Provide Insight into the Molecular Pathogenesis of Pouchitis and Ulcerative Colitis.

Huang Y, Dalal S, Antonopoulos D, Hubert N, Raffals LH, Dolan K, Weber C, Messer JS, Jabri B, Bendelac A, Eren AM, Rubin DT, Sogin M, Chang EB.

Inflamm Bowel Dis. 2017 Mar;23(3):366-378. doi: 10.1097/MIB.0000000000001027.

22.

Patient-Specific Bacteroides Genome Variants in Pouchitis.

Vineis JH, Ringus DL, Morrison HG, Delmont TO, Dalal S, Raffals LH, Antonopoulos DA, Rubin DT, Eren AM, Chang EB, Sogin ML.

MBio. 2016 Nov 15;7(6). pii: e01713-16. doi: 10.1128/mBio.01713-16.

23.

Editorial: New Insights into Microbial Ecology through Subtle Nucleotide Variation.

Eren AM, Sogin ML, Maignien L.

Front Microbiol. 2016 Aug 24;7:1318. doi: 10.3389/fmicb.2016.01318. eCollection 2016. No abstract available.

24.

Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes.

Bálint M, Bahram M, Eren AM, Faust K, Fuhrman JA, Lindahl B, O'Hara RB, Öpik M, Sogin ML, Unterseher M, Tedersoo L.

FEMS Microbiol Rev. 2016 Sep;40(5):686-700. doi: 10.1093/femsre/fuw017. Epub 2016 Jun 29. Review.

PMID:
27358393
25.

Bacterial communities in penile skin, male urethra, and vaginas of heterosexual couples with and without bacterial vaginosis.

Zozaya M, Ferris MJ, Siren JD, Lillis R, Myers L, Nsuami MJ, Eren AM, Brown J, Taylor CM, Martin DH.

Microbiome. 2016 Apr 19;4:16. doi: 10.1186/s40168-016-0161-6.

26.
27.

Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea, Antarctica.

Delmont TO, Eren AM, Vineis JH, Post AF.

Front Microbiol. 2015 Oct 26;6:1090. doi: 10.3389/fmicb.2015.01090. eCollection 2015.

28.

Extensive Modulation of the Fecal Metagenome in Children With Crohn's Disease During Exclusive Enteral Nutrition.

Quince C, Ijaz UZ, Loman N, Eren AM, Saulnier D, Russell J, Haig SJ, Calus ST, Quick J, Barclay A, Bertz M, Blaut M, Hansen R, McGrogan P, Russell RK, Edwards CA, Gerasimidis K.

Am J Gastroenterol. 2015 Dec;110(12):1718-29; quiz 1730. doi: 10.1038/ajg.2015.357. Epub 2015 Nov 3.

29.

Anvi'o: an advanced analysis and visualization platform for 'omics data.

Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, Delmont TO.

PeerJ. 2015 Oct 8;3:e1319. doi: 10.7717/peerj.1319. eCollection 2015.

30.

Comparison of Sewage and Animal Fecal Microbiomes by Using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups.

Fisher JC, Eren AM, Green HC, Shanks OC, Morrison HG, Vineis JH, Sogin ML, McLellan SL.

Appl Environ Microbiol. 2015 Oct;81(20):7023-33. doi: 10.1128/AEM.01524-15. Epub 2015 Jul 31.

31.

Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics.

Delmont TO, Eren AM, Maccario L, Prestat E, Esen ÖC, Pelletier E, Le Paslier D, Simonet P, Vogel TM.

Front Microbiol. 2015 Apr 30;6:358. doi: 10.3389/fmicb.2015.00358. eCollection 2015.

32.

The gut microbiota of rural papua new guineans: composition, diversity patterns, and ecological processes.

Martínez I, Stegen JC, Maldonado-Gómez MX, Eren AM, Siba PM, Greenhill AR, Walter J.

Cell Rep. 2015 Apr 28;11(4):527-38. doi: 10.1016/j.celrep.2015.03.049. Epub 2015 Apr 16.

33.

Sewage reflects the microbiomes of human populations.

Newton RJ, McLellan SL, Dila DK, Vineis JH, Morrison HG, Eren AM, Sogin ML.

MBio. 2015 Feb 24;6(2):e02574. doi: 10.1128/mBio.02574-14.

34.

Dynamics of tongue microbial communities with single-nucleotide resolution using oligotyping.

Mark Welch JL, Utter DR, Rossetti BJ, Mark Welch DB, Eren AM, Borisy GG.

Front Microbiol. 2014 Nov 7;5:568. doi: 10.3389/fmicb.2014.00568. eCollection 2014.

35.

Blautia and Prevotella sequences distinguish human and animal fecal pollution in Brazil surface waters.

Koskey AM, Fisher JC, Eren AM, Ponce-Terashima R, Reis MG, Blanton RE, McLellan SL.

Environ Microbiol Rep. 2014 Dec;6(6):696-704. doi: 10.1111/1758-2229.12189. Epub 2014 Jul 9.

36.

Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences.

Eren AM, Morrison HG, Lescault PJ, Reveillaud J, Vineis JH, Sogin ML.

ISME J. 2015 Mar 17;9(4):968-79. doi: 10.1038/ismej.2014.195.

37.

Discovering new indicators of fecal pollution.

McLellan SL, Eren AM.

Trends Microbiol. 2014 Dec;22(12):697-706. doi: 10.1016/j.tim.2014.08.002. Epub 2014 Sep 5. Review.

38.

Oligotyping analysis of the human oral microbiome.

Eren AM, Borisy GG, Huse SM, Mark Welch JL.

Proc Natl Acad Sci U S A. 2014 Jul 15;111(28):E2875-84. doi: 10.1073/pnas.1409644111. Epub 2014 Jun 25.

39.

A single genus in the gut microbiome reflects host preference and specificity.

Eren AM, Sogin ML, Morrison HG, Vineis JH, Fisher JC, Newton RJ, McLellan SL.

ISME J. 2015 Jan;9(1):90-100. doi: 10.1038/ismej.2014.97. Epub 2014 Jun 17.

40.

SeaBase: a multispecies transcriptomic resource and platform for gene network inference.

Fischer AH, Mozzherin D, Eren AM, Lans KD, Wilson N, Cosentino C, Smith J.

Integr Comp Biol. 2014 Jul;54(2):250-63. doi: 10.1093/icb/icu065. Epub 2014 Jun 6.

PMID:
24907201
41.

Humpback whale populations share a core skin bacterial community: towards a health index for marine mammals?

Apprill A, Robbins J, Eren AM, Pack AA, Reveillaud J, Mattila D, Moore M, Niemeyer M, Moore KM, Mincer TJ.

PLoS One. 2014 Mar 26;9(3):e90785. doi: 10.1371/journal.pone.0090785. eCollection 2014.

42.

VAMPS: a website for visualization and analysis of microbial population structures.

Huse SM, Mark Welch DB, Voorhis A, Shipunova A, Morrison HG, Eren AM, Sogin ML.

BMC Bioinformatics. 2014 Feb 5;15:41. doi: 10.1186/1471-2105-15-41.

43.

Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis.

Young VB, Raffals LH, Huse SM, Vital M, Dai D, Schloss PD, Brulc JM, Antonopoulos DA, Arrieta RL, Kwon JH, Reddy KG, Hubert NA, Grim SL, Vineis JH, Dalal S, Morrison HG, Eren AM, Meyer F, Schmidt TM, Tiedje JM, Chang EB, Sogin ML.

Microbiome. 2013 Mar 4;1(1):9. doi: 10.1186/2049-2618-1-9.

44.

Ecological succession and stochastic variation in the assembly of Arabidopsis thaliana phyllosphere communities.

Maignien L, DeForce EA, Chafee ME, Eren AM, Simmons SL.

MBio. 2014 Jan 21;5(1):e00682-13. doi: 10.1128/mBio.00682-13.

45.

Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data.

Eren AM, Maignien L, Sul WJ, Murphy LG, Grim SL, Morrison HG, Sogin ML.

Methods Ecol Evol. 2013 Dec 1;4(12). doi: 10.1111/2041-210X.12114.

46.

A filtering method to generate high quality short reads using illumina paired-end technology.

Eren AM, Vineis JH, Morrison HG, Sogin ML.

PLoS One. 2013 Jun 17;8(6):e66643. doi: 10.1371/journal.pone.0066643. Print 2013. Erratum in: PLoS One. 2013;8(6). doi:10.1371/annotation/afa5c40d-c604-46ae-84c4-82cb92193a5e.

47.

DRISEE overestimates errors in metagenomic sequencing data.

Eren AM, Morrison HG, Huse SM, Sogin ML.

Brief Bioinform. 2014 Sep;15(5):783-7. doi: 10.1093/bib/bbt010. Epub 2013 May 22.

48.

Sewage reflects the distribution of human faecal Lachnospiraceae.

McLellan SL, Newton RJ, Vandewalle JL, Shanks OC, Huse SM, Eren AM, Sogin ML.

Environ Microbiol. 2013 Aug;15(8):2213-27. doi: 10.1111/1462-2920.12092. Epub 2013 Feb 25.

49.

Histamine-2 receptor blockers alter the fecal microbiota in premature infants.

Gupta RW, Tran L, Norori J, Ferris MJ, Eren AM, Taylor CM, Dowd SE, Penn D.

J Pediatr Gastroenterol Nutr. 2013 Apr;56(4):397-400. doi: 10.1097/MPG.0b013e318282a8c2.

PMID:
23254444
50.

Exploring the diversity of Gardnerella vaginalis in the genitourinary tract microbiota of monogamous couples through subtle nucleotide variation.

Eren AM, Zozaya M, Taylor CM, Dowd SE, Martin DH, Ferris MJ.

PLoS One. 2011;6(10):e26732. doi: 10.1371/journal.pone.0026732. Epub 2011 Oct 25.

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