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Items: 1 to 20 of 108

1.

Profiling microbial strains in urban environments using metagenomic sequencing data.

Zolfo M, Asnicar F, Manghi P, Pasolli E, Tett A, Segata N.

Biol Direct. 2018 May 9;13(1):9. doi: 10.1186/s13062-018-0211-z.

2.

Strain-level microbial epidemiology and population genomics from shotgun metagenomics.

Scholz M, Ward DV, Pasolli E, Tolio T, Zolfo M, Asnicar F, Truong DT, Tett A, Morrow AL, Segata N.

Nat Methods. 2016 May;13(5):435-8. doi: 10.1038/nmeth.3802. Epub 2016 Mar 21.

PMID:
26999001
3.

MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach.

Brown BL, Watson M, Minot SS, Rivera MC, Franklin RB.

Gigascience. 2017 Mar 1;6(3):1-10. doi: 10.1093/gigascience/gix007.

4.

PanFP: pangenome-based functional profiles for microbial communities.

Jun SR, Robeson MS, Hauser LJ, Schadt CW, Gorin AA.

BMC Res Notes. 2015 Sep 26;8:479. doi: 10.1186/s13104-015-1462-8.

5.

Uncovering oral Neisseria tropism and persistence using metagenomic sequencing.

Donati C, Zolfo M, Albanese D, Tin Truong D, Asnicar F, Iebba V, Cavalieri D, Jousson O, De Filippo C, Huttenhower C, Segata N.

Nat Microbiol. 2016 May 27;1(7):16070. doi: 10.1038/nmicrobiol.2016.70.

PMID:
27572971
6.

Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome.

Jones BV, Sun F, Marchesi JR.

BMC Genomics. 2010 Jan 19;11:46. doi: 10.1186/1471-2164-11-46.

7.

Species classifier choice is a key consideration when analysing low-complexity food microbiome data.

Walsh AM, Crispie F, O'Sullivan O, Finnegan L, Claesson MJ, Cotter PD.

Microbiome. 2018 Mar 20;6(1):50. doi: 10.1186/s40168-018-0437-0.

8.

MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples.

Zolfo M, Tett A, Jousson O, Donati C, Segata N.

Nucleic Acids Res. 2017 Jan 25;45(2):e7. doi: 10.1093/nar/gkw837. Epub 2016 Sep 19.

9.

Metagenomic characterization of ambulances across the USA.

O'Hara NB, Reed HJ, Afshinnekoo E, Harvin D, Caplan N, Rosen G, Frye B, Woloszynek S, Ounit R, Levy S, Butler E, Mason CE.

Microbiome. 2017 Sep 22;5(1):125. doi: 10.1186/s40168-017-0339-6.

10.

Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation.

Beaulaurier J, Zhu S, Deikus G, Mogno I, Zhang XS, Davis-Richardson A, Canepa R, Triplett EW, Faith JJ, Sebra R, Schadt EE, Fang G.

Nat Biotechnol. 2018 Jan;36(1):61-69. doi: 10.1038/nbt.4037. Epub 2017 Dec 11.

11.

HuMiChip2 for strain level identification and functional profiling of human microbiomes.

Tu Q, Li J, Shi Z, Chen Y, Lin L, Li J, Wang H, Yan J, Zhou Q, Li X, Li L, Zhou J, He Z.

Appl Microbiol Biotechnol. 2017 Jan;101(1):423-435. doi: 10.1007/s00253-016-7910-0. Epub 2016 Oct 12.

12.

Metagenomics: Probing pollutant fate in natural and engineered ecosystems.

Bouhajja E, Agathos SN, George IF.

Biotechnol Adv. 2016 Dec;34(8):1413-1426. doi: 10.1016/j.biotechadv.2016.10.006. Epub 2016 Nov 5. Review.

PMID:
27825829
13.

The evolutionary signal in metagenome phyletic profiles predicts many gene functions.

Vidulin V, Šmuc T, Džeroski S, Supek F.

Microbiome. 2018 Jul 10;6(1):129. doi: 10.1186/s40168-018-0506-4.

14.

Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis.

Dubinkina VB, Ischenko DS, Ulyantsev VI, Tyakht AV, Alexeev DG.

BMC Bioinformatics. 2016 Jan 16;17:38. doi: 10.1186/s12859-015-0875-7.

15.

Strain/species identification in metagenomes using genome-specific markers.

Tu Q, He Z, Zhou J.

Nucleic Acids Res. 2014 Apr;42(8):e67. doi: 10.1093/nar/gku138. Epub 2014 Feb 12.

16.

Selection of marker genes for genetic barcoding of microorganisms and binning of metagenomic reads by Barcoder software tools.

Rotimi AM, Pierneef R, Reva ON.

BMC Bioinformatics. 2018 Aug 30;19(1):309. doi: 10.1186/s12859-018-2320-1.

17.

A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes.

Gkanogiannis A, Gazut S, Salanoubat M, Kanj S, Brüls T.

BMC Bioinformatics. 2016 Aug 19;17(1):311. doi: 10.1186/s12859-016-1186-3.

18.

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography.

Nayfach S, Rodriguez-Mueller B, Garud N, Pollard KS.

Genome Res. 2016 Nov;26(11):1612-1625. Epub 2016 Oct 18.

19.

Strain-Level Metagenomic Analysis of the Fermented Dairy Beverage Nunu Highlights Potential Food Safety Risks.

Walsh AM, Crispie F, Daari K, O'Sullivan O, Martin JC, Arthur CT, Claesson MJ, Scott KP, Cotter PD.

Appl Environ Microbiol. 2017 Aug 1;83(16). pii: e01144-17. doi: 10.1128/AEM.01144-17. Print 2017 Aug 15.

20.

Vikodak--A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets.

Nagpal S, Haque MM, Mande SS.

PLoS One. 2016 Feb 5;11(2):e0148347. doi: 10.1371/journal.pone.0148347. eCollection 2016.

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