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Items: 1 to 20 of 132

1.

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.

2.

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.

3.

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.

PMID:
27734124
4.

Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes.

Wang M, Doak TG, Ye Y.

Genome Biol. 2015 Nov 2;16:243. doi: 10.1186/s13059-015-0804-0.

5.

Recovering complete and draft population genomes from metagenome datasets.

Sangwan N, Xia F, Gilbert JA.

Microbiome. 2016 Mar 8;4:8. doi: 10.1186/s40168-016-0154-5. Review.

6.

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.

Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW.

Genome Res. 2015 Jul;25(7):1043-55. doi: 10.1101/gr.186072.114. Epub 2015 May 14.

7.

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets.

Wu YW, Simmons BA, Singer SW.

Bioinformatics. 2016 Feb 15;32(4):605-7. doi: 10.1093/bioinformatics/btv638. Epub 2015 Oct 29.

PMID:
26515820
8.

Strain/species-specific probe design for microbial identification microarrays.

Tu Q, He Z, Deng Y, Zhou J.

Appl Environ Microbiol. 2013 Aug;79(16):5085-8. doi: 10.1128/AEM.01124-13. Epub 2013 Jun 7.

9.

MetaGeniE: characterizing human clinical samples using deep metagenomic sequencing.

Rawat A, Engelthaler DM, Driebe EM, Keim P, Foster JT.

PLoS One. 2014 Nov 3;9(11):e110915. doi: 10.1371/journal.pone.0110915. eCollection 2014.

10.

Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing.

Tsai YC, Conlan S, Deming C; NISC Comparative Sequencing Program, Segre JA, Kong HH, Korlach J, Oh J.

MBio. 2016 Feb 9;7(1):e01948-15. doi: 10.1128/mBio.01948-15.

11.

Using populations of human and microbial genomes for organism detection in metagenomes.

Ames SK, Gardner SN, Marti JM, Slezak TR, Gokhale MB, Allen JE.

Genome Res. 2015 Jul;25(7):1056-67. doi: 10.1101/gr.184879.114. Epub 2015 Apr 29.

12.

Estimating DNA coverage and abundance in metagenomes using a gamma approximation.

Hooper SD, Dalevi D, Pati A, Mavromatis K, Ivanova NN, Kyrpides NC.

Bioinformatics. 2010 Feb 1;26(3):295-301. doi: 10.1093/bioinformatics/btp687. Epub 2009 Dec 14.

13.

Further analysis reveals new gut microbiome markers of type 2 diabetes mellitus.

Wang X, Xu X, Xia Y.

Antonie Van Leeuwenhoek. 2017 Mar;110(3):445-453. doi: 10.1007/s10482-016-0805-3. Epub 2016 Dec 10.

PMID:
27943013
14.

Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities.

Suenaga H.

Environ Microbiol. 2012 Jan;14(1):13-22. doi: 10.1111/j.1462-2920.2011.02438.x. Epub 2011 Mar 1. Review.

PMID:
21366818
15.

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.

16.

Intrinsic correlation of oligonucleotides: a novel genomic signature for metagenome analysis.

Ding X, Cao CC, Sun X.

J Theor Biol. 2014 Jul 21;353:9-18. doi: 10.1016/j.jtbi.2014.02.039. Epub 2014 Mar 11.

PMID:
24631045
17.

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.

18.

MetaID: a novel method for identification and quantification of metagenomic samples.

Srinivasan SM, Guda C.

BMC Genomics. 2013;14 Suppl 8:S4. doi: 10.1186/1471-2164-14-S8-S4. Epub 2013 Dec 9.

19.

A metagenome-wide association study of gut microbiota in type 2 diabetes.

Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, Liang S, Zhang W, Guan Y, Shen D, Peng Y, Zhang D, Jie Z, Wu W, Qin Y, Xue W, Li J, Han L, Lu D, Wu P, Dai Y, Sun X, Li Z, Tang A, Zhong S, Li X, Chen W, Xu R, Wang M, Feng Q, Gong M, Yu J, Zhang Y, Zhang M, Hansen T, Sanchez G, Raes J, Falony G, Okuda S, Almeida M, LeChatelier E, Renault P, Pons N, Batto JM, Zhang Z, Chen H, Yang R, Zheng W, Li S, Yang H, Wang J, Ehrlich SD, Nielsen R, Pedersen O, Kristiansen K, Wang J.

Nature. 2012 Oct 4;490(7418):55-60. doi: 10.1038/nature11450. Epub 2012 Sep 26.

PMID:
23023125
20.

Recruiting human microbiome shotgun data to site-specific reference genomes.

Xie G, Lo CC, Scholz M, Chain PS.

PLoS One. 2014 Jan 15;9(1):e84963. doi: 10.1371/journal.pone.0084963. eCollection 2014.

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