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Items: 1 to 20 of 97

1.

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC.

Nat Methods. 2017 Nov;14(11):1063-1071. doi: 10.1038/nmeth.4458. Epub 2017 Oct 2.

2.

CAMISIM: simulating metagenomes and microbial communities.

Fritz A, Hofmann P, Majda S, Dahms E, Dröge J, Fiedler J, Lesker TR, Belmann P, DeMaere MZ, Darling AE, Sczyrba A, Bremges A, McHardy AC.

Microbiome. 2019 Feb 8;7(1):17. doi: 10.1186/s40168-019-0633-6.

3.

AMBER: Assessment of Metagenome BinnERs.

Meyer F, Hofmann P, Belmann P, Garrido-Oter R, Fritz A, Sczyrba A, McHardy AC.

Gigascience. 2018 Jun 1;7(6). doi: 10.1093/gigascience/giy069.

4.

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.

5.

Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes.

Papudeshi B, Haggerty JM, Doane M, Morris MM, Walsh K, Beattie DT, Pande D, Zaeri P, Silva GGZ, Thompson F, Edwards RA, Dinsdale EA.

BMC Genomics. 2017 Nov 28;18(1):915. doi: 10.1186/s12864-017-4294-1.

6.

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.

7.

Assessing taxonomic metagenome profilers with OPAL.

Meyer F, Bremges A, Belmann P, Janssen S, McHardy AC, Koslicki D.

Genome Biol. 2019 Mar 4;20(1):51. doi: 10.1186/s13059-019-1646-y.

8.

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.

9.

Taxonomic binning of metagenome samples generated by next-generation sequencing technologies.

Dröge J, McHardy AC.

Brief Bioinform. 2012 Nov;13(6):646-55. doi: 10.1093/bib/bbs031. Epub 2012 Jul 31.

PMID:
22851513
10.

Large-scale machine learning for metagenomics sequence classification.

Vervier K, Mahé P, Tournoud M, Veyrieras JB, Vert JP.

Bioinformatics. 2016 Apr 1;32(7):1023-32. doi: 10.1093/bioinformatics/btv683. Epub 2015 Nov 20.

11.

Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods.

Dröge J, Gregor I, McHardy AC.

Bioinformatics. 2015 Mar 15;31(6):817-24. doi: 10.1093/bioinformatics/btu745. Epub 2014 Nov 10.

12.

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
13.

Classification of metagenomic sequences: methods and challenges.

Mande SS, Mohammed MH, Ghosh TS.

Brief Bioinform. 2012 Nov;13(6):669-81. doi: 10.1093/bib/bbs054. Epub 2012 Sep 8. Review.

PMID:
22962338
14.

MetaCluster-TA: taxonomic annotation for metagenomic data based on assembly-assisted binning.

Wang Y, Leung H, Yiu S, Chin F.

BMC Genomics. 2014;15 Suppl 1:S12. doi: 10.1186/1471-2164-15-S1-S12. Epub 2014 Jan 24.

15.

ICoVeR - an interactive visualization tool for verification and refinement of metagenomic bins.

Broeksema B, Calusinska M, McGee F, Winter K, Bongiovanni F, Goux X, Wilmes P, Delfosse P, Ghoniem M.

BMC Bioinformatics. 2017 May 2;18(1):233. doi: 10.1186/s12859-017-1653-5.

16.

Exploiting topic modeling to boost metagenomic reads binning.

Zhang R, Cheng Z, Guan J, Zhou S.

BMC Bioinformatics. 2015;16 Suppl 5:S2. doi: 10.1186/1471-2105-16-S5-S2. Epub 2015 Mar 18.

17.

Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist's Perspective - Not Only Size Matters!

Vollmers J, Wiegand S, Kaster AK.

PLoS One. 2017 Jan 18;12(1):e0169662. doi: 10.1371/journal.pone.0169662. eCollection 2017.

18.

Binning metagenomic contigs by coverage and composition.

Alneberg J, Bjarnason BS, de Bruijn I, Schirmer M, Quick J, Ijaz UZ, Lahti L, Loman NJ, Andersson AF, Quince C.

Nat Methods. 2014 Nov;11(11):1144-6. doi: 10.1038/nmeth.3103. Epub 2014 Sep 14.

PMID:
25218180
19.

MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling.

Piro VC, Matschkowski M, Renard BY.

Microbiome. 2017 Aug 14;5(1):101. doi: 10.1186/s40168-017-0318-y.

20.

CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision.

Herath D, Tang SL, Tandon K, Ackland D, Halgamuge SK.

BMC Bioinformatics. 2017 Dec 28;18(Suppl 16):571. doi: 10.1186/s12859-017-1967-3.

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