690 related articles for article (PubMed ID: 29227468)
1. 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. PubMed ID: 29227468
[TBL] [Abstract][Full Text] [Related]
2. Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands.
Maguire F; Jia B; Gray KL; Lau WYV; Beiko RG; Brinkman FSL
Microb Genom; 2020 Oct; 6(10):. PubMed ID: 33001022
[TBL] [Abstract][Full Text] [Related]
3. Evaluating
Vosloo S; Huo L; Anderson CL; Dai Z; Sevillano M; Pinto A
Microbiol Spectr; 2021 Dec; 9(3):e0143421. PubMed ID: 34730411
[TBL] [Abstract][Full Text] [Related]
4. 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; 18(1):915. PubMed ID: 29183281
[TBL] [Abstract][Full Text] [Related]
5. Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system.
Somerville V; Lutz S; Schmid M; Frei D; Moser A; Irmler S; Frey JE; Ahrens CH
BMC Microbiol; 2019 Jun; 19(1):143. PubMed ID: 31238873
[TBL] [Abstract][Full Text] [Related]
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; 17(1):311. PubMed ID: 27542753
[TBL] [Abstract][Full Text] [Related]
7. 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. PubMed ID: 25218180
[TBL] [Abstract][Full Text] [Related]
8. Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes.
Lin HH; Liao YC
Sci Rep; 2016 Apr; 6():24175. PubMed ID: 27067514
[TBL] [Abstract][Full Text] [Related]
9. Accurate Binning of Metagenomic Contigs Using Composition, Coverage, and Assembly Graphs.
Mallawaarachchi V; Lin Y
J Comput Biol; 2022 Dec; 29(12):1357-1376. PubMed ID: 36367700
[TBL] [Abstract][Full Text] [Related]
10. 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; 19(1):309. PubMed ID: 30165813
[TBL] [Abstract][Full Text] [Related]
11. Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets.
Yue Y; Huang H; Qi Z; Dou HM; Liu XY; Han TF; Chen Y; Song XJ; Zhang YH; Tu J
BMC Bioinformatics; 2020 Jul; 21(1):334. PubMed ID: 32723290
[TBL] [Abstract][Full Text] [Related]
12. HiFine: integrating Hi-C-based and shotgun-based methods to refine binning of metagenomic contigs.
Du Y; Sun F
Bioinformatics; 2022 May; 38(11):2973-2979. PubMed ID: 35482530
[TBL] [Abstract][Full Text] [Related]
13. Unsupervised Binning of Metagenomic Assembled Contigs Using Improved Fuzzy C-Means Method.
Liu Y; Hou T; Kang B; Liu F
IEEE/ACM Trans Comput Biol Bioinform; 2017; 14(6):1459-1467. PubMed ID: 27295684
[TBL] [Abstract][Full Text] [Related]
14. 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; 18(Suppl 16):571. PubMed ID: 29297295
[TBL] [Abstract][Full Text] [Related]
15. Generation of a Metagenomics Proximity Ligation 3C Library of a Mammalian Gut Microbiota.
Foutel-Rodier T; Thierry A; Koszul R; Marbouty M
Methods Enzymol; 2018; 612():183-195. PubMed ID: 30502941
[TBL] [Abstract][Full Text] [Related]
16. A new metagenome binning method based on gene uniqueness.
Kang Y; Wan C; Lu S; Fu Z; Chen AK; Lu Z
Genes Genomics; 2020 Aug; 42(8):883-892. PubMed ID: 32506266
[TBL] [Abstract][Full Text] [Related]
17. CoCoNet: an efficient deep learning tool for viral metagenome binning.
Arisdakessian CG; Nigro OD; Steward GF; Poisson G; Belcaid M
Bioinformatics; 2021 Sep; 37(18):2803-2810. PubMed ID: 33822891
[TBL] [Abstract][Full Text] [Related]
18. GraphBin: refined binning of metagenomic contigs using assembly graphs.
Mallawaarachchi V; Wickramarachchi A; Lin Y
Bioinformatics; 2020 Jun; 36(11):3307-3313. PubMed ID: 32167528
[TBL] [Abstract][Full Text] [Related]
19. Recovery of strain-resolved genomes from human microbiome through an integration framework of single-cell genomics and metagenomics.
Arikawa K; Ide K; Kogawa M; Saeki T; Yoda T; Endoh T; Matsuhashi A; Takeyama H; Hosokawa M
Microbiome; 2021 Oct; 9(1):202. PubMed ID: 34641955
[TBL] [Abstract][Full Text] [Related]
20. Improved metagenome binning and assembly using deep variational autoencoders.
Nissen JN; Johansen J; Allesøe RL; Sønderby CK; Armenteros JJA; Grønbech CH; Jensen LJ; Nielsen HB; Petersen TN; Winther O; Rasmussen S
Nat Biotechnol; 2021 May; 39(5):555-560. PubMed ID: 33398153
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
