146 related articles for article (PubMed ID: 31581946)
1. A machine learning-based service for estimating quality of genomes using PATRIC.
Parrello B; Butler R; Chlenski P; Olson R; Overbeek J; Pusch GD; Vonstein V; Overbeek R
BMC Bioinformatics; 2019 Oct; 20(1):486. PubMed ID: 31581946
[TBL] [Abstract][Full Text] [Related]
2. Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC.
Parrello B; Butler R; Chlenski P; Pusch GD; Overbeek R
PLoS One; 2021; 16(4):e0250092. PubMed ID: 33857229
[TBL] [Abstract][Full Text] [Related]
3. 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. PubMed ID: 25977477
[TBL] [Abstract][Full Text] [Related]
4. 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]
5. MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function.
Keegan KP; Glass EM; Meyer F
Methods Mol Biol; 2016; 1399():207-33. PubMed ID: 26791506
[TBL] [Abstract][Full Text] [Related]
6. PATRIC as a unique resource for studying antimicrobial resistance.
Antonopoulos DA; Assaf R; Aziz RK; Brettin T; Bun C; Conrad N; Davis JJ; Dietrich EM; Disz T; Gerdes S; Kenyon RW; Machi D; Mao C; Murphy-Olson DE; Nordberg EK; Olsen GJ; Olson R; Overbeek R; Parrello B; Pusch GD; Santerre J; Shukla M; Stevens RL; VanOeffelen M; Vonstein V; Warren AS; Wattam AR; Xia F; Yoo H
Brief Bioinform; 2019 Jul; 20(4):1094-1102. PubMed ID: 28968762
[TBL] [Abstract][Full Text] [Related]
7. MetaVW: Large-Scale Machine Learning for Metagenomics Sequence Classification.
Vervier K; Mahé P; Vert JP
Methods Mol Biol; 2018; 1807():9-20. PubMed ID: 30030800
[TBL] [Abstract][Full Text] [Related]
8. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST).
Overbeek R; Olson R; Pusch GD; Olsen GJ; Davis JJ; Disz T; Edwards RA; Gerdes S; Parrello B; Shukla M; Vonstein V; Wattam AR; Xia F; Stevens R
Nucleic Acids Res; 2014 Jan; 42(Database issue):D206-14. PubMed ID: 24293654
[TBL] [Abstract][Full Text] [Related]
9. EvalDNA: a machine learning-based tool for the comprehensive evaluation of mammalian genome assembly quality.
MacDonald ML; Lee KH
BMC Bioinformatics; 2021 Nov; 22(1):570. PubMed ID: 34837948
[TBL] [Abstract][Full Text] [Related]
10. MEGAnnotator: a user-friendly pipeline for microbial genomes assembly and annotation.
Lugli GA; Milani C; Mancabelli L; van Sinderen D; Ventura M
FEMS Microbiol Lett; 2016 Apr; 363(7):. PubMed ID: 26936607
[TBL] [Abstract][Full Text] [Related]
11. Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center.
Wattam AR; Brettin T; Davis JJ; Gerdes S; Kenyon R; Machi D; Mao C; Olson R; Overbeek R; Pusch GD; Shukla MP; Stevens R; Vonstein V; Warren A; Xia F; Yoo H
Methods Mol Biol; 2018; 1704():79-101. PubMed ID: 29277864
[TBL] [Abstract][Full Text] [Related]
12. Removing contaminants from databases of draft genomes.
Lu J; Salzberg SL
PLoS Comput Biol; 2018 Jun; 14(6):e1006277. PubMed ID: 29939994
[TBL] [Abstract][Full Text] [Related]
13. Antimicrobial Resistance Prediction in PATRIC and RAST.
Davis JJ; Boisvert S; Brettin T; Kenyon RW; Mao C; Olson R; Overbeek R; Santerre J; Shukla M; Wattam AR; Will R; Xia F; Stevens R
Sci Rep; 2016 Jun; 6():27930. PubMed ID: 27297683
[TBL] [Abstract][Full Text] [Related]
14. Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center.
Wattam AR; Davis JJ; Assaf R; Boisvert S; Brettin T; Bun C; Conrad N; Dietrich EM; Disz T; Gabbard JL; Gerdes S; Henry CS; Kenyon RW; Machi D; Mao C; Nordberg EK; Olsen GJ; Murphy-Olson DE; Olson R; Overbeek R; Parrello B; Pusch GD; Shukla M; Vonstein V; Warren A; Xia F; Yoo H; Stevens RL
Nucleic Acids Res; 2017 Jan; 45(D1):D535-D542. PubMed ID: 27899627
[TBL] [Abstract][Full Text] [Related]
15. A RESTful API for accessing microbial community data for MG-RAST.
Wilke A; Bischof J; Harrison T; Brettin T; D'Souza M; Gerlach W; Matthews H; Paczian T; Wilkening J; Glass EM; Desai N; Meyer F
PLoS Comput Biol; 2015 Jan; 11(1):e1004008. PubMed ID: 25569221
[TBL] [Abstract][Full Text] [Related]
16. Human contamination in bacterial genomes has created thousands of spurious proteins.
Breitwieser FP; Pertea M; Zimin AV; Salzberg SL
Genome Res; 2019 Jun; 29(6):954-960. PubMed ID: 31064768
[TBL] [Abstract][Full Text] [Related]
17. Accessing the SEED genome databases via Web services API: tools for programmers.
Disz T; Akhter S; Cuevas D; Olson R; Overbeek R; Vonstein V; Stevens R; Edwards RA
BMC Bioinformatics; 2010 Jun; 11():319. PubMed ID: 20546611
[TBL] [Abstract][Full Text] [Related]
18. PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database.
Davis JJ; Gerdes S; Olsen GJ; Olson R; Pusch GD; Shukla M; Vonstein V; Wattam AR; Yoo H
Front Microbiol; 2016; 7():118. PubMed ID: 26903996
[TBL] [Abstract][Full Text] [Related]
19. COGNIZER: A Framework for Functional Annotation of Metagenomic Datasets.
Bose T; Haque MM; Reddy C; Mande SS
PLoS One; 2015; 10(11):e0142102. PubMed ID: 26561344
[TBL] [Abstract][Full Text] [Related]
20. CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning.
Chklovski A; Parks DH; Woodcroft BJ; Tyson GW
Nat Methods; 2023 Aug; 20(8):1203-1212. PubMed ID: 37500759
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]