184 related articles for article (PubMed ID: 34871418)
1. Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes.
Andreopoulos WB; Geller AM; Lucke M; Balewski J; Clum A; Ivanova NN; Levy A
Nucleic Acids Res; 2022 Feb; 50(3):e17. PubMed ID: 34871418
[TBL] [Abstract][Full Text] [Related]
2. Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores.
Schwengers O; Barth P; Falgenhauer L; Hain T; Chakraborty T; Goesmann A
Microb Genom; 2020 Oct; 6(10):. PubMed ID: 32579097
[TBL] [Abstract][Full Text] [Related]
3. Classification of bacterial plasmid and chromosome derived sequences using machine learning.
Zou X; Nguyen M; Overbeek J; Cao B; Davis JJ
PLoS One; 2022; 17(12):e0279280. PubMed ID: 36525447
[TBL] [Abstract][Full Text] [Related]
4. PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer.
Tang X; Shang J; Ji Y; Sun Y
Nucleic Acids Res; 2023 Aug; 51(15):e83. PubMed ID: 37427782
[TBL] [Abstract][Full Text] [Related]
5. pYR4 From a Norwegian Isolate of
Wrobel A; Ottoni C; Leo JC; Linke D
Front Cell Infect Microbiol; 2018; 8():373. PubMed ID: 30460204
[TBL] [Abstract][Full Text] [Related]
6. Plasmids Shaped the Recent Emergence of the Major Nosocomial Pathogen Enterococcus faecium.
Arredondo-Alonso S; Top J; McNally A; Puranen S; Pesonen M; Pensar J; Marttinen P; Braat JC; Rogers MRC; van Schaik W; Kaski S; Willems RJL; Corander J; Schürch AC
mBio; 2020 Feb; 11(1):. PubMed ID: 32047136
[No Abstract] [Full Text] [Related]
7. SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies.
Aytan-Aktug D; Grigorjev V; Szarvas J; Clausen PTLC; Munk P; Nguyen M; Davis JJ; Aarestrup FM; Lund O
Microbiol Spectr; 2022 Dec; 10(6):e0264122. PubMed ID: 36377945
[TBL] [Abstract][Full Text] [Related]
8. The sequence of a 1.8-mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways.
Medema MH; Trefzer A; Kovalchuk A; van den Berg M; Müller U; Heijne W; Wu L; Alam MT; Ronning CM; Nierman WC; Bovenberg RA; Breitling R; Takano E
Genome Biol Evol; 2010 Jul; 2():212-24. PubMed ID: 20624727
[TBL] [Abstract][Full Text] [Related]
9. PlasBin-flow: a flow-based MILP algorithm for plasmid contigs binning.
Mane A; Faizrahnemoon M; Vinař T; Brejová B; Chauve C
Bioinformatics; 2023 Jun; 39(39 Suppl 1):i288-i296. PubMed ID: 37387134
[TBL] [Abstract][Full Text] [Related]
10. Identification of the conjugative and mobilizable plasmid fragments in the plasmidome using sequence signatures.
Fang Z; Zhou H
Microb Genom; 2020 Nov; 6(11):. PubMed ID: 33074084
[TBL] [Abstract][Full Text] [Related]
11. Conjugative plasmids interact with insertion sequences to shape the horizontal transfer of antimicrobial resistance genes.
Che Y; Yang Y; Xu X; Břinda K; Polz MF; Hanage WP; Zhang T
Proc Natl Acad Sci U S A; 2021 Feb; 118(6):. PubMed ID: 33526659
[TBL] [Abstract][Full Text] [Related]
12. Plasmer: an Accurate and Sensitive Bacterial Plasmid Prediction Tool Based on Machine Learning of Shared k-mers and Genomic Features.
Zhu Q; Gao S; Xiao B; He Z; Hu S
Microbiol Spectr; 2023 Jun; 11(3):e0464522. PubMed ID: 37191574
[TBL] [Abstract][Full Text] [Related]
13. RFPlasmid: predicting plasmid sequences from short-read assembly data using machine learning.
van der Graaf-van Bloois L; Wagenaar JA; Zomer AL
Microb Genom; 2021 Nov; 7(11):. PubMed ID: 34846288
[TBL] [Abstract][Full Text] [Related]
14. Exploring the evolutionary dynamics of plasmids: the Acinetobacter pan-plasmidome.
Fondi M; Bacci G; Brilli M; Papaleo MC; Mengoni A; Vaneechoutte M; Dijkshoorn L; Fani R
BMC Evol Biol; 2010 Feb; 10():59. PubMed ID: 20181243
[TBL] [Abstract][Full Text] [Related]
15. mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species.
Arredondo-Alonso S; Rogers MRC; Braat JC; Verschuuren TD; Top J; Corander J; Willems RJL; Schürch AC
Microb Genom; 2018 Nov; 4(11):. PubMed ID: 30383524
[TBL] [Abstract][Full Text] [Related]
16. GraphPlas: Refined Classification of Plasmid Sequences Using Assembly Graphs.
Wickramarachchi A; Lin Y
IEEE/ACM Trans Comput Biol Bioinform; 2022; 19(1):57-67. PubMed ID: 34029192
[TBL] [Abstract][Full Text] [Related]
17. Detection of plasmid contigs in draft genome assemblies using customized Kraken databases.
Gomi R; Wyres KL; Holt KE
Microb Genom; 2021 Apr; 7(4):. PubMed ID: 33826492
[TBL] [Abstract][Full Text] [Related]
18. F Plasmids Are the Major Carriers of Antibiotic Resistance Genes in Human-Associated Commensal Escherichia coli.
Stephens C; Arismendi T; Wright M; Hartman A; Gonzalez A; Gill M; Pandori M; Hess D
mSphere; 2020 Aug; 5(4):. PubMed ID: 32759337
[TBL] [Abstract][Full Text] [Related]
19. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing.
Carattoli A; Zankari E; García-Fernández A; Voldby Larsen M; Lund O; Villa L; Møller Aarestrup F; Hasman H
Antimicrob Agents Chemother; 2014 Jul; 58(7):3895-903. PubMed ID: 24777092
[TBL] [Abstract][Full Text] [Related]
20. PlasForest: a homology-based random forest classifier for plasmid detection in genomic datasets.
Pradier L; Tissot T; Fiston-Lavier AS; Bedhomme S
BMC Bioinformatics; 2021 Jun; 22(1):349. PubMed ID: 34174810
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]