HOTSPOT: hierarchical host prediction for assembled plasmid contigs with transformer

Critical Assessment of Metagenome Interpretation: the second round of challenges

(2022) Fernando Meyer et al.   NATURE METHODS

PlasmidHostFinder: Prediction of Plasmid Hosts Using Random Forest

(2022) Derya Aytan-Aktug et al.   mSystems

COPLA, a taxonomic classifier of plasmids

(2021) Santiago Redondo-Salvo et al.   BMC BIOINFORMATICS

Large-scale network analysis captures biological features of bacterial plasmids

(2020) Mislav Acman et al.   Nature Communications

Analysis of COMPASS, a New Comprehensive Plasmid Database Revealed Prevalence of Multireplicon and Extensive Diversity of IncF Plasmids

(2020) Pierre-Emmanuel Douarre et al.   Frontiers in Microbiology

Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids

(2020) Santiago Redondo-Salvo et al.   Nature Communications

Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores

(2020) Oliver Schwengers et al.   Microbial Genomics

Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance

(2020) James Robertson et al.   Microbial Genomics

Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands

(2020) Finlay Maguire et al.   Microbial Genomics

Linking the resistome and plasmidome to the microbiome

(2019) Thibault Stalder et al.   ISME Journal

PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures

(2018) Pawel S Krawczyk et al.   NUCLEIC ACIDS RESEARCH

Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation

(2017) John Beaulaurier et al.   NATURE BIOTECHNOLOGY

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy

(2015) Masaki Shintani et al.   Frontiers in Microbiology

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community

(2014) Uli Klümper et al.   ISME Journal

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Strain/species identification in metagenomes using genome-specific markers

(2014) Qichao Tu et al.   NUCLEIC ACIDS RESEARCH

Broad host range plasmids

(2013) Aayushi Jain et al.   FEMS MICROBIOLOGY LETTERS

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

Mobilizable narrow host range plasmids as natural suicide vectors enabling horizontal gene transfer among distantly related bacterial species

(2011) Maria Smorawinska et al.   FEMS MICROBIOLOGY LETTERS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

What traits are carried on mobile genetic elements and why?

(2010) D J Rankin et al.   HEREDITY