Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

(2020) Kishwar Shafin et al.   NATURE BIOTECHNOLOGY

DNA Features Viewer: a sequence annotation formatting and plotting library for Python

(2020) Valentin Zulkower et al.   BIOINFORMATICS

HyAsP, a greedy tool for plasmids identification

(2019) Robert Müller et al.   BIOINFORMATICS

Plasmid detection and assembly in genomic and metagenomic datasets

(2019) Dmitry Antipov et al.   GENOME RESEARCH

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Toxins, Targets, and Triggers: An Overview of Toxin-Antitoxin Biology

(2018) Alexander Harms et al.   MOLECULAR CELL

PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures

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

PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads

(2018) Märt Roosaare et al.   PeerJ

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

pYR4 From a Norwegian Isolate of Yersinia ruckeri Is a Putative Virulence Plasmid Encoding Both a Type IV Pilus and a Type IV Secretion System

(2018) Agnieszka Wrobel et al.   Frontiers in Cellular and Infection Microbiology

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Ordering the mob: Insights into replicon and MOB typing schemes from analysis of a curated dataset of publicly available plasmids

(2017) Alex Orlek et al.   PLASMID

Mob/oriT, a mobilizable site-specific recombination system for unmarked genetic manipulation in Bacillus thuringiensis and Bacillus cereus

(2016) Pengxia Wang et al.   Microbial Cell Factories

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

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

Toxin Plasmids of Clostridium perfringens

(2013) J. Li et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

A vast collection of microbial genes that are toxic to bacteria

(2012) A. Kimelman et al.   GENOME RESEARCH

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

The stb Operon Balances the Requirements for Vegetative Stability and Conjugative Transfer of Plasmid R388

(2011) Catherine Guynet et al.   PLoS Genetics

cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data

(2010) Fengfeng Zhou et al.   BIOINFORMATICS

Microreview: Type IV secretion systems: versatility and diversity in function

(2010) Karin Wallden et al.   CELLULAR MICROBIOLOGY

The Pseudomonas aeruginosa Pathogenicity Island PAPI-1 Is Transferred via a Novel Type IV Pilus

(2010) M. Q. Carter et al.   JOURNAL OF BACTERIOLOGY

Mobility of Plasmids

(2010) C. Smillie et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Introducing the bacterial ‘chromid’: not a chromosome, not a plasmid

(2010) Peter W. Harrison et al.   TRENDS IN MICROBIOLOGY

An SOS Inhibitor that Binds to Free RecA Protein: The PsiB Protein

(2009) Vessela Petrova et al.   MOLECULAR CELL

ACLAME: A CLAssification of Mobile genetic Elements, update 2010

(2009) Raphaël Leplae et al.   NUCLEIC ACIDS RESEARCH