PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures

Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!

(2017) John Vollmers et al.   PLoS One

Analysis of the Genome and Mobilome of a Dissimilatory Arsenate Reducing Aeromonas sp. O23A Reveals Multiple Mechanisms for Heavy Metal Resistance and Metabolism

(2017) Witold Uhrynowski et al.   Frontiers in Microbiology

A network-driven approach for genome-wide association mapping

(2016) Seunghak Lee et al.   BIOINFORMATICS

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

Physiological and Metagenomic Analyses of Microbial Mats Involved in Self-Purification of Mine Waters Contaminated with Heavy Metals

(2016) Lukasz Drewniak et al.   Frontiers in Microbiology

Review of Antimicrobial Resistance in the Environment and Its Relevance to Environmental Regulators

(2016) Andrew C. Singer et al.   Frontiers in Microbiology

TensorFlow: Biology’s Gateway to Deep Learning?

(2016) Ladislav Rampasek et al.   Cell Systems

Classification of Metagenomics Data at Lower Taxonomic Level Using a Robust Supervised Classifier

(2015) Tao Hou et al.   Evolutionary Bioinformatics

Bacterial clade with the ribosomal RNA operon on a small plasmid rather than the chromosome

(2015) Mizue Anda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Strategies and approaches in plasmidome studies—uncovering plasmid diversity disregarding of linear elements?

(2015) Julián R. Dib et al.   Frontiers in Microbiology

Exploring antibiotic resistance genes and metal resistance genes in plasmid metagenomes from wastewater treatment plants

(2015) An-Dong Li 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

Hundreds of Circular Novel Plasmids and DNA Elements Identified in a Rat Cecum Metamobilome

(2014) Tue Sparholt Jørgensen et al.   PLoS One

Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences

(2014) Val F. Lanza et al.   PLoS Genetics

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Plasmids and the spread of resistance

(2013) Alessandra Carattoli   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Community-wide plasmid gene mobilization and selection

(2013) Vladimir Sentchilo et al.   ISME Journal

A method for purifying high quality and high yield plasmid DNA for metagenomic and deep sequencing approaches

(2013) Aya Brown Kav et al.   JOURNAL OF MICROBIOLOGICAL METHODS

The plasmidome of a Salmonella enterica serovar Derby isolated from pork meat

(2013) Anne Bleicher et al.   PLASMID

Plasmidome-Analysis of ESBL-Producing Escherichia coli Using Conventional Typing and High-Throughput Sequencing

(2013) Alma Brolund et al.   PLoS One

Mobile elements, zoonotic pathogens and commensal bacteria: conduits for the delivery of resistance genes into humans, production animals and soil microbiota

(2013) Steven P. Djordjevic et al.   Frontiers in Microbiology

Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands

(2012) Jon Bohlin et al.   BMC GENOMICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Insights into the bovine rumen plasmidome

(2012) A. B. Kav et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Taxonomic metagenome sequence assignment with structured output models

(2011) Kaustubh R Patil et al.   NATURE METHODS

Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition

(2011) Isaam Saeed et al.   NUCLEIC ACIDS RESEARCH

Pyrosequencing of Antibiotic-Contaminated River Sediments Reveals High Levels of Resistance and Gene Transfer Elements

(2011) Erik Kristiansson et al.   PLoS One

Plasmid Metagenome Reveals High Levels of Antibiotic Resistance Genes and Mobile Genetic Elements in Activated Sludge

(2011) Tong Zhang et al.   PLoS One

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

(2010) Fengfeng Zhou et al.   BIOINFORMATICS

Exploring the evolutionary dynamics of plasmids: the Acinetobacter pan-plasmidome

(2010) Marco Fondi et al.   BMC EVOLUTIONARY BIOLOGY

Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome

(2010) Brian V Jones et al.   BMC GENOMICS

Mobility of Plasmids

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

A Primer on Metagenomics

(2010) John C. Wooley et al.   PLoS Computational Biology

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Metagenomic signatures of 86 microbial and viral metagenomes

(2009) Dana Willner et al.   ENVIRONMENTAL MICROBIOLOGY

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

Barcodes for genomes and applications

(2008) Fengfeng Zhou et al.   BMC BIOINFORMATICS

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes

(2008) Jon Bohlin et al.   BMC GENOMICS

Patchy distribution of flexible genetic elements in bacterial populations mediates robustness to environmental uncertainty

(2008) Holger Heuer et al.   FEMS MICROBIOLOGY ECOLOGY

Insight into the plasmid metagenome of wastewater treatment plant bacteria showing reduced susceptibility to antimicrobial drugs analysed by the 454-pyrosequencing technology

(2008) Rafael Szczepanowski et al.   JOURNAL OF BIOTECHNOLOGY

Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes

(2008) Haruo Suzuki et al.   NUCLEIC ACIDS RESEARCH

Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes

(2008) Jon Bohlin et al.   PLoS Computational Biology