Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes

Characteristics of ARG-carrying plasmidome in the cultivable microbial community from wastewater treatment system under high oxytetracycline concentration

(2018) Yanhong Shi et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

KBase: The United States Department of Energy Systems Biology Knowledgebase

(2018) Adam P Arkin et al.   NATURE BIOTECHNOLOGY

Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning

(2018) Zhili He et al.   mBio

Large plasmidome of dairy Lactococcus lactis subsp. lactis biovar diacetylactis FM03P encodes technological functions and appears highly unstable

(2018) Oscar van Mastrigt et al.   BMC GENOMICS

Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation

(2017) Andrew J. King et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Identification of IncA/C Plasmid Replication and Maintenance Genes and Development of a Plasmid Multi-Locus Sequence-Typing Scheme

(2016) Steven J. Hancock et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Diverse gene functions in a soil mobilome

(2016) Wenting Luo et al.   SOIL BIOLOGY & BIOCHEMISTRY

Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community

(2016) Christopher L. Hemme et al.   mBio

Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors

(2015) Mark B. Smith et al.   mBio

Genomic and metabolic analysis of fluoranthene degradation pathway in Celeribacter indicus P73T

(2015) Junwei Cao et al.   Scientific Reports

Comparative metagenomics reveals impact of contaminants on groundwater microbiomes

(2015) Christopher L. Hemme et al.   Frontiers in Microbiology

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

(2015) Julián R. Dib 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

An Improved Method for Including Upper Size Range Plasmids in Metamobilomes

(2014) Anders Norman et al.   PLoS One

An auto-inducible mechanism for ionic liquid resistance in microbial biofuel production

(2014) Thomas L. Ruegg et al.   Nature Communications

Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids

(2014) A. San Millan et al.   Nature Communications

Exploring the role of CheA3 in Desulfovibrio vulgaris Hildenborough motility

(2014) Jayashree Ray et al.   Frontiers in Microbiology

The Comprehensive Antibiotic Resistance Database

(2013) Andrew G. McArthur et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Distribution-Based Clustering: Using Ecology To Refine the Operational Taxonomic Unit

(2013) Sarah P. Preheim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Degradation of acetochlor by consortium of two bacterial strains and cloning of a novel amidase gene involved in acetochlor-degrading pathway

(2013) Yi Li et al.   BIORESOURCE TECHNOLOGY

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

BacMet: antibacterial biocide and metal resistance genes database

(2013) Chandan Pal et al.   NUCLEIC ACIDS RESEARCH

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

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

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

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

(2011) Tong Zhang et al.   PLoS One

Horizontal Gene Exchange in Environmental Microbiota

(2011) Rustam I. Aminov   Frontiers in Microbiology

Circoletto: visualizing sequence similarity with Circos

(2010) N. Darzentas   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Frequency and diversity of small cryptic plasmids in the genus Rahnella

(2010) Wilfried Rozhon et al.   BMC MICROBIOLOGY

Strategies for culture of ‘unculturable’ bacteria

(2010) Sonia R. Vartoukian et al.   FEMS MICROBIOLOGY LETTERS

Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community

(2010) Christopher L Hemme et al.   ISME Journal

Mobility of Plasmids

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

TADB: a web-based resource for Type 2 toxin–antitoxin loci in bacteria and archaea

(2010) Yucheng Shao et al.   NUCLEIC ACIDS RESEARCH

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

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

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

ACLAME: A CLAssification of Mobile genetic Elements, update 2010

(2009) Raphaël Leplae et al.   NUCLEIC ACIDS RESEARCH

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

(2008) F Meyer et al.   BMC BIOINFORMATICS

ARDB--Antibiotic Resistance Genes Database

(2008) B. Liu et al.   NUCLEIC ACIDS RESEARCH