MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data

Effects of a Saccharomyces cerevisiae fermentation product on liver abscesses, fecal microbiome, and resistome in feedlot cattle raised without antibiotics

(2019) Katherine L. Huebner et al.   Scientific Reports

Identification and reconstruction of novel antibiotic resistance genes from metagenomes

(2019) Fanny Berglund et al.   Microbiome

Macrolide Resistance in MORDOR I — A Cluster-Randomized Trial in Niger

(2019) Thuy Doan et al.   NEW ENGLAND JOURNAL OF MEDICINE

Antibiotic-Resistance Genes in Waste Water

(2018) Antti Karkman et al.   TRENDS IN MICROBIOLOGY

The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants—but not always

(2018) Johan Bengtsson-Palme   Microbiome

Investigating Effects of Tulathromycin Metaphylaxis on the Fecal Resistome and Microbiome of Commercial Feedlot Cattle Early in the Feeding Period

(2018) Enrique Doster et al.   Frontiers in Microbiology

Prediction of the intestinal resistome by a three-dimensional structure-based method

(2018) Etienne Ruppé et al.   Nature Microbiology

Antibiotic resistome in a large-scale healthy human gut microbiota deciphered by metagenomic and network analyses

(2017) Jie Feng et al.   ENVIRONMENTAL MICROBIOLOGY

Unexpected persistence of extended-spectrum β-lactamase-producing Enterobacteriaceae in the faecal microbiota of hospitalised patients treated with imipenem

(2017) N. Grall et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

Sampling the mobile gene pool: innovation via horizontal gene transfer in bacteria

(2017) James P. J. Hall et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The antibiotic resistome: gene flow in environments, animals and human beings

(2017) Yongfei Hu et al.   Frontiers of Medicine

Singularity: Scientific containers for mobility of compute

(2017) Gregory M. Kurtzer et al.   PLoS One

Antimicrobial resistance surveillance in the genomic age

(2016) Andrew G. McArthur et al.   Annals of the New York Academy of Sciences

Consolidating and Exploring Antibiotic Resistance Gene Data Resources

(2016) Basil Britto Xavier et al.   JOURNAL OF CLINICAL MICROBIOLOGY

MEGARes: an antimicrobial resistance database for high throughput sequencing

(2016) Steven M. Lakin et al.   NUCLEIC ACIDS RESEARCH

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

(2016) Baofeng Jia et al.   NUCLEIC ACIDS RESEARCH

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Antimicrobial resistance—a threat to the world’s sustainable development

(2016) Dušan Jasovský et al.   UPSALA JOURNAL OF MEDICAL SCIENCES

Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential

(2015) Chandan Pal et al.   BMC GENOMICS

Metagenomic Assembly Reveals Hosts of Antibiotic Resistance Genes and the Shared Resistome in Pig, Chicken, and Human Feces

(2015) Liping Ma et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes

(2015) Bing Li et al.   ISME Journal

Horizontal gene transfer: building the web of life

(2015) Shannon M. Soucy et al.   NATURE REVIEWS GENETICS

Polypharmacology modelling using proteochemometrics (PCM): recent methodological developments, applications to target families, and future prospects

(2015) Isidro Cortés-Ciriano et al.   MedChemComm

Antimicrobial resistance: a global multifaceted phenomenon

(2015) Francesca Prestinaci et al.   Pathogens and Global Health

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Metagenomic epidemiology: a new frontier

(2014) Stephen S Francis et al.   JOURNAL OF EPIDEMIOLOGY AND COMMUNITY HEALTH

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

What is a resistance gene? Ranking risk in resistomes

(2014) José L. Martínez et al.   NATURE REVIEWS MICROBIOLOGY

Metagenomic Frameworks for Monitoring Antibiotic Resistance in Aquatic Environments

(2013) Jesse A. Port et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

BacMet: antibacterial biocide and metal resistance genes database

(2013) Chandan Pal et al.   NUCLEIC ACIDS RESEARCH

Antimicrobial resistance: a global view from the 2013 World Healthcare-Associated Infections Forum

(2013) Angela Huttner et al.   Antimicrobial Resistance and Infection Control

Metagenomic epidemiology: a public health need for the control of antimicrobial resistance

(2012) F. Baquero   CLINICAL MICROBIOLOGY AND INFECTION

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Call of the wild: antibiotic resistance genes in natural environments

(2010) Heather K. Allen et al.   NATURE REVIEWS MICROBIOLOGY

Updated Functional Classification of  -Lactamases

(2009) K. Bush et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Ecology and evolution of antibiotic resistance

(2009) F. Baquero et al.   Environmental Microbiology Reports