Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes

Contributions and Challenges of High Throughput qPCR for Determining Antimicrobial Resistance in the Environment: A Critical Review

(2019) Hassan Waseem et al.   MOLECULES

Plasmid DNA contaminant in molecular reagents

(2019) N. Wally et al.   Scientific Reports

Clinical metagenomics

(2019) Charles Y. Chiu et al.   NATURE REVIEWS GENETICS

Sequencing-based methods and resources to study antimicrobial resistance

(2019) Manish Boolchandani et al.   NATURE REVIEWS GENETICS

Capturing sequence diversity in metagenomes with comprehensive and scalable probe design

(2019) Hayden C. Metsky et al.   NATURE BIOTECHNOLOGY

FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences

(2019) Jenai Quan et al.   NUCLEIC ACIDS RESEARCH

MrBait: universal identification and design of targeted-enrichment capture probes

(2018) Tyler K Chafin et al.   BIOINFORMATICS

The paradox of HBV evolution as revealed from a 16th century mummy

(2018) Zoe Patterson Ross et al.   PLoS Pathogens

Travel and the Spread of Drug-Resistant Bacteria

(2018) Kevin L. Schwartz et al.   Current Infectious Disease Reports

In-depth resistome analysis by targeted metagenomics

(2018) Val F. Lanza et al.   Microbiome

Recognizing the reagent microbiome

(2018) Marcus C. de Goffau et al.   Nature Microbiology

BacCapSeq: a Platform for Diagnosis and Characterization of Bacterial Infections

(2018) Orchid M. Allicock et al.   mBio

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations

(2018) Raphael Eisenhofer et al.   TRENDS IN MICROBIOLOGY

Next-generation approaches to understand and combat the antibiotic resistome

(2017) Terence S. Crofts et al.   NATURE REVIEWS MICROBIOLOGY

A molecular portrait of maternal sepsis from Byzantine Troy

(2017) Alison M Devault et al.   eLife

Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing

(2017) Noelle R. Noyes et al.   Microbiome

17 th Century Variola Virus Reveals the Recent History of Smallpox

(2016) Ana T. Duggan et al.   CURRENT BIOLOGY

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

GenBank

(2016) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

The structure and diversity of human, animal and environmental resistomes

(2016) Chandan Pal et al.   Microbiome

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

A General Method for Rapid Determination of Antibiotic Susceptibility and Species in Bacterial Infections

(2014) Anja Mezger et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Rapid point of care diagnostic tests for viral and bacterial respiratory tract infections—needs, advances, and future prospects

(2014) Alimuddin Zumla et al.   LANCET INFECTIOUS DISEASES

Yersinia pestis and the Plague of Justinian 541–543 AD: a genomic analysis

(2014) David M Wagner et al.   LANCET INFECTIOUS DISEASES

Ancient Whole Genome Enrichment Using Baits Built from Modern DNA

(2014) Jacob M. Enk et al.   MOLECULAR BIOLOGY AND EVOLUTION

Targeted sequencing for gene discovery and quantification using RNA CaptureSeq

(2014) Tim R Mercer et al.   Nature Protocols

Scalable metagenomic taxonomy classification using a reference genome database

(2013) Sasha K. Ames et al.   BIOINFORMATICS

Progress on the development of rapid methods for antimicrobial susceptibility testing

(2013) M. R. Pulido et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Antibiotic resistance—the need for global solutions

(2013) Ramanan Laxminarayan et al.   LANCET INFECTIOUS DISEASES

The Culturable Soil Antibiotic Resistome: A Community of Multi-Drug Resistant Bacteria

(2013) Fiona Walsh et al.   PLoS One

Proliferation of Multidrug-Resistant New Delhi Metallo-β-lactamase Genes in Municipal Wastewater Treatment Plants in Northern China

(2013) Yi Luo et al.   Environmental Science & Technology Letters

Pre-capture multiplexing improves efficiency and cost-effectiveness of targeted genomic enrichment

(2012) A Eliot Shearer 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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens

(2012) K. J. Forsberg et al.   SCIENCE

BamTools: a C++ API and toolkit for analyzing and managing BAM files

(2011) D. W. Barnett et al.   BIOINFORMATICS

Performance comparison of exome DNA sequencing technologies

(2011) Michael J Clark et al.   NATURE BIOTECHNOLOGY

Specific Capture and Whole-Genome Sequencing of Viruses from Clinical Samples

(2011) Daniel P. Depledge et al.   PLoS One

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prevalence of integrons and a newdfrA17variant in Gram-negative bacilli which cause community-acquired infections

(2010) Cemal Sandalli et al.   MICROBIOLOGY AND IMMUNOLOGY

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

Call of the wild: antibiotic resistance genes in natural environments

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Efficient oligonucleotide probe selection for pan-genomic tiling arrays

(2009) Adam M Phillippy et al.   BMC BIOINFORMATICS

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY