Characterizing Phage Genomes for Therapeutic Applications

Early MinION™ nanopore single-molecule sequencing technology enables the characterization of hepatitis B virus genetic complexity in clinical samples

(2018) Virginie Sauvage et al.   PLoS One

A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria

(2018) Kathryn M. Kauffman et al.   NATURE

Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches

(2017) Stephen Hayes et al.   Viruses-Basel

Prophage Integrase Typing Is a Useful Indicator of Genomic Diversity in Salmonella enterica

(2017) Anna Colavecchio et al.   Frontiers in Microbiology

De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms

(2017) Francesca Giordano et al.   Scientific Reports

PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data

(2017) Julian R. Garneau et al.   Scientific Reports

Personalized Therapeutic Cocktail of Wild Environmental Phages Rescues Mice from Acinetobacter baumannii Wound Infections

(2016) James M. Regeimbal et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Software-based analysis of bacteriophage genomes, physical ends, and packaging strategies

(2016) Bryan D. Merrill et al.   BMC GENOMICS

Phages, Fitness, Virulence, and Synergy: A Novel Approach for the Therapy of Infections Caused by Pseudomonas aeruginosa

(2016) Charles W. Stratton   JOURNAL OF INFECTIOUS DISEASES

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform

(2016) Po-E Li et al.   NUCLEIC ACIDS RESEARCH

Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation

(2016) Ana Laura Grazziotin et al.   NUCLEIC ACIDS RESEARCH

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt 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

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes

(2016) Branko Rihtman et al.   PeerJ

Oxford Nanopore MinION Sequencing and Genome Assembly

(2016) Hengyun Lu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

A new perspective on lysogeny: prophages as active regulatory switches of bacteria

(2015) Ron Feiner et al.   NATURE REVIEWS MICROBIOLOGY

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures

(2015) Tracey Allen K. Freitas et al.   NUCLEIC ACIDS RESEARCH

VFDB 2016: hierarchical and refined dataset for big data analysis—10 years on

(2015) Lihong Chen et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: 2015 update

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Temperate and lytic bacteriophages programmed to sensitize and kill antibiotic-resistant bacteria

(2015) Ido Yosef et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

What Can We Learn from a Metagenomic Analysis of a Georgian Bacteriophage Cocktail?

(2015) Henrike Zschach et al.   Viruses-Basel

Inhibition of Biofilm Formation by T7 Bacteriophages Producing Quorum-Quenching Enzymes

(2014) Ruoting Pei et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Rapid evaluation and quality control of next generation sequencing data with FaQCs

(2014) Chien-Chi Lo et al.   BMC BIOINFORMATICS

Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology

(2014) Molly K Gibson et al.   ISME Journal

Beyond the Chromosome: The Prevalence of Unique Extra-Chromosomal Bacteriophages with Integrated Virulence Genes in Pathogenic Staphylococcus aureus

(2014) Bryan Utter et al.   PLoS One

Standards for Sequencing Viral Genomes in the Era of High-Throughput Sequencing

(2014) J. T. Ladner et al.   mBio

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

(2014) Bas E. Dutilh et al.   Nature Communications

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Deep sequencing of phage display libraries to support antibody discovery

(2013) Ulla Ravn et al.   METHODS

A Genomic-Scale Artificial MicroRNA Library as a Tool to Investigate the Functionally Redundant Gene Space in Arabidopsis

(2013) F. Hauser et al.   PLANT CELL

PHACTS, a computational approach to classifying the lifestyle of phages

(2012) Katelyn McNair et al.   BIOINFORMATICS

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

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

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Template-based protein structure modeling using the RaptorX web server

(2012) Morten Källberg et al.   Nature Protocols

Reversing Bacterial Resistance to Antibiotics by Phage-Mediated Delivery of Dominant Sensitive Genes

(2011) Rotem Edgar et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing

(2010) Ernesto Picardi et al.   NUCLEIC ACIDS RESEARCH

Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy

(2009) T. K. Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Bad Bugs, No Drugs: No ESKAPE! An Update from the Infectious Diseases Society of America

(2008) Helen W. Boucher et al.   CLINICAL INFECTIOUS DISEASES

Federal Funding for the Study of Antimicrobial Resistance in Nosocomial Pathogens: No ESKAPE

(2008) Louis B. Rice   JOURNAL OF INFECTIOUS DISEASES

ARDB--Antibiotic Resistance Genes Database

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