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

Analysis of whole genome sequencing for the Escherichia coli O157:H7 typing phages

(2015) Lauren A Cowley et al.   BMC GENOMICS

Genomic and proteomic characterization of two novel siphovirus infecting the sedentary facultative epibiont cyanobacteriumAcaryochloris marina

(2015) Yi-Wah Chan et al.   ENVIRONMENTAL MICROBIOLOGY

The cost of phage resistance in a plant pathogenic bacterium is context-dependent

(2015) Sean Meaden et al.   EVOLUTION

A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes

(2015) Joshua S Weitz et al.   ISME Journal

Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice

(2015) Adina Howe et al.   ISME Journal

Spontaneous Deletion of an “ORFanage” Region Facilitates Host Adaptation in a “Photosynthetic” Cyanophage

(2015) Richard J. Puxty et al.   PLoS One

Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters

(2015) Jeremy J. Barr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Patterns and ecological drivers of ocean viral communities

(2015) J. R. Brum et al.   SCIENCE

Revisiting phage therapy: new applications for old resources

(2015) Franklin L. Nobrega et al.   TRENDS IN MICROBIOLOGY

Whole genome sequence comparison of ten diagnostic brucellaphages propagated on two Brucella abortus hosts

(2015) Ekaterine Tevdoradze et al.   Virology Journal

Bacteriophages isolated from Lake Michigan demonstrate broad host-range across several bacterial phyla

(2015) Kema Malki et al.   Virology Journal

Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes

(2015) Michael Baym et al.   PLoS One

Exploiting gut bacteriophages for human health

(2014) Marion Dalmasso et al.   TRENDS IN MICROBIOLOGY

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

(2014) Simon Roux et al.   eLife

Comparative genomics defines the core genome of the growing N4-like phage genus and identifies N4-like Roseophage specific genes

(2014) Jacqueline Z.-M. Chan et al.   Frontiers in Microbiology

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

GAGE-B: an evaluation of genome assemblers for bacterial organisms

(2013) Tanja Magoc et al.   BIOINFORMATICS

Estimates of viral abundance in soils are strongly influenced by extraction and enumeration methods

(2013) Kurt E. Williamson et al.   BIOLOGY AND FERTILITY OF SOILS

Phage infection of an environmentally relevant marine bacterium alters host metabolism and lysate composition

(2013) Nana Yaw D Ankrah et al.   ISME Journal

DPS – A rapid method for genome sequencing of DNA-containing bacteriophages directly from a single plaque

(2013) Witold Kot et al.   JOURNAL OF VIROLOGICAL METHODS

Abundant SAR11 viruses in the ocean

(2013) Yanlin Zhao et al.   NATURE

Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome

(2013) Sheetal R. Modi et al.   NATURE

The Pacific Ocean Virome (POV): A Marine Viral Metagenomic Dataset and Associated Protein Clusters for Quantitative Viral Ecology

(2013) Bonnie L. Hurwitz et al.   PLoS One

Genome of a SAR116 bacteriophage shows the prevalence of this phage type in the oceans

(2013) I. Kang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacteriophage adhering to mucus provide a non-host-derived immunity

(2013) J. J. Barr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Viral metagenomics analysis of planktonic viruses in East Lake, Wuhan, China

(2013) Xingyi Ge et al.   VIROLOGICA SINICA

Qualimap: evaluating next-generation sequencing alignment data

(2012) Fernando García-Alcalde et al.   BIOINFORMATICS

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

The limitations of draft assemblies for understanding prokaryotic adaptation and evolution

(2012) N. Ricker et al.   GENOMICS

Viral Metagenomics: A Tool for Virus Discovery and Diversity in Aquaculture

(2012) S. V. Alavandi et al.   Indian Journal of Virology

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

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

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

A novel lineage of myoviruses infecting cyanobacteria is widespread in the oceans

(2012) G. Sabehi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development ofphoHas a Novel Signature Gene for Assessing Marine Phage Diversity

(2011) Dawn B. Goldsmith et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Evaluation of a Transposase Protocol for Rapid Generation of Shotgun High-Throughput Sequencing Libraries from Nanogram Quantities of DNA

(2011) Rachel Marine et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Repetitive DNA and next-generation sequencing: computational challenges and solutions

(2011) Todd J. Treangen et al.   NATURE REVIEWS GENETICS

Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism

(2011) L. R. Thompson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Viral metagenomics as an emerging and powerful tool in veterinary medicine

(2011) Anne-Lie Blomström   VETERINARY QUARTERLY

Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies

(2010) Sébastien Boisvert et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Analysis of High-Throughput Sequencing and Annotation Strategies for Phage Genomes

(2010) Matthew R. Henn et al.   PLoS One

ABACAS: algorithm-based automatic contiguation of assembled sequences

(2009) S. Assefa et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Metagenomic signatures of 86 microbial and viral metagenomes

(2009) Dana Willner et al.   ENVIRONMENTAL MICROBIOLOGY

Comparative genomics of marine cyanomyoviruses reveals the widespread occurrence ofSynechococcushost genes localized to a hyperplastic region: implications for mechanisms of cyanophage evolution

(2009) Andrew D. Millard et al.   ENVIRONMENTAL MICROBIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

The Headful Packaging Nuclease of Bacteriophage T4

(2008) Tanfis I. Alam et al.   MOLECULAR MICROBIOLOGY