Optimization and evaluation of viral metagenomic amplification and sequencing procedures toward a genome-level resolution of the human fecal DNA virome

Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates the severity of DSS colitis

(2022) Anshul Sinha et al.   Microbiome

Long-read metagenomics using PromethION uncovers oral bacteriophages and their interaction with host bacteria

(2021) Koji Yahara et al.   Nature Communications

Characterization of the gut DNA and RNA viromes in a cohort of Chinese residents and visiting Pakistanis

(2021) Qiulong Yan et al.   Virus Evolution

Biases in Viral Metagenomics-Based Detection, Cataloguing and Quantification of Bacteriophage Genomes in Human Faeces, a Review

(2021) Julie Callanan et al.   Microorganisms

Comparison of ultrafiltration and iron chloride flocculation in the preparation of aquatic viromes from contrasting sample types

(2021) Kathryn Langenfeld et al.   PeerJ

Thousands of previously unknown phages discovered in whole-community human gut metagenomes

(2021) Sean Benler et al.   Microbiome

Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens

(2021) Ryan Cook et al.   Microbiome

Fecal filtrate transplantation protects against necrotizing enterocolitis

(2021) Anders Brunse et al.   ISME Journal

BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

(2021) Mosè Manni et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages

(2021) Kristopher Kieft et al.   Nature Communications

Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome

(2021) Stephen Nayfach et al.   Nature Microbiology

Gut dsDNA virome shows diversity and richness alterations associated with childhood obesity and metabolic syndrome

(2021) Shirley Bikel et al.   iScience

Alterations in the Gut Virome in Obesity and Type 2 Diabetes Mellitus

(2021) Keli Yang et al.   GASTROENTEROLOGY

Faecal virome transplantation decreases symptoms of type 2 diabetes and obesity in a murine model

(2020) Torben Sølbeck Rasmussen et al.   GUT

The dynamics of the stool virome in very early onset inflammatory bowel disease

(2020) Guanxiang Liang et al.   Journal of Crohns & Colitis

The stepwise assembly of the neonatal virome is modulated by breastfeeding

(2020) Guanxiang Liang et al.   NATURE

Intestinal Virome Signature Associated With Severity of Nonalcoholic Fatty Liver Disease

(2020) Sonja Lang et al.   GASTROENTEROLOGY

Intestinal virome in patients with alcoholic hepatitis

(2020) Lu Jiang et al.   HEPATOLOGY

VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

(2020) Kristopher Kieft et al.   Microbiome

Improved high-molecular-weight DNA extraction, nanopore sequencing and metagenomic assembly from the human gut microbiome

(2020) Dylan G. Maghini et al.   Nature Protocols

Gut mucosal virome alterations in ulcerative colitis

(2019) Tao Zuo et al.   GUT

Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands

(2019) Joanna Warwick-Dugdale et al.   PeerJ

Potential roles of gut microbiome and metabolites in modulating ALS in mice

(2019) Eran Blacher et al.   NATURE

A simple, reproducible and cost-effective procedure to analyse gut phageome: from phage isolation to bioinformatic approach

(2019) Camille d’Humières et al.   Scientific Reports

OUP accepted manuscript

(2018)   BIOINFORMATICS

DL-endopeptidases function as both cell wall hydrolases and poly-γ-glutamic acid hydrolases

(2018) Tatsuya Fukushima et al.   MICROBIOLOGY-SGM

Deciphering the Human Virome with Single-Virus Genomics and Metagenomics

(2018) Maria de la Cruz Peña et al.   Viruses-Basel

Reproducible protocols for metagenomic analysis of human faecal phageomes

(2018) Andrey N. Shkoporov et al.   Microbiome

Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses

(2018) Marcos Parras-Moltó et al.   Microbiome

Interaction of Human Enteric Viruses with Microbial Compounds: Implication for Virus Persistence and Disinfection Treatments

(2017) Prunelle Waldman et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Enterotypes in the landscape of gut microbial community composition

(2017) Paul I. Costea et al.   Nature Microbiology

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Towards quantitative viromics for both double-stranded and single-stranded DNA viruses

(2016) Simon Roux et al.   PeerJ

Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications

(2015) Lei Huang et al.   Annual Review of Genomics and Human Genetics

Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes

(2015) Manuel Kleiner et al.   BMC GENOMICS

Gut DNA viromes of Malawian twins discordant for severe acute malnutrition

(2015) Alejandro Reyes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis

(2015) Nádia Conceição-Neto et al.   Scientific Reports

Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut

(2015) Josué L. Castro-Mejía et al.   Microbiome

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

(2014) Marten Boetzer et al.   BMC BIOINFORMATICS

Identification of Diversity-Generating Retroelements in Human Microbiomes

(2014) Yuzhen Ye   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

GapFiller: a de novo assembly approach to fill the gap within paired reads

(2012) Francesca Nadalin et al.   BMC BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Genomic DNA amplification by the multiple displacement amplification (MDA) method: Figure 1

(2009) Roger S. Lasken   BIOCHEMICAL SOCIETY TRANSACTIONS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

(2009) Iwanka Kozarewa et al.   NATURE METHODS

Laboratory procedures to generate viral metagenomes

(2009) Rebecca V Thurber et al.   Nature Protocols

Whole Genome Amplification and De novo Assembly of Single Bacterial Cells

(2009) Sébastien Rodrigue et al.   PLoS One