A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases

Massive expansion of human gut bacteriophage diversity

(2021) Luis F. Camarillo-Guerrero et al.   CELL

Streamlining CRISPR spacer-based bacterial host predictions to decipher the viral dark matter

(2021) Moïra B Dion et al.   NUCLEIC ACIDS RESEARCH

Evolution of Microbial Genomics: Conceptual Shifts over a Quarter Century

(2021) Eugene V. Koonin et al.   TRENDS IN MICROBIOLOGY

Phage-specific metabolic reprogramming of virocells

(2020) Cristina Howard-Varona et al.   ISME Journal

Global Organization and Proposed Megataxonomy of the Virus World

(2020) Eugene V. Koonin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Clades of huge phages from across Earth’s ecosystems

(2020) Basem Al-Shayeb et al.   NATURE

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Phage liquid crystalline droplets form occlusive sheaths that encapsulate and protect infectious rod-shaped bacteria

(2020) Abul K. Tarafder et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery of several thousand highly diverse circular DNA viruses

(2020) Michael J Tisza et al.   eLife

The intestinal virome in children with cystic fibrosis differs from healthy controls

(2020) Michael J. Coffey et al.   PLoS One

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

(2020) Kristopher Kieft et al.   Microbiome

Molecular Mechanisms of CRISPR-Cas Immunity in Bacteria

(2020) Philip M. Nussenzweig et al.   Annual Review of Genetics

The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut

(2020) Ann C. Gregory et al.   Cell Host & Microbe

Flexible genes establish widespread bacteriophage pan-genomes in cryoconite hole ecosystems

(2020) Christopher M. Bellas et al.   Nature Communications

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

(2020) Stephen Nayfach et al.   NATURE BIOTECHNOLOGY

Cenote-Taker 2 democratizes virus discovery and sequence annotation

(2020) Michael J Tisza et al.   Virus Evolution

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

Phage Therapy in the Postantibiotic Era

(2019) Fernando L. Gordillo Altamirano et al.   CLINICAL MICROBIOLOGY REVIEWS

Gut Virome Analysis of Cameroonians Reveals High Diversity of Enteric Viruses, Including Potential Interspecies Transmitted Viruses

(2019) Claude Kwe Yinda et al.   mSphere

Bacterial ‘Grounded’ Prophages: Hotspots for Genetic Renovation and Innovation

(2019) Bhaskar Chandra Mohan Ramisetty et al.   Frontiers in Genetics

Bacteriophage trigger antiviral immunity and prevent clearance of bacterial infection

(2019) Johanna M. Sweere et al.   SCIENCE

Novel insights from uncultivated genomes of the global human gut microbiome

(2019) Stephen Nayfach et al.   NATURE

Gut mucosal virome alterations in ulcerative colitis

(2019) Tao Zuo et al.   GUT

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

(2019) Ann C. Gregory et al.   CELL

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

(2019) Ho Bin Jang et al.   NATURE BIOTECHNOLOGY

Moving beyond P values: data analysis with estimation graphics

(2019) Joses Ho et al.   NATURE METHODS

CRISPR–Cas in mobile genetic elements: counter-defence and beyond

(2019) Guilhem Faure et al.   NATURE REVIEWS MICROBIOLOGY

Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes

(2019) Simon Roux et al.   Nature Microbiology

Redondoviridae, a Family of Small, Circular DNA Viruses of the Human Oro-Respiratory Tract Associated with Periodontitis and Critical Illness

(2019) Arwa A. Abbas et al.   Cell Host & Microbe

Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease

(2019) Rohit Loomba et al.   Cell Metabolism

What is (not) known about the dynamics of the human gut virome in health and disease

(2019) Leen Beller et al.   Current Opinion in Virology

The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific

(2019) Andrey N. Shkoporov et al.   Cell Host & Microbe

Detecting contamination in viromes using ViromeQC

(2019) Moreno Zolfo et al.   NATURE BIOTECHNOLOGY

Gut Bacteriophage: Current Understanding and Challenges

(2019) Thomas D. S. Sutton et al.   Frontiers in Endocrinology

Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease

(2019) Adam G. Clooney et al.   Cell Host & Microbe

Discordant transmission of bacteria and viruses from mothers to babies at birth

(2019) Rabia Maqsood et al.   Microbiome

OUP accepted manuscript

(2018)   BIOINFORMATICS

Alterations in Enteric Virome Are Associated With Colorectal Cancer and Survival Outcomes

(2018) Geicho Nakatsu et al.   GASTROENTEROLOGY

Current understanding of the human microbiome

(2018) Jack A Gilbert et al.   NATURE MEDICINE

Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes

(2018) Jeffrey K. Cornuault et al.   Microbiome

A human gut phage catalog correlates the gut phageome with type 2 diabetes

(2018) Yingfei Ma et al.   Microbiome

Reproducible protocols for metagenomic analysis of human faecal phageomes

(2018) Andrey N. Shkoporov et al.   Microbiome

Metatranscriptome of human faecal microbial communities in a cohort of adult men

(2018) Galeb S. Abu-Ali et al.   Nature Microbiology

Enteric Virome and Bacterial Microbiota in Children with Ulcerative Colitis and Crohnʼs Disease

(2018) Melissa A. Fernandes et al.   JOURNAL OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION

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

(2018) Kathryn M. Kauffman et al.   NATURE

Minimum Information about an Uncultivated Virus Genome (MIUViG)

(2018) Simon Roux et al.   NATURE BIOTECHNOLOGY

Metagenomic Discovery of 83 New Human Papillomavirus Types in Patients with Immunodeficiency

(2018) Diana V. Pastrana et al.   mSphere

Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates

(2017) Matthew R. Olm et al.   GENOME RESEARCH

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

Ménage à trois in the human gut: interactions between host, bacteria and phages

(2017) Mohammadali Khan Mirzaei et al.   NATURE REVIEWS MICROBIOLOGY

Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children

(2017) Guoyan Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The gut microbiome in atherosclerotic cardiovascular disease

(2017) Zhuye Jie et al.   Nature Communications

Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients

(2017) J. R. Bedarf et al.   Genome Medicine

Intestinal Dysbiosis and Rheumatoid Arthritis: A Link between Gut Microbiota and the Pathogenesis of Rheumatoid Arthritis

(2017) Gabriel Horta-Baas et al.   Journal of Immunology Research

Gut microbiota dysbiosis contributes to the development of hypertension

(2017) Jing Li et al.   Microbiome

A myovirus encoding both photosystem I and II proteins enhances cyclic electron flow in infected Prochlorococcus cells

(2017) Svetlana Fridman et al.   Nature Microbiology

Human Microbiota-Associated Mice: A Model with Challenges

(2016) Marie-Claire Arrieta et al.   Cell Host & Microbe

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

Interconnected microbiomes and resistomes in low-income human habitats

(2016) Erica C. Pehrsson et al.   NATURE

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

(2016) David Paez-Espino et al.   NUCLEIC ACIDS RESEARCH

Healthy human gut phageome

(2016) Pilar Manrique et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unique Features of Ethnic Mongolian Gut Microbiome revealed by metagenomic analysis

(2016) Wenjun Liu et al.   Scientific Reports

Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

(2016) Anna Heintz-Buschart et al.   Nature Microbiology

Piggyback-the-Winner in host-associated microbial communities

(2016) Cynthia B Silveira et al.   npj Biofilms and Microbiomes

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

(2015) Jason M. Norman et al.   CELL

Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life

(2015) Fredrik Bäckhed et al.   Cell Host & Microbe

Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota

(2015) Simone Rampelli et al.   CURRENT BIOLOGY

Gut Virome Sequencing in Children With Early Islet Autoimmunity: Figure 1

(2015) Lenka Kramná et al.   DIABETES CARE

The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment

(2015) Xuan Zhang et al.   NATURE MEDICINE

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

Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks

(2015) W B Langdon   BioData Mining

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Occurrence and Diversity of CRISPR-Cas Systems in the Genus Bifidobacterium

(2015) Alexandra E. Briner et al.   PLoS One

Alterations of the human gut microbiome in liver cirrhosis

(2014) Nan Qin et al.   NATURE

Biogeography and individuality shape function in the human skin metagenome

(2014) Julia Oh et al.   NATURE

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

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

Evidence for metaviromic islands in marine phages

(2014) Carolina Megumi Mizuno et al.   Frontiers in Microbiology

Machine learning for neuroimaging with scikit-learn

(2014) Alexandre Abraham et al.   Frontiers in Neuroinformatics

Assessing the Human Gut Microbiota in Metabolic Diseases

(2013) F. Karlsson et al.   DIABETES

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity

(2013) Kimberley D. Seed et al.   NATURE

Gut metagenome in European women with normal, impaired and diabetic glucose control

(2013) Fredrik H. Karlsson et al.   NATURE

Rapid evolution of the human gut virome

(2013) S. Minot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

clusterMaker: a multi-algorithm clustering plugin for Cytoscape

(2012) John H Morris et al.   BMC BIOINFORMATICS

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Emerging view of the human virome

(2012) Kristine M. Wylie et al.   Translational Research

The human gut virome: Inter-individual variation and dynamic response to diet

(2011) S. Minot et al.   GENOME RESEARCH

Evolution and classification of the CRISPR–Cas systems

(2011) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

Succession of microbial consortia in the developing infant gut microbiome

(2010) J. E. Koenig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Host-parasite coevolution and patterns of adaptation across time and space

(2008) S. GANDON et al.   JOURNAL OF EVOLUTIONARY BIOLOGY