Global overview and major challenges of host prediction methods for uncultivated phages

VPF-Class: Taxonomic assignment and host prediction of uncultivated viruses based on viral protein families

(2021) Joan Carles Pons et al.   BIOINFORMATICS

Prokaryotic virus host predictor: a Gaussian model for host prediction of prokaryotic viruses in metagenomics

(2021) Congyu Lu et al.   BMC BIOLOGY

Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins

(2021) Dimitri Boeckaerts et al.   Scientific Reports

Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features

(2021) Natalya Yutin et al.   Nature Communications

MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut

(2021) Martial Marbouty et al.   eLife

Interaction dynamics and virus–host range for estuarine actinophages captured by epicPCR

(2021) Eric G. Sakowski et al.   Nature Microbiology

SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts

(2021) Ruoshi Zhang et al.   BIOINFORMATICS

Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens

(2021) Emma Guerin et al.   Microbiome

Giant virus diversity and host interactions through global metagenomics

(2020) Frederik Schulz et al.   NATURE

Phage diversity, genomics and phylogeny

(2020) Moïra B. Dion et al.   NATURE REVIEWS MICROBIOLOGY

VIDHOP, viral host prediction with Deep Learning

(2020) Florian Mock et al.   BIOINFORMATICS

Insights into the dynamics between viruses and their hosts in a hot spring microbial mat

(2020) Jessica K. Jarett et al.   ISME Journal

Standardized bacteriophage purification for personalized phage therapy

(2020) Tiffany Luong et al.   Nature Protocols

Adsorption sequencing (AdsorpSeq) as a rapid method to link environmental bacteriophages to hosts

(2020) Patrick A. de Jonge et al.   iScience

High proportions of bacteria and archaea across most biomes remain uncultured

(2019) Andrew D. Steen et al.   ISME Journal

Defining the human gut host–phage network through single-cell viral tagging

(2019) Mária Džunková et al.   Nature Microbiology

Evolution of BACON Domain Tandem Repeats in crAssphage and Novel Gut Bacteriophage Lineages

(2019) Patrick A. de Jonge et al.   Viruses-Basel

Predicting virus-host association by Kernelized logistic matrix factorization and similarity network fusion

(2019) Dan Liu et al.   BMC BIOINFORMATICS

Charting the Complexity of the Marine Microbiome through Single-Cell Genomics

(2019) Maria G. Pachiadaki et al.   CELL

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

(2019) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

A virus or more in (nearly) every cell: ubiquitous networks of virus–host interactions in extreme environments

(2018) Jacob H. Munson-McGee et al.   ISME Journal

Rapid quantification of bacteriophages and their bacterial hosts in vitro and in vivo using droplet digital PCR

(2018) Norma M. Morella et al.   JOURNAL OF VIROLOGICAL METHODS

Phage puppet masters of the marine microbial realm

(2018) Mya Breitbart et al.   Nature Microbiology

Host-linked soil viral ecology along a permafrost thaw gradient

(2018) Joanne B. Emerson et al.   Nature Microbiology

Viral and metabolic controls on high rates of microbial sulfur and carbon cycling in wetland ecosystems

(2018) Paula Dalcin Martins et al.   Microbiome

Limitations of Correlation-Based Inference in Complex Virus-Microbe Communities

(2018) Ashley R. Coenen et al.   mSystems

Computational prediction of inter-species relationships through omics data analysis and machine learning

(2018) Diogo Manuel Carvalho Leite et al.   BMC BIOINFORMATICS

Minimum Information about an Uncultivated Virus Genome (MIUViG)

(2018) Simon Roux et al.   NATURE BIOTECHNOLOGY

ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis

(2018) Andrey N. Shkoporov et al.   Nature Communications

Temporal dynamics of uncultured viruses: a new dimension in viral diversity

(2017) Ksenia Arkhipova et al.   ISME Journal

Lysogeny in nature: mechanisms, impact and ecology of temperate phages

(2017) Cristina Howard-Varona et al.   ISME Journal

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans

(2017) Felipe H. Coutinho et al.   Nature Communications

Editorial: Virus Discovery by Metagenomics: The (Im)possibilities

(2017) Bas E. Dutilh et al.   Frontiers in Microbiology

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut

(2017) Natalya Yutin et al.   Nature Microbiology

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

(2016) Simon Roux et al.   NATURE

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

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

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

Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences

(2016) Nathan A. Ahlgren et al.   NUCLEIC ACIDS RESEARCH

HostPhinder: A Phage Host Prediction Tool

(2016) Julia Villarroel et al.   Viruses-Basel

Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems

(2016) David Burstein et al.   Nature Communications

Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton

(2015) Jessica M Labonté et al.   ISME Journal

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

(2015) Ron Feiner et al.   NATURE REVIEWS MICROBIOLOGY

Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

(2015) Simon Roux et al.   eLife

Using Signature Genes as Tools To Assess Environmental Viral Ecology and Diversity

(2014) Evelien M. Adriaenssens et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Viral tagging reveals discrete populations in Synechococcus viral genome sequence space

(2014) Li Deng et al.   NATURE

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

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

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

(2014) Simon Roux et al.   eLife

Single-cell and population level viral infection dynamics revealed by phageFISH, a method to visualize intracellular and free viruses

(2013) Elke Allers et al.   ENVIRONMENTAL MICROBIOLOGY

Expanding the Marine Virosphere Using Metagenomics

(2013) Carolina Megumi Mizuno et al.   PLoS Genetics

Probing Individual Environmental Bacteria for Viruses by Using Microfluidic Digital PCR

(2011) A. D. Tadmor et al.   SCIENCE

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS