iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria

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

(2021) Dimitri Boeckaerts et al.   Scientific Reports

Metagenomic tools in microbial ecology research

(2021) Neslihan Taş et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains

(2021) Adam J. Hockenberry et al.   PeerJ

HoPhage: an ab initio tool for identifying hosts of phage fragments from metaviromes

(2021) Jie Tan et al.   BIOINFORMATICS

DeepHost: phage host prediction with convolutional neural network

(2021) Wang Ruohan et al.   BRIEFINGS IN BIOINFORMATICS

GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

(2021) Donovan H Parks et al.   NUCLEIC ACIDS RESEARCH

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

(2021) Clément Coclet et al.   Current Opinion in Virology

Integrating Viral Metagenomics into an Ecological Framework

(2021) Pacifica Sommers et al.   Annual Review of Virology

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

(2021) Stephen Nayfach et al.   Nature Microbiology

PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences

(2021) Andrzej Zielezinski et al.   BIOINFORMATICS

Taxonomy-aware, sequence similarity ranking reliably predicts phage–host relationships

(2021) Andrzej Zielezinski et al.   BMC BIOLOGY

Mapping CRISPR spaceromes reveals vast host-specific viromes of prokaryotes

(2020) Sergey A. Shmakov et al.   Communications Biology

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

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

Phage or foe: an insight into the impact of viral predation on microbial communities

(2018) Lucía Fernández et al.   ISME Journal

KBase: The United States Department of Energy Systems Biology Knowledgebase

(2018) Adam P Arkin et al.   NATURE BIOTECHNOLOGY

Evaluation of the novel crAssphage marker for sewage pollution tracking in storm drain outfalls in Tampa, Florida

(2018) Warish Ahmed et al.   WATER RESEARCH

Host-linked soil viral ecology along a permafrost thaw gradient

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

Minimum Information about an Uncultivated Virus Genome (MIUViG)

(2018) Simon Roux et al.   NATURE BIOTECHNOLOGY

Genomes OnLine database (GOLD) v.7: updates and new features

(2018) Supratim Mukherjee et al.   NUCLEIC ACIDS RESEARCH

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

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

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

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

(2017) Natalya Yutin et al.   Nature Microbiology

Smoothing Parameter and Model Selection for General Smooth Models

(2016) Simon N. Wood et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Plankton networks driving carbon export in the oligotrophic ocean

(2016) Lionel Guidi et al.   NATURE

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

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Molecular Bases and Role of Viruses in the Human Microbiome

(2014) Shira R. Abeles et al.   JOURNAL OF MOLECULAR BIOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

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

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

Metagenomic Evaluation of the Highly Abundant Human Gut Bacteriophage CrAssphage for Source Tracking of Human Fecal Pollution

(2014) Elyse Stachler et al.   Environmental Science & Technology Letters

Crass: identification and reconstruction of CRISPR from unassembled metagenomic data

(2013) Connor T. Skennerton et al.   NUCLEIC ACIDS RESEARCH

Probing Individual Environmental Bacteria for Viruses by Using Microfluidic Digital PCR

(2011) A. D. Tadmor et al.   SCIENCE

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS