Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: Viruses, plasmids, and more

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

(2021) Stephen Nayfach et al.   Nature Microbiology

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

Clades of huge phages from across Earth’s ecosystems

(2020) Basem Al-Shayeb et al.   NATURE

A pneumonia outbreak associated with a new coronavirus of probable bat origin

(2020) Peng Zhou et al.   NATURE

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

Origin of viruses: primordial replicators recruiting capsids from hosts

(2019) Mart Krupovic et al.   NATURE REVIEWS MICROBIOLOGY

Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids

(2019) Darius Kazlauskas et al.   Nature Communications

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

(2019) Simon Roux et al.   Nature Microbiology

Evolution of satellite plasmids can prolong the maintenance of newly acquired accessory genes in bacteria

(2019) Xue Zhang et al.   Nature Communications

Vast diversity of prokaryotic virus genomes encoding double jelly-roll major capsid proteins uncovered by genomic and metagenomic sequence analysis

(2018) Natalya Yutin et al.   Virology Journal

Clustering huge protein sequence sets in linear time

(2018) Martin Steinegger et al.   Nature Communications

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes

(2018) David Paez-Espino et al.   NUCLEIC ACIDS RESEARCH

The so far farthest reaches of the double jelly roll capsid protein fold

(2018) Carmen San Martín et al.   Virology Journal

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Diversity and evolution of class 2 CRISPR–Cas systems

(2017) Sergey Shmakov et al.   NATURE REVIEWS MICROBIOLOGY

The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes

(2017) Sergey A. Shmakov et al.   mBio

MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes

(2017) Abraham G. Moller et al.   PeerJ

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

(2017) Jie Ren et al.   Microbiome

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

(2017) Natalya Yutin et al.   Nature Microbiology

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

CRISPRDetect: A flexible algorithm to define CRISPR arrays

(2016) Ambarish Biswas et al.   BMC GENOMICS

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

An updated evolutionary classification of CRISPR–Cas systems

(2015) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses

(2014) Mart Krupovic et al.   Biology Direct

An Allometric Relationship between the Genome Length and Virion Volume of Viruses

(2014) J. Cui et al.   JOURNAL OF VIROLOGY

circRNA Biogenesis Competes with Pre-mRNA Splicing

(2014) Reut Ashwal-Fluss et al.   MOLECULAR CELL

Degenerate target sites mediate rapid primed CRISPR adaptation

(2014) P. C. Fineran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

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

(2013) Kimberley D. Seed et al.   NATURE

Crass: identification and reconstruction of CRISPR from unassembled metagenomic data

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

Origins of HIV and the AIDS Pandemic

(2013) P. M. Sharp et al.   Cold Spring Harbor Perspectives in Medicine

CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes

(2013) Quan Zhang et al.   GENOME BIOLOGY

CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome

(2012) A. Stern et al.   GENOME RESEARCH

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

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

Site-specific recombination systems in filamentous phages

(2012) Ahmed Askora et al.   MOLECULAR GENETICS AND GENOMICS

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Evolution and Diversity of the Microviridae Viral Family through a Collection of 81 New Complete Genomes Assembled from Virome Reads

(2012) Simon Roux et al.   PLoS One

Use of Cellular CRISPR (Clusters of Regularly Interspaced Short Palindromic Repeats) Spacer-Based Microarrays for Detection of Viruses in Environmental Samples

(2010) J. C. Snyder et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities

(2008) A. F. Andersson et al.   SCIENCE