相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。Pharokka: a fast scalable bacteriophage annotation tool
George Bouras et al.
BIOINFORMATICS (2023)
High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems
Sean Meaden et al.
CURRENT BIOLOGY (2022)
GenBank
Eric W. Sayers et al.
NUCLEIC ACIDS RESEARCH (2022)
Metagenomic methylation patterns resolve bacterial genomes of unusual size and structural complexity
Elizabeth G. Wilbanks et al.
ISME JOURNAL (2022)
Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities
Vincent Somerville et al.
MICROBIOME (2022)
clinker & clustermap.js: automatic generation of gene cluster comparison figures
Cameron L. M. Gilchrist et al.
BIOINFORMATICS (2021)
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation
Wenjun Li et al.
NUCLEIC ACIDS RESEARCH (2021)
Twelve years of SAMtools and BCFtools
Petr Danecek et al.
GIGASCIENCE (2021)
A Roadmap for Genome-Based Phage Taxonomy
Dann Turner et al.
VIRUSES-BASEL (2021)
BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains
Adam J. Hockenberry et al.
PEERJ (2021)
Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages
Kristopher Kieft et al.
NATURE COMMUNICATIONS (2021)
CRISPRclassify: Repeat-Based Classification of CRISPR Loci
Matthew A. Nethery et al.
CRISPR JOURNAL (2021)
Pfam: The protein families database in 2021
Jaina Mistry et al.
NUCLEIC ACIDS RESEARCH (2021)
The arms race between bacteria and their phage foes
Hannah G. Hampton et al.
NATURE (2020)
METAVIRALSPADES: assembly of viruses from metagenomic data
Dmitry Antipov et al.
BIOINFORMATICS (2020)
VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences
Kristopher Kieft et al.
MICROBIOME (2020)
Lysogeny in the oceans: Lessons from cultivated model systems and a reanalysis of its prevalence
Matthew J. Tuttle et al.
ENVIRONMENTAL MICROBIOLOGY (2020)
Infection with Bacteroides Phage BV01 Alters the Host Transcriptome and Bile Acid Metabolism in a Common Human Gut Microbe
Danielle E. Campbell et al.
CELL REPORTS (2020)
Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities
Manuel Kleiner et al.
MICROBIOME (2020)
PHANOTATE: a novel approach to gene identification in phage genomes
Katelyn McNair et al.
BIOINFORMATICS (2019)
Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks
Ho Bin Jang et al.
NATURE BIOTECHNOLOGY (2019)
Phage puppet masters of the marine microbial realm
Mya Breitbart et al.
NATURE MICROBIOLOGY (2018)
Metapopulation Structure of CRISPR-Cas Immunity in Pseudomonas aeruginosa and Its Viruses
Whitney E. England et al.
MSYSTEMS (2018)
VCFR: a package to manipulate and visualize variant call format data in R
Brian J. Knaus et al.
MOLECULAR ECOLOGY RESOURCES (2017)
Sampling the mobile gene pool: innovation via horizontal gene transfer in bacteria
James P. J. Hall et al.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2017)
Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity
Simon Roux et al.
PEERJ (2017)
PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data
Julian R. Garneau et al.
SCIENTIFIC REPORTS (2017)
ISEScan: automated identification of insertion sequence elements in prokaryotic genomes
Zhiqun Xie et al.
BIOINFORMATICS (2017)
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
Nuala A. O'Leary et al.
NUCLEIC ACIDS RESEARCH (2016)
The Phyre2 web portal for protein modeling, prediction and analysis
Lawrence A. Kelley et al.
NATURE PROTOCOLS (2015)
Patterns and ecological drivers of ocean viral communities
Jennifer R. Brum et al.
SCIENCE (2015)
NCBI Viral Genomes Resource
J. Rodney Brister et al.
NUCLEIC ACIDS RESEARCH (2015)
Antagonistic Coevolution of Marine Planktonic Viruses and Their Hosts
Jennifer B. H. Martiny et al.
ANNUAL REVIEW OF MARINE SCIENCE, VOL 6 (2014)
Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony M. Bolger et al.
BIOINFORMATICS (2014)
Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh
Elizabeth G. Wilbanks et al.
ENVIRONMENTAL MICROBIOLOGY (2014)
CRISPR-Induced Distributed Immunity in Microbial Populations
Lauren M. Childs et al.
PLOS ONE (2014)
Sulfur Oxidation Genes in Diverse Deep-Sea Viruses
Karthik Anantharaman et al.
SCIENCE (2014)
Bacteria-phage coevolution as a driver of ecological and evolutionary processes in microbial communities
Britt Koskella et al.
FEMS MICROBIOLOGY REVIEWS (2014)
Bacteriophage Orphan DNA Methyltransferases: Insights from Their Bacterial Origin, Function, and Occurrence
James Murphy et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2013)
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
Helga Thorvaldsdottir et al.
BRIEFINGS IN BIOINFORMATICS (2013)
Phage mutations in response to CRISPR diversification in a bacterial population
Christine L. Sun et al.
ENVIRONMENTAL MICROBIOLOGY (2013)
Crass: identification and reconstruction of CRISPR from unassembled metagenomic data
Connor T. Skennerton et al.
NUCLEIC ACIDS RESEARCH (2013)
CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems
Sita J. Lange et al.
NUCLEIC ACIDS RESEARCH (2013)
Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
NATURE METHODS (2012)
A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity
Martin Jinek et al.
SCIENCE (2012)
FIMO: scanning for occurrences of a given motif
Charles E. Grant et al.
BIOINFORMATICS (2011)
The human gut virome: Inter-individual variation and dynamic response to diet
Samuel Minot et al.
GENOME RESEARCH (2011)
Accelerated Profile HMM Searches
Sean R. Eddy
PLOS COMPUTATIONAL BIOLOGY (2011)
CRISPR/Cas, the Immune System of Bacteria and Archaea
Philippe Horvath et al.
SCIENCE (2010)
BLAST plus : architecture and applications
Christiam Camacho et al.
BMC BIOINFORMATICS (2009)
Viral biogeography revealed by signatures in Sulfolobus islandicus genomes
Nicole L. Held et al.
ENVIRONMENTAL MICROBIOLOGY (2009)
Short motif sequences determine the targets of the prokaryotic CRISPR defence system
F. J. M. Mojica et al.
MICROBIOLOGY-SGM (2009)
Virus population dynamics and acquired virus resistance in natural microbial communities
Anders F. Andersson et al.
SCIENCE (2008)
Phage response to CRISPR-Encoded resistance in Streptococcus thermophilus
Helene Deveau et al.
JOURNAL OF BACTERIOLOGY (2008)
CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats
Charles Bland et al.
BMC BIOINFORMATICS (2007)
Exploring the Vast Diversity of Marine Viruses
Mya Breitbart et al.
OCEANOGRAPHY (2007)
CRISPR provides acquired resistance against viruses in prokaryotes
Rodolphe Barrangou et al.
SCIENCE (2007)
Evolutionary conservation of sequence and secondary structures in CRISPR repeats
Victor Kunin et al.
GENOME BIOLOGY (2007)
DNA-DNA hybridization values and their relationship to whole-genome sequence similarities
Johan Goris et al.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2007)
Mauve: Multiple alignment of conserved genomic sequence with rearrangements
ACE Darling et al.
GENOME RESEARCH (2004)
WebLogo: A sequence logo generator
GE Crooks et al.
GENOME RESEARCH (2004)
Identification of genes that are associated with DNA repeats in prokaryotes
R Jansen et al.
MOLECULAR MICROBIOLOGY (2002)
Biological significance of a family of regularly spaced repeats in the genomes of Archaea, bacteria and mitochondria
FJM Mojica et al.
MOLECULAR MICROBIOLOGY (2000)
分享论文
