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。ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models
Diego Darriba et al.
MOLECULAR BIOLOGY AND EVOLUTION (2020)
Structural Insights Into the Transcriptional Regulation of HigBA Toxin-Antitoxin System by Antitoxin HigA in Pseudomonas aeruginosa
Ying Liu et al.
FRONTIERS IN MICROBIOLOGY (2020)
Autographivirinae Bacteriophage Arno 160 Infects Pectobacterium carotovorum via Depolymerization of the Bacterial O-Polysaccharide
Mikhail M. Shneider et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)
The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks
Alexander E. Gorbalenya et al.
NATURE MICROBIOLOGY (2020)
Molecular Characterization and Comparative Genomic Analysis of vB_PaeP_YA3, a Novel Temperate Bacteriophage ofPseudomonas aeruginosa
Xinyan Yu et al.
FRONTIERS IN MICROBIOLOGY (2020)
VIRIDIC-A Novel Tool to Calculate the Intergenomic Similarities of Prokaryote-Infecting Viruses
Cristina Moraru et al.
VIRUSES-BASEL (2020)
Origin and Evolution of Studiervirinae Bacteriophages Infecting Pectobacterium: Horizontal Transfer Assists Adaptation to New Niches
Peter V. Evseev et al.
MICROORGANISMS (2020)
Classifying the Unclassified: A Phage Classification Method
Cynthia Maria Chibani et al.
VIRUSES-BASEL (2019)
Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales
Soo Jen Low et al.
NATURE MICROBIOLOGY (2019)
The role of 3D genome organization in development and cell differentiation
Hui Zheng et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2019)
Temperate Bacteriophages from Chronic Pseudomonas aeruginosa Lung Infections Show Disease-Specific Changes in Host Range and Modulate Antimicrobial Susceptibility
Mohammad A. Tariq et al.
MSYSTEMS (2019)
Pelagiphages in the Podoviridae family integrate into host genomes
Yanlin Zhao et al.
ENVIRONMENTAL MICROBIOLOGY (2019)
Changing Rates of Chronic Pseudomonas aeruginosa Infections in Cystic Fibrosis: A Population-Based Cohort Study
Matthew R. Crull et al.
CLINICAL INFECTIOUS DISEASES (2018)
A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core
Lukas Zimmermann et al.
JOURNAL OF MOLECULAR BIOLOGY (2018)
Gene Co-occurrence Networks Reflect Bacteriophage Ecology and Evolution
Jason W. Shapiro et al.
MBIO (2018)
A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection
Norman Goodacre et al.
MSPHERE (2018)
Cryo-EM structure of the bacteriophage T4 isometric head at 3.3-Å resolution and its relevance to the assembly of icosahedral viruses
Zhenguo Chen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
Adsorption of Bacteriophages on Bacterial Cells
A. V. Letarov et al.
BIOCHEMISTRY-MOSCOW (2017)
A large-scale evaluation of algorithms to calculate average nucleotide identity
Seok-Hwan Yoon et al.
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY (2017)
ViPTree: the viral proteomic tree server
Yosuke Nishimura et al.
BIOINFORMATICS (2017)
OrthoANI: An improved algorithm and software for calculating average nucleotide identity
Imchang Lee et al.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2016)
Emerging Roles of Toxin-Antitoxin Modules in Bacterial Pathogenesis
Barbara Kedzierska et al.
MOLECULES (2016)
Common Evolutionary Origin of Procapsid Proteases, Phage Tail Tubes, and Tubes of Bacterial Type VI Secretion Systems
Andrei Fokine et al.
STRUCTURE (2016)
Chronic wound infections: the role of Pseudomonas aeruginosa and Staphylococcus aureus
Raffaele Serra et al.
EXPERT REVIEW OF ANTI-INFECTIVE THERAPY (2015)
The Phyre2 web portal for protein modeling, prediction and analysis
Lawrence A. Kelley et al.
NATURE PROTOCOLS (2015)
Bacteriophage lambda: Early pioneer and still relevant
Sherwood R. Casjens et al.
VIROLOGY (2015)
Phage ΦPan70, a Putative Temperate Phage, Controls Pseudomonas aeruginosa in Planktonic, Biofilm and Burn Mouse Model Assays
Angela V. Holguin et al.
VIRUSES-BASEL (2015)
Phylogenetic Distribution of CRISPR-Cas Systems in Antibiotic-Resistant Pseudomonas aeruginosa
Alex van Belkum et al.
MBIO (2015)
Comparative Genomic and Phylogenomic Analyses Reveal a Conserved Core Genome Shared by Estuarine and Oceanic Cyanopodoviruses
Sijun Huang et al.
PLOS ONE (2015)
The Phylogenetic Likelihood Library
T. Flouri et al.
SYSTEMATIC BIOLOGY (2015)
Prokka: rapid prokaryotic genome annotation
Torsten Seemann
BIOINFORMATICS (2014)
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Alexandros Stamatakis
BIOINFORMATICS (2014)
Phage Lysis: Three Steps, Three Choices, One Outcome
Ryland Young
JOURNAL OF MICROBIOLOGY (2014)
Isolation and characterization of novel soilborne lytic bacteriophages infecting Dickeya spp. biovar 3 ('D. solani')
R. Czajkowski et al.
PLANT PATHOLOGY (2014)
A novel Pseudomonas aeruginosa Bacteriophage, Ab31, a Chimera Formed from Temperate Phage PAJU2 and P. putida Lytic Phage AF: Characteristics and Mechanism of Bacterial Resistance
Libera Latino et al.
PLOS ONE (2014)
Capsid expansion mechanism of bacteriophage T7 revealed by multistate atomic models derived from cryo-EM reconstructions
Fei Guo et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Phage cluster relationships identified through single gene analysis
Kyle C. Smith et al.
BMC GENOMICS (2013)
Genomes of marine cyanopodoviruses reveal multiple origins of diversity
S. J. Labrie et al.
ENVIRONMENTAL MICROBIOLOGY (2013)
Functional Domains of the HK97 Capsid Maturation Protease and the Mechanisms of Protein Encapsidation
Robert L. Duda et al.
JOURNAL OF MOLECULAR BIOLOGY (2013)
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Kazutaka Katoh et al.
MOLECULAR BIOLOGY AND EVOLUTION (2013)
Phage Lambda P Protein: Trans-Activation, Inhibition Phenotypes and their Suppression
Sidney Hayes et al.
VIRUSES-BASEL (2013)
Expanding the Marine Virosphere Using Metagenomics
Carolina Megumi Mizuno et al.
PLOS GENETICS (2013)
The Spanin Complex Is Essential for Lambda Lysis
Joel Berry et al.
JOURNAL OF BACTERIOLOGY (2012)
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Anton Bankevich et al.
JOURNAL OF COMPUTATIONAL BIOLOGY (2012)
Easyfig: a genome comparison visualizer
Mitchell J. Sullivan et al.
BIOINFORMATICS (2011)
Structure of the Three N-Terminal Immunoglobulin Domains of the Highly Immunogenic Outer Capsid Protein from a T4-Like Bacteriophage
Andrei Fokine et al.
JOURNAL OF VIROLOGY (2011)
Search and clustering orders of magnitude faster than BLAST
Robert C. Edgar
BIOINFORMATICS (2010)
Prodigal: prokaryotic gene recognition and translation initiation site identification
Doug Hyatt et al.
BMC BIOINFORMATICS (2010)
Assembly and Maturation of the Bacteriophage Lambda Procapsid: gpC Is the Viral Protease
Elizabeth Medina et al.
JOURNAL OF MOLECULAR BIOLOGY (2010)
FastTree 2-Approximately Maximum-Likelihood Trees for Large Alignments
Morgan N. Price et al.
PLOS ONE (2010)
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
Salvador Capella-Gutierrez et al.
BIOINFORMATICS (2009)
FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix
Morgan N. Price et al.
MOLECULAR BIOLOGY AND EVOLUTION (2009)
Functional domains of the bacteriophage P2 scaffolding protein: Identification of residues involved in assembly and protease activity
Jenny R. Chang et al.
VIROLOGY (2009)
An improved general amino acid replacement matrix
Si Quang Le et al.
MOLECULAR BIOLOGY AND EVOLUTION (2008)
Evolutionary history of bacteriophages with double-stranded DNA genomes
Galina Glazko et al.
BIOLOGY DIRECT (2007)
Virioplankton 'pegylation': Use of PEG (polyethylene glycol) to concentrate and purify viruses in pelagic ecosystems
J. Colombet et al.
JOURNAL OF MICROBIOLOGICAL METHODS (2007)
Phage Lambda CIII: A Protease Inhibitor Regulating the Lysis-Lysogeny Decision
Oren Kobiler et al.
PLOS ONE (2007)
Propagating the missing bacteriophages: a large bacteriophage in a new class
Philip Serwer et al.
VIROLOGY JOURNAL (2007)
Beyond the sequence: Cellular organization of genome function
Tom Misteli
CELL (2007)
RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Alexandros Stamatakis
BIOINFORMATICS (2006)
Comparative genomic analysis of 18 Pseudomonas aeruginosa bacteriophages
T Kwan et al.
JOURNAL OF BACTERIOLOGY (2006)
The HHpred interactive server for protein homology detection and structure prediction
J Söding et al.
NUCLEIC ACIDS RESEARCH (2005)
The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs
P Schattner et al.
NUCLEIC ACIDS RESEARCH (2005)
Identification of the receptor-binding protein in 936-species lactococcal bacteriophages
K Dupont et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2004)
Phages and the evolution of bacterial pathogens:: From genomic rearrangements to lysogenic conversion
H Brüssow et al.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2004)
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences
D Laslett et al.
NUCLEIC ACIDS RESEARCH (2004)
UCSF chimera - A visualization system for exploratory research and analysis
EF Pettersen et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
MrBayes 3: Bayesian phylogenetic inference under mixed models
F Ronquist et al.
BIOINFORMATICS (2003)
Type IV pilin structure and assembly:: X-ray and EM analyses of Vibrio cholerae toxin-coregulated pilus and Pseudomonas aeruginosa PAK pilin
L Craig et al.
MOLECULAR CELL (2003)
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
K Katoh et al.
NUCLEIC ACIDS RESEARCH (2002)
Gene products encoded in the ninR region of phage λ participate in Red-mediated recombination
TA Tarkowski et al.
GENES TO CELLS (2002)
Phage genomics:: Small is beautiful
H Brüssow et al.
CELL (2002)
MRBAYES: Bayesian inference of phylogenetic trees
JP Huelsenbeck et al.
BIOINFORMATICS (2001)
Genomic sequences of bacteriophages HK97 and HK022: Pervasive genetic mosaicism in the lambdoid bacteriophages
RJ Juhala et al.
JOURNAL OF MOLECULAR BIOLOGY (2000)
Genomic sequence and analysis of the atypical temperate bacteriophage N15
V Ravin et al.
JOURNAL OF MOLECULAR BIOLOGY (2000)