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。Insights from genome-wide approaches to identify variants associated to phenotypes at pan-genome scale: Application to L-monocytogenes' ability to grow in cold conditions
Lena Fritsch et al.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY (2019)
Tracing outbreaks with machine learning
Nicole E. Wheeler
NATURE REVIEWS MICROBIOLOGY (2019)
The European Nucleotide Archive in 2018
Peter W. Harrison et al.
NUCLEIC ACIDS RESEARCH (2019)
Zoonotic Source Attribution of Salmonella enterica Serotype Typhimurium Using Genomic Surveillance Data, United States
Shaokang Zhang et al.
EMERGING INFECTIOUS DISEASES (2019)
Intestine specific regulation of pig cytidine-5′-monophospho-N-acetylneuraminic acid hydroxylase gene for N-glycolylneuraminic acid biosynthesis
Kwon-Ho Song et al.
SCIENTIFIC REPORTS (2019)
UFBoot2: Improving the Ultrafast Bootstrap Approximation
Diep Thi Hoang et al.
MOLECULAR BIOLOGY AND EVOLUTION (2018)
Effects of dietary valine: lysine ratio on the performance, amino acid composition of tissues and mRNA expression of genes involved in branched-chain amino acid metabolism of weaned piglets
Ye Tong Xu et al.
ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES (2018)
Effects of glutamate and aspartate on growth performance, serum amino acids, and amino acid transporters in piglets
Yuying Li et al.
FOOD AND AGRICULTURAL IMMUNOLOGY (2018)
Thimerosal changes protein conformation and increase the rate of fibrillation in physiological conditions: Spectroscopic studies using bovine serum albumin (BSA)
Joao Cesar N. Santos et al.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES (2018)
Population genomics of bacterial host adaptation
Samuel K. Sheppard et al.
NATURE REVIEWS GENETICS (2018)
Role of a single noncoding nucleotide in the evolution of an epidemic African clade of Salmonella
Disa L. Hammarlof et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)
Evolution of Salmonella within Hosts
Jennifer R. Tanner et al.
TRENDS IN MICROBIOLOGY (2018)
A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination
Caitlin Collins et al.
PLOS COMPUTATIONAL BIOLOGY (2018)
A genomic overview of the population structure of Salmonella
Nabil-Fareed Alikhan et al.
PLOS GENETICS (2018)
Aspartate metabolism is involved in the maintenance of enterohaemorrhagic Escherichia coli O157:H7 in bovine intestinal content
Yolande Bertin et al.
ENVIRONMENTAL MICROBIOLOGY (2018)
Genome-wide identification of geographical segregated genetic markers in Salmonella enterica serovar Typhimurium variant 4,[5],12:i:-
Federica Palma et al.
SCIENTIFIC REPORTS (2018)
A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events
Magali Jaillard et al.
PLOS GENETICS (2018)
Microbial genome-wide association studies: lessons from human GWAS
Robert A. Power et al.
NATURE REVIEWS GENETICS (2017)
UniProt: the universal protein knowledgebase
Alex Bateman et al.
NUCLEIC ACIDS RESEARCH (2017)
Local genes for local bacteria: Evidence of allopatry in the genomes of transatlantic Campylobacter populations
Ben Pascoe et al.
MOLECULAR ECOLOGY (2017)
ModelFinder: fast model selection for accurate phylogenetic estimates
Subha Kalyaanamoorthy et al.
NATURE METHODS (2017)
Evolution of Salmonella-Host Cell Interactions through a Dynamic Bacterial Genome
Bushra Ilyas et al.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY (2017)
Pan-genome Analyses of the Species Salmonella enterica, and Identification of Genomic Markers Predictive for Species, Subspecies, and Serovar
Chad R. Laing et al.
FRONTIERS IN MICROBIOLOGY (2017)
A novel hypothesis-unbiased method for Gene Ontology enrichment based on transcriptome data
Mario Fruzangohar et al.
PLOS ONE (2017)
First gene-ontology enrichment analysis based on bacterial coregenome variants: insights into adaptations of Salmonella serovars to mammalian- and avian-hosts
Arnaud Felten et al.
BMC MICROBIOLOGY (2017)
An Oxidative Central Metabolism Enables Salmonella to Utilize Microbiota-Derived Succinate
Luisella Spiga et al.
CELL HOST & MICROBE (2017)
Tracing Origins of the Salmonella Bareilly Strain Causing a Food-borne Outbreak in the United States
Maria Hoffmann et al.
JOURNAL OF INFECTIOUS DISEASES (2016)
MultiQC: summarize analysis results for multiple tools and samples in a single report
Philip Ewels et al.
BIOINFORMATICS (2016)
RNA helicases in bacteria
Vanessa Khemici et al.
CURRENT OPINION IN MICROBIOLOGY (2016)
Conserved Features in the Structure, Mechanism, and Biogenesis of the Inverse Autotransporter Protein Family
Eva Heinz et al.
GENOME BIOLOGY AND EVOLUTION (2016)
A network-based analysis of colon cancer splicing changes reveals a tumorigenesis-favoring regulatory pathway emanating from ELK1
Dror Hollander et al.
GENOME RESEARCH (2016)
Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance
Christopher A. Desjardins et al.
NATURE GENETICS (2016)
Bacterial GWAS: not just gilding the lily
John A. Lees et al.
NATURE REVIEWS MICROBIOLOGY (2016)
Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes
John A. Lees et al.
NATURE COMMUNICATIONS (2016)
Identifying lineage effects when controlling for population structure improves power in bacterial association studies
Sarah G. Earle et al.
NATURE MICROBIOLOGY (2016)
The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies
Catherine E. Yoshida et al.
PLOS ONE (2016)
Genome-Wide Association Study of HIV Whole Genome Sequences Validated using Drug Resistance
Robert A. Power et al.
PLOS ONE (2016)
Extraction and Characterization of Refined K-carrageenan of Red Algae [Kappaphycus alvarezii (Doty ex PC Silva, 1996)] Originated from Karimun Jawa Islands
Godras Jati Manuhara et al.
2ND INTERNATIONAL SYMPOSIUM ON AQUATIC PRODUCTS PROCESSING AND HEALTH, ISAPPROSH 2015 (2016)
Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary
Ola Brynildsrud et al.
GENOME BIOLOGY (2016)
Mash: fast genome and metagenome distance estimation using MinHash
Brian D. Ondov et al.
GENOME BIOLOGY (2016)
MEDUSA: a multi-draft based scaffolder
Emanuele Bosi et al.
BIOINFORMATICS (2015)
Roary: rapid large-scale prokaryote pan genome analysis
Andrew J. Page et al.
BIOINFORMATICS (2015)
The advent of genome-wide association studies for bacteria
Peter E. Chen et al.
CURRENT OPINION IN MICROBIOLOGY (2015)
A Male-Specific Genetic Map of the Microcrustacean Daphnia pulex Based on Single-Sperm Whole-Genome Sequencing
Sen Xu et al.
GENETICS (2015)
Genetic architecture of artemisinin-resistant Plasmodium falciparum
Olivo Miotto et al.
NATURE GENETICS (2015)
The Evolution of Campylobacter jejuni and Campylobacter coli
Samuel K. Sheppard et al.
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2015)
ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
Xavier Didelot et al.
PLOS COMPUTATIONAL BIOLOGY (2015)
BOG: R-package for Bacterium and virus analysis of Orthologous Groups
Jincheol Park et al.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2015)
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
Lam-Tung Nguyen et al.
MOLECULAR BIOLOGY AND EVOLUTION (2015)
Patterns of genome evolution that have accompanied host adaptation in Salmonella
Gemma C. Langridge et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
First Complete Genome Sequence of a Salmonella enterica subsp. enterica Serovar Derby Strain Associated with Pork in France
Annaelle Kerouanton et al.
GENOME ANNOUNCEMENTS (2015)
Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony M. Bolger et al.
BIOINFORMATICS (2014)
Mercury exposure in a large subantarctic avian community
Alice Carravieri et al.
ENVIRONMENTAL POLLUTION (2014)
Dissecting Vancomycin-Intermediate Resistance in Staphylococcus aureus Using Genome-Wide Association
Md Tauqeer Alam et al.
GENOME BIOLOGY AND EVOLUTION (2014)
Predicting the virulence of MRSA from its genome sequence
Maisem Laabei et al.
GENOME RESEARCH (2014)
Prioritizing Disease-Linked Variants, Genes, and Pathways with an Interactive Whole-Genome Analysis Pipeline
In-Hee Lee et al.
HUMAN MUTATION (2014)
When to use the Bonferroni correction
Richard A. Armstrong
OPHTHALMIC AND PHYSIOLOGICAL OPTICS (2014)
GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers
Sebastian Juenemann et al.
PLOS ONE (2014)
Bacterial Phylogenetic Reconstruction from Whole Genomes Is Robust to Recombination but Demographic Inference Is Not
Jessica Hedge et al.
MBIO (2014)
Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology
Timothy D. Read et al.
GENOME MEDICINE (2014)
Comprehensive Identification of Single Nucleotide Polymorphisms Associated with Beta-lactam Resistance within Pneumococcal Mosaic Genes
Claire Chewapreecha et al.
PLOS GENETICS (2014)
QUAST: quality assessment tool for genome assemblies
Alexey Gurevich et al.
BIOINFORMATICS (2013)
Genomic diversity and adaptation of Salmonella enterica serovar Typhimurium from analysis of six genomes of different phage types
Stanley Pang et al.
BMC GENOMICS (2013)
Pharmacology of polymyxins: new insights into an 'old' class of antibiotics
Tony Velkov et al.
FUTURE MICROBIOLOGY (2013)
EptC of Campylobacter jejuni Mediates Phenotypes Involved in Host Interactions and Virulence
Thomas W. Cullen et al.
INFECTION AND IMMUNITY (2013)
The PriA Replication Restart Protein Blocks Replicase Access Prior to Helicase Assembly and Directs Template Specificity through Its ATPase Activity
Carol M. Manhart et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2013)
Expression Divergence between Escherichia coli and Salmonella enterica serovar Typhimurium Reflects Their Lifestyles
Pieter Meysman et al.
MOLECULAR BIOLOGY AND EVOLUTION (2013)
Ultrafast Approximation for Phylogenetic Bootstrap
Bui Quang Minh et al.
MOLECULAR BIOLOGY AND EVOLUTION (2013)
Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis
Maha R. Farhat et al.
NATURE GENETICS (2013)
Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity
Svetlana A. Shabalina et al.
NUCLEIC ACIDS RESEARCH (2013)
Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter
Samuel K. Sheppard et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Identification of the YfgF MASE1 domain as a modulator of bacterial responses to aspartate
Melissa Lacey et al.
OPEN BIOLOGY (2013)
Neutral Genomic Microevolution of a Recently Emerged Pathogen, Salmonella enterica Serovar Agona
Zhemin Zhou et al.
PLOS GENETICS (2013)
A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control
Istvan Bartha et al.
ELIFE (2013)
Animal salmonelloses: a brief review of host adaptation and host specificity of Salmonella spp.
Grammato Evangelopoulou et al.
VETERINARY WORLD (2013)
Effects of Disinfection on Legionella spp., Eukarya, and Biofilms in a Hot Water System
Maha Farhat et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2012)
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Anton Bankevich et al.
JOURNAL OF COMPUTATIONAL BIOLOGY (2012)
Iron Availability Increases the Pathogenic Potential of Salmonella Typhimurium and Other Enteric Pathogens at the Intestinal Epithelial Interface
Guus A. M. Kortman et al.
PLOS ONE (2012)
Livestock-associated Staphylococcus aureus: origin, evolution and public health threat
J. Ross Fitzgerald
TRENDS IN MICROBIOLOGY (2012)
phytools: an R package for phylogenetic comparative biology (and other things)
Liam J. Revell
METHODS IN ECOLOGY AND EVOLUTION (2012)
Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift
Pablo Cingolani et al.
Frontiers in Genetics (2012)
Comparative Genomics of 28 Salmonella enterica Isolates: Evidence for CRISPR-Mediated Adaptive Sublineage Evolution
W. Florian Fricke et al.
JOURNAL OF BACTERIOLOGY (2011)
Toxicokinetics of Mercury after Long-Term Repeated Exposure to Thimerosal-Containing Vaccine
Lars Barregard et al.
TOXICOLOGICAL SCIENCES (2011)
Salmonella bongori Provides Insights into the Evolution of the Salmonellae
Maria Fookes et al.
PLOS PATHOGENS (2011)
Host Association of Campylobacter Genotypes Transcends Geographic Variation
Samuel K. Sheppard et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2010)
The Global Burden of Nontyphoidal Salmonella Gastroenteritis
Shannon E. Majowicz et al.
CLINICAL INFECTIOUS DISEASES (2010)
The F plasmid transfer activator TraJ is a dimeric helix-turn-helix DNA-binding protein
J. Manuel Rodriguez-Maillard et al.
FEMS MICROBIOLOGY LETTERS (2010)
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
Aaron McKenna et al.
GENOME RESEARCH (2010)
Genotype imputation for genome-wide association studies
Jonathan Marchini et al.
NATURE REVIEWS GENETICS (2010)
Supplement 2003-2007 (No. 47) to the White-Kauffmann-Le Minor scheme
Martine Guibourdenche et al.
RESEARCH IN MICROBIOLOGY (2010)
Impact of recombination on bacterial evolution
Xavier Didelot et al.
TRENDS IN MICROBIOLOGY (2010)
Isoleucine and valine supplementation of crude protein-reduced diets for pigs aged 5-8 weeks
J. V. Norgaard et al.
ANIMAL FEED SCIENCE AND TECHNOLOGY (2009)
Variation in Salmonella enterica Serovar Typhi IncHI1 Plasmids during the Global Spread of Resistant Typhoid Fever
Minh-Duy Phan et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2009)
Biopython: freely available Python tools for computational molecular biology and bioinformatics
Peter J. A. Cock et al.
BIOINFORMATICS (2009)
HicA of Escherichia coli Defines a Novel Family of Translation-Independent mRNA Interferases in Bacteria and Archaea
Mikkel G. Jorgensen et al.
JOURNAL OF BACTERIOLOGY (2009)
GENOME-WIDE ASSOCIATION STUDIES Validating, augmenting and refining genome-wide association signals
John P. A. Ioannidis et al.
NATURE REVIEWS GENETICS (2009)
Limitations of dietary isoleucine and valine in broiler chick diets
A. Corzo et al.
POULTRY SCIENCE (2009)
Recent human-to-poultry host jump, adaptation, and pandemic spread of Staphylococcus aureus
Bethan V. Lowder et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Estimation of significance thresholds for genomewide association scans
Frank Dudbridge et al.
GENETIC EPIDEMIOLOGY (2008)
Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways
Nicholas R. Thomson et al.
GENOME RESEARCH (2008)
Evolution of genes on the Salmonella Virulence plasmid phylogeny revealed from sequencing of the virulence plasmids of S. enterica serotype Dublin and comparative analysis
Chishih Chu et al.
GENOMICS (2008)
Improved detection of overrepresentation of Gene-Ontology annotations with parentchild analysis
Steffen Grossmann et al.
BIOINFORMATICS (2007)
PLINK: A tool set for whole-genome association and population-based linkage analyses
Shaun Purcell et al.
AMERICAN JOURNAL OF HUMAN GENETICS (2007)
Replicating genotype-phenotype associations
Stephen J. Chanock et al.
NATURE (2007)
The use of vaccination in poultry production
S. Marangon et al.
REVUE SCIENTIFIQUE ET TECHNIQUE-OFFICE INTERNATIONAL DES EPIZOOTIES (2007)
Roles of E-coli double-strand-break-repair proteins in stress-induced mutation
AS He et al.
DNA REPAIR (2006)
Differences in gene content between Salmonella enterica serovar enteritidis isolates and comparison to closely related serovars gallinarum and Dublin
S Porwollik et al.
JOURNAL OF BACTERIOLOGY (2005)
The cyanobacterial phytochrome Cph2 inhibits phototaxis towards blue light
A Wilde et al.
MOLECULAR MICROBIOLOGY (2002)
Salmonella enterica serotype Typhimurium and its host-adapted variants
W Rabsch et al.
INFECTION AND IMMUNITY (2002)
The RihA, RihB, and RihC ribonucleoside hydrolases of Escherichia coli -: Substrate specificity, gene expression and regulation
C Petersen et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2001)
Genetic and functional analysis of a PmrA-PmrB-regulated locus necessary for lipopolysaccharide modification, antimicrobial peptide resistance, and oral virulence of Salmonella enterica serovar typhimurium
JS Gunn et al.
INFECTION AND IMMUNITY (2000)
Incidence of Salmonella in fish and seafood
ML Heinitz et al.
JOURNAL OF FOOD PROTECTION (2000)