(Q37971380)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22199376%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

title

Pathogen comparative genomics in the next-generation sequencing era: genome alignments, pangenomics and metagenomics (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22199376%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

1 reference

1 reference

1 reference

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22199376%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

Chien-Chi Lo

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22199376%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

Patrick S Chain

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22199376%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

author name string

Bin Hu

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22199376%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

Shawn R Starkenburg

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22199376%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

publication date

1 November 2011

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22199376%20AND%20SRC:MED&resulttype=core&format=json

Briefings in functional genomics

19 January 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22199376%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

volume

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22199376%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

issue

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22199376%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

page(s)

322-333

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22199376%20AND%20SRC:MED&resulttype=core&format=json

Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray

19 January 2020

cites work

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Assessment of comparative genomic hybridization experiment by an in situ synthesized CombiMatrix microarray with Yersinia pestis vaccine strain EV76 DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Comparing whole genomes using DNA microarrays

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Comparative analysis of epidermal growth factor receptor mutations and gene amplification as predictors of gefitinib efficacy in Japanese patients with nonsmall cell lung cancer

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Comparative analysis of insulin gene promoters: implications for diabetes research

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Comparative analyses of multi-species sequences from targeted genomic regions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Comparative genomics and evolutionary trajectories of viral ATP dependent DNA-packaging systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Genome sequence of enterohaemorrhagic Escherichia coli O157:H7

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Genomic islands in pathogenic and environmental microorganisms

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

21 January 2018

The microbial pan-genome

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome"

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Building the sequence map of the human pan-genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Estimating the size of the bacterial pan-genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

A catalog of reference genomes from the human microbiome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Comparative genomics: the bacterial pan-genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Efficient oligonucleotide probe selection for pan-genomic tiling arrays

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Next-generation DNA sequencing methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Genome sequence of Yersinia pestis KIM

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Whole-Genome Analyses of Speciation Events in Pathogenic Brucellae

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Complete Genome Sequence of Yersinia pestis Strains Antiqua and Nepal516: Evidence of Gene Reduction in an Emerging Pathogen

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Comparative genomics of Staphylococcus aureus musculoskeletal isolates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Factors characterizing Staphylococcus epidermidis invasiveness determined by comparative genomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Comparative genomic analysis of Vibrio cholerae: genes that correlate with cholera endemic and pandemic disease.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

A simple, fast, and accurate method of phylogenomic inference

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Toward Automatic Reconstruction of a Highly Resolved Tree of Life

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Burkholderia cenocepacia strains isolated from cystic fibrosis patients are apparently more invasive and more virulent than rhizosphere strains

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Molecular evolutionary consequences of niche restriction in Francisella tularensis, a facultative intracellular pathogen

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Microevolution and history of the plague bacillus, Yersinia pestis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Genome sequence of Yersinia pestis, the causative agent of plague

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Pathogenomics of the virulence plasmids of Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Multiple antimicrobial resistance in plague: an emerging public health risk

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Recombination and insertion events involving the botulinum neurotoxin complex genes in Clostridium botulinum types A, B, E and F and Clostridium butyricum type E strains

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

The genome of a pathogenic rhodococcus: cooptive virulence underpinned by key gene acquisitions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Coding-sequence determinants of gene expression in Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Synonymous but not the same: the causes and consequences of codon bias

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Identification of a universal Group B streptococcus vaccine by multiple genome screen

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Diversity considerations in HIV-1 vaccine selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Pathogenic Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Functional characterization of the antibiotic resistance reservoir in the human microflora

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Microbial forensics: DNA fingerprinting of Bacillus anthracis (anthrax).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Humans and evolutionary and ecological forces shaped the phylogeography of recently emerged diseases

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Within-host evolution of Burkholderia pseudomallei in four cases of acute melioidosis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Fast and accurate short read alignment with Burrows-Wheeler transform

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Evaluation of next-generation sequencing software in mapping and assembly

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Fast algorithms for large-scale genome alignment and comparison

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

An applications-focused review of comparative genomics tools: capabilities, limitations and future challenges

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Improving SNP discovery by base alignment quality

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Prodigal: prokaryotic gene recognition and translation initiation site identification

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Identifying bacterial genes and endosymbiont DNA with Glimmer

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

MetaGene: prokaryotic gene finding from environmental genome shotgun sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Mauve: multiple alignment of conserved genomic sequence with rearrangements

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

The RAST Server: rapid annotations using subsystems technology

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

IMG ER: a system for microbial genome annotation expert review and curation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Ergatis: a web interface and scalable software system for bioinformatics workflows

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

DIYA: a bacterial annotation pipeline for any genomics lab.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

RATT: Rapid Annotation Transfer Tool

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Integrative genomics viewer

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Tablet--next generation sequence assembly visualization

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

ACT: the Artemis Comparison Tool

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

De novo assembly and analysis of RNA-seq data.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Velvet: algorithms for de novo short read assembly using de Bruijn graphs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

De novo assembly of human genomes with massively parallel short read sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Short read fragment assembly of bacterial genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

ABySS: a parallel assembler for short read sequence data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Microindel detection in short-read sequence data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

SOAP2: an improved ultrafast tool for short read alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

mrsFAST: a cache-oblivious algorithm for short-read mapping.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

CloudBurst: highly sensitive read mapping with MapReduce

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

BFAST: an alignment tool for large scale genome resequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Genomics. Genome project standards in a new era of sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Sensitive and accurate detection of copy number variants using read depth of coverage

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Reactome: a database of reactions, pathways and biological processes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

21 January 2018

The microbial reactome.

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Reactome: a knowledge base of biologic pathways and processes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Reactome knowledgebase of human biological pathways and processes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

High-throughput generation, optimization and analysis of genome-scale metabolic models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Population diversity and dynamics of Streptococcus mitis, Streptococcus oralis, and Streptococcus infantis in the upper respiratory tracts of adults, determined by a nonculture strategy

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Evolution of Streptococcus pneumoniae and its close commensal relatives.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Comparative transcriptomics in Yersinia pestis: a global view of environmental modulation of gene expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

Comparative Analyses of Transcriptional Profiles in Mouse Organs Using a Pneumonic Plague Model after Infection with Wild-Type Yersinia pestis CO92 and Its Braun Lipoprotein Mutant

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042

The role of Hfq in bacterial pathogens

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELR042