Bioinformatics Aspects of Foodborne Pathogen Research (Q58112596)

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Identification and correction of systematic error in high-throughput sequence data

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Characterizing and measuring bias in sequence data

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Fast gapped-read alignment with Bowtie 2

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Fast and accurate short read alignment with Burrows-Wheeler transform

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Prospective Whole-Genome Sequencing Enhances National Surveillance of Listeria monocytogenes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

When whole-genome alignments just won't work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

De novo assembly and genotyping of variants using colored de Bruijn graphs

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

High-throughput microbial population genomics using the Cortex variation assembler

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

A whole-genome assembly of Drosophila

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

The automatic annotation of bacterial genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Prokka: rapid prokaryotic genome annotation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Lysergic acid diethylamide- and mescaline-induced attenuation of the effect of punishment in the rat

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Complete genome sequence of Salmonella enterica serovar Typhimurium LT2

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

The RAST Server: rapid annotations using subsystems technology

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Improved microbial gene identification with GLIMMER

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Prodigal: prokaryotic gene recognition and translation initiation site identification

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Ten years of pan-genome analyses

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

ITEP: an integrated toolkit for exploration of microbial pan-genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

An efficient algorithm for large-scale detection of protein families

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Basic local alignment search tool

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Roary: rapid large-scale prokaryote pan genome analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

CD-HIT: accelerated for clustering the next-generation sequencing data

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Application of phylogenetic networks in evolutionary studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Long-branch attraction bias and inconsistency in Bayesian phylogenetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

A gateway for phylogenetic analysis powered by grid computing featuring GARLI 2.0.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Short tree, long tree, right tree, wrong tree: new acquisition bias corrections for inferring SNP phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

A likelihood approach to estimating phylogeny from discrete morphological character data

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

BEAST: Bayesian evolutionary analysis by sampling trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

The effect of recombination on the accuracy of phylogeny estimation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

ClonalFrameML: efficient inference of recombination in whole bacterial genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Detection of recombination events in bacterial genomes from large population samples

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Bacterial phylogenetic reconstruction from whole genomes is robust to recombination but demographic inference is not.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Genome sequence of enterohaemorrhagic Escherichia coli O157:H7

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Performance comparison of benchtop high-throughput sequencing platforms

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Assemblathon 1: a competitive assessment of de novo short read assembly methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Anthrax molecular epidemiology and forensics: using the appropriate marker for different evolutionary scales

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Real-time genomic epidemiological evaluation of human Campylobacter isolates by use of whole-genome multilocus sequence typing

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing of Listeria monocytogenes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Environmental genome shotgun sequencing of the Sargasso Sea

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Comparative Analysis of 16S and 23S rRNA Sequences of Listeria Species

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

QIIME allows analysis of high-throughput community sequencing data

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Search and clustering orders of magnitude faster than BLAST

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Analysis of 16S rRNA environmental sequences using MEGAN

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Season, irrigation, leaf age, and Escherichia coli inoculation influence the bacterial diversity in the lettuce phyllosphere

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Bayesian community-wide culture-independent microbial source tracking

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Evaluation of bacterial contamination in raw milk, ultra-high temperature milk and infant formula using single molecule, real-time sequencing technology

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Application of metagenomic sequencing to food safety: detection of Shiga Toxin-producing Escherichia coli on fresh bagged spinach

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Potential impact of recombination on sitewise approaches for detecting positive natural selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

Impacts of culture-independent diagnostic practices on public health surveillance for bacterial enteric pathogens

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/978-3-319-43751-4_4

CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data

31 March 2020

1 reference

COCI

https://opencitations.net/index/coci/api/v1/citations/10.7717/PEERJ-CS.20