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

Improving SNP discovery by base alignment quality

(2011) H. Li   BIOINFORMATICS

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

(2011) Alexej Abyzov et al.   BIOINFORMATICS

Evaluation of next-generation sequencing software in mapping and assembly

(2011) Suying Bao et al.   JOURNAL OF HUMAN GENETICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

RATT: Rapid Annotation Transfer Tool

(2011) Thomas D. Otto et al.   NUCLEIC ACIDS RESEARCH

Microindel detection in short-read sequence data

(2010) Peter Krawitz et al.   BIOINFORMATICS

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery

(2010) Fereydoun Hormozdiari et al.   BIOINFORMATICS

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

(2010) J. Orvis et al.   BIOINFORMATICS

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

(2010) Bruno Zeitouni et al.   BIOINFORMATICS

Assessment of Comparative Genomic Hybridization Experiment by an in situ Synthesized CombiMatrix Microarray with Yersinia pestis Vaccine Strain EV76 DNA

(2010) Yuan-Hai YOU et al.   BIOMEDICAL AND ENVIRONMENTAL SCIENCES

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

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

(2010) Jeffrey Martin et al.   BMC GENOMICS

Comparative Analyses of Transcriptional Profiles in Mouse Organs Using a Pneumonic Plague Model after Infection with Wild-TypeYersinia pestisCO92 and Its Braun Lipoprotein Mutant

(2010) Cristi L. Galindo et al.   COMPARATIVE AND FUNCTIONAL GENOMICS

The role of Hfq in bacterial pathogens

(2010) Yanjie Chao et al.   CURRENT OPINION IN MICROBIOLOGY

Evolutionary Dynamics of Complete Campylobacter Pan-Genomes and the Bacterial Species Concept

(2010) Tristan Lefébure et al.   Genome Biology and Evolution

Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies

(2010) Sébastien Boisvert et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity

(2010) Giovanna Morelli et al.   NATURE GENETICS

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

(2010) Faraz Hach et al.   NATURE METHODS

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

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

(2010) Joshua B. Plotkin et al.   NATURE REVIEWS GENETICS

Reactome: a database of reactions, pathways and biological processes

(2010) D. Croft et al.   NUCLEIC ACIDS RESEARCH

A Catalog of Reference Genomes from the Human Microbiome

(2010) et al.   SCIENCE

The Genome of a Pathogenic Rhodococcus: Cooptive Virulence Underpinned by Key Gene Acquisitions

(2010) Michal Letek et al.   PLoS Genetics

Within-Host Evolution of Burkholderia pseudomallei in Four Cases of Acute Melioidosis

(2010) Erin P. Price et al.   PLoS Pathogens

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

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

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

(2010) Claudio Donati et al.   GENOME BIOLOGY

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

(2009) Bas E. Dutilh et al.   BIOINFORMATICS

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

(2009) Zia Khan et al.   BIOINFORMATICS

DIYA: a bacterial annotation pipeline for any genomics lab

(2009) Andrew C. Stewart et al.   BIOINFORMATICS

CloudBurst: highly sensitive read mapping with MapReduce

(2009) M. C. Schatz   BIOINFORMATICS

Tablet--next generation sequence assembly visualization

(2009) I. Milne et al.   BIOINFORMATICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

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

(2009) Victor M. Markowitz et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Efficient oligonucleotide probe selection for pan-genomic tiling arrays

(2009) Adam M Phillippy et al.   BMC BIOINFORMATICS

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

(2009) Karen K Hill et al.   BMC BIOLOGY

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

(2009) S. Yoon et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

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

(2009) R. Li et al.   GENOME RESEARCH

Pathogenomics of the Virulence Plasmids of Escherichia coli

(2009) T. J. Johnson et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

Building the sequence map of the human pan-genome

(2009) Ruiqiang Li et al.   NATURE BIOTECHNOLOGY

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

(2009) Iwanka Kozarewa et al.   NATURE METHODS

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

(2009) Ken Chen et al.   NATURE METHODS

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

(2009) Paul S. Keim et al.   NATURE REVIEWS MICROBIOLOGY

Sequencing the species pan-genome

(2009) Stephen Bentley   NATURE REVIEWS MICROBIOLOGY

BFAST: An Alignment Tool for Large Scale Genome Resequencing

(2009) Nils Homer et al.   PLoS One

Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing

(2009) D. R. Yoder-Himes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome Project Standards in a New Era of Sequencing

(2009) P. S. G. Chain et al.   SCIENCE

Coding-Sequence Determinants of Gene Expression in Escherichia coli

(2009) G. Kudla et al.   SCIENCE

Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora

(2009) M. O. A. Sommer et al.   SCIENCE

Estimating the size of the bacterial pan-genome

(2009) Pascal Lapierre et al.   TRENDS IN GENETICS

The microbial reactome

(2009) Manuel Ferrer   Microbial Biotechnology

Molecular Evolutionary Consequences of Niche Restriction in Francisella tularensis, a Facultative Intracellular Pathogen

(2009) Pär Larsson et al.   PLoS Pathogens

Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses

(2009) Xiyin Wang et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Microbial Forensics: DNA Fingerprinting ofBacillus anthracis(Anthrax)

(2008) Paul Keim et al.   ANALYTICAL CHEMISTRY

Next-Generation DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Comparative genomics: the bacterial pan-genome

(2008) Hervé Tettelin et al.   CURRENT OPINION IN MICROBIOLOGY

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

(2008) Luisa Pirone et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Population Diversity and Dynamics of Streptococcus mitis, Streptococcus oralis, and Streptococcus infantis in the Upper Respiratory Tracts of Adults, Determined by a Nonculture Strategy

(2008) M. Bek-Thomsen et al.   INFECTION AND IMMUNITY

The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates

(2008) D. A. Rasko et al.   JOURNAL OF BACTERIOLOGY

Comparing whole genomes using DNA microarrays

(2008) David Gresham et al.   NATURE REVIEWS GENETICS

Evolution of Streptococcus pneumoniae and Its Close Commensal Relatives

(2008) Mogens Kilian et al.   PLoS One

A simple, fast, and accurate method of phylogenomic inference

(2008) Martin Wu et al.   GENOME BIOLOGY

Short read fragment assembly of bacterial genomes

(2007) M. J. Chaisson et al.   GENOME RESEARCH

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

(2007) Lakshminarayan M. Iyer et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY