Whole genome sequencing of the monomorphic pathogen Mycobacterium bovis reveals local differentiation of cattle clinical isolates

Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations

(2017) Rafal Mostowy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Epidemiological investigation of bovine tuberculosis outbreaks in Uruguay (2011–2013)

(2017) Catalina Picasso et al.   PREVENTIVE VETERINARY MEDICINE

Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages

(2016) Jody E. Phelan et al.   BMC GENOMICS

Molecular Typing of Mycobacterium bovis from Cattle Reared in Midwest Brazil

(2016) Ricardo César Tavares Carvalho et al.   PLoS One

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Phylogeny to function: PE/PPE protein evolution and impact onMycobacterium tuberculosispathogenicity

(2015) S. Fishbein et al.   MOLECULAR MICROBIOLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Genome-wide association study identifies novel loci associated with resistance to bovine tuberculosis

(2014) M L Bermingham et al.   HEREDITY

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

(2014) Bastian Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

(2014) Francesc Coll et al.   Nature Communications

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

CISA: Contig Integrator for Sequence Assembly of Bacterial Genomes

(2013) Shin-Hung Lin et al.   PLoS One

The Role of Selection in Shaping Diversity of Natural M. tuberculosis Populations

(2013) Caitlin S. Pepperell et al.   PLoS Pathogens

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Single Nucleotide Polymorphisms in the Mycobacterium bovis Genome Resolve Phylogenetic Relationships

(2012) D. Joshi et al.   JOURNAL OF CLINICAL MICROBIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs

(2012) Martin T Swain et al.   Nature Protocols

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Bacterial Cell Surface Heterogeneity: A Pathogen's Disguise

(2012) Henny C. van der Mei et al.   PLoS Pathogens

Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift

(2012) Pablo Cingolani et al.   Frontiers in Genetics

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

Copy-Number Variation: The Balance between Gene Dosage and Expression in Drosophila melanogaster

(2011) Jun Zhou et al.   Genome Biology and Evolution

European 2 – A clonal complex of Mycobacterium bovis dominant in the Iberian Peninsula

(2011) Sabrina Rodriguez-Campos et al.   INFECTION GENETICS AND EVOLUTION

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

African 2, a Clonal Complex of Mycobacterium bovis Epidemiologically Important in East Africa

(2010) S. Berg et al.   JOURNAL OF BACTERIOLOGY

Dosage Sensitivity Shapes the Evolution of Copy-Number Varied Regions

(2010) Benjamin Schuster-Böckler et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

African 1, an Epidemiologically Important Clonal Complex of Mycobacterium bovis Dominant in Mali, Nigeria, Cameroon, and Chad

(2009) B. Muller et al.   JOURNAL OF BACTERIOLOGY

Genotyping of Genetically Monomorphic Bacteria: DNA Sequencing in Mycobacterium tuberculosis Highlights the Limitations of Current Methodologies

(2009) Iñaki Comas et al.   PLoS One

Mycobacterium bovis at the animal–human interface: A problem, or not?

(2009) Anita Luise Michel et al.   VETERINARY MICROBIOLOGY

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

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

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

Frequent Homologous Recombination Events in Mycobacterium tuberculosis PE/PPE Multigene Families: Potential Role in Antigenic Variability

(2008) A. Karboul et al.   JOURNAL OF BACTERIOLOGY