A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes

'Add, stir and reduce': Yersinia spp. as model bacteria for pathogen evolution

(2016) Alan McNally et al.   NATURE REVIEWS MICROBIOLOGY

Loss of Multicellular Behavior in Epidemic African Nontyphoidal Salmonella enterica Serovar Typhimurium ST313 Strain D23580

(2016) Larissa A. Singletary et al.   mBio

Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host

(2016) Elizabeth J. Klemm et al.   Nature Microbiology

Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies

(2015) Lars Barquist et al.   Annual Review of Genetics

HMMvar-func: a new method for predicting the functional outcome of genetic variants

(2015) Mingming Liu et al.   BMC BIOINFORMATICS

Regional Isolation Drives Bacterial Diversification within Cystic Fibrosis Lungs

(2015) Peter Jorth et al.   Cell Host & Microbe

Taking the pseudo out of pseudogenes

(2015) Ian Goodhead et al.   CURRENT OPINION IN MICROBIOLOGY

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

(2015) Sergey Koren et al.   CURRENT OPINION IN MICROBIOLOGY

The Evaluation of Tools Used to Predict the Impact of Missense Variants Is Hindered by Two Types of Circularity

(2015) Dominik G. Grimm et al.   HUMAN MUTATION

A single natural nucleotide mutation alters bacterial pathogen host tropism

(2015) David Viana et al.   NATURE GENETICS

Twenty years of bacterial genome sequencing

(2015) Nicholas J. Loman et al.   NATURE REVIEWS MICROBIOLOGY

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Allelic variation contributes to bacterial host specificity

(2015) Min Yue et al.   Nature Communications

Signatures of Adaptation in Human Invasive Salmonella Typhimurium ST313 Populations from Sub-Saharan Africa

(2015) Chinyere K. Okoro et al.   PLoS Neglected Tropical Diseases

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis

(2014) Rasmus Lykke Marvig et al.   NATURE GENETICS

Parallel independent evolution of pathogenicity within the genus Yersinia

(2014) S. Reuter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Patterns of genome evolution that have accompanied host adaptation inSalmonella

(2014) Gemma C. Langridge et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative Analysis of Salmonella Genomes Identifies a Metabolic Network for Escalating Growth in the Inflamed Gut

(2014) S.-P. Nuccio et al.   mBio

Comprehensive Identification of Single Nucleotide Polymorphisms Associated with Beta-lactam Resistance within Pneumococcal Mosaic Genes

(2014) Claire Chewapreecha et al.   PLoS Genetics

Salmonella Pathogenicity and Host Adaptation in Chicken-Associated Serovars

(2013) S. L. Foley et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

(2013) J. M. Monk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Epidemic of Extended-Spectrum- -Lactamase-Producing Escherichia coli ST131 Is Driven by a Single Highly Pathogenic Subclone, H30-Rx

(2013) L. B. Price et al.   mBio

Bacterial Adaptation through Loss of Function

(2013) Alison K. Hottes et al.   PLoS Genetics

Developing insights into the mechanisms of evolution of bacterial pathogens from whole-genome sequences

(2012) Josephine Bryant et al.   Future Microbiology

Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models

(2012) Hashem A. Shihab et al.   HUMAN MUTATION

Invasive non-typhoidal salmonella disease: an emerging and neglected tropical disease in Africa

(2012) Nicholas A Feasey et al.   LANCET

Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study

(2012) Simon R Harris et al.   LANCET INFECTIOUS DISEASES

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa

(2012) Chinyere K Okoro et al.   NATURE GENETICS

High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity

(2012) Nicholas J. Loman et al.   NATURE REVIEWS MICROBIOLOGY

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

Evidence for several waves of global transmission in the seventh cholera pandemic

(2011) Ankur Mutreja et al.   NATURE

Predicting the functional impact of protein mutations: application to cancer genomics

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Gene Decay in Shigella as an Incipient Stage of Host-Adaptation

(2011) Ye Feng et al.   PLoS One

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

The Extinction Dynamics of Bacterial Pseudogenes

(2010) Chih-Horng Kuo et al.   PLoS Genetics

Over-optimism in bioinformatics research

(2009) A.-L. Boulesteix   BIOINFORMATICS

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways

(2008) N. R. Thomson et al.   GENOME RESEARCH

Domain-Based and Family-Specific Sequence Identity Thresholds Increase the Levels of Reliable Protein Function Transfer

(2008) Sarah Addou et al.   JOURNAL OF MOLECULAR BIOLOGY

The Population Genetics of dN/dS

(2008) Sergey Kryazhimskiy et al.   PLoS Genetics