Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis

ACE: adaptive cluster expansion for maximum entropy graphical model inference

(2016) J. P. Barton et al.   BIOINFORMATICS

The Maximum Entropy Fallacy Redux?

(2016) Erik Aurell   PLoS Computational Biology

Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean?

(2016) Erik van Nimwegen   PLoS Computational Biology

Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models

(2016) Hugo Jacquin et al.   PLoS Computational Biology

Identification of pneumococcal colonization determinants in the stringent response pathway facilitated by genomic diversity

(2015) Yuan Li et al.   BMC GENOMICS

The advent of genome-wide association studies for bacteria

(2015) Peter E Chen et al.   CURRENT OPINION IN MICROBIOLOGY

Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1

(2015) Matteo Figliuzzi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Epidemic Clones, Oceanic Gene Pools, and Eco-LD in the Free Living Marine Pathogen Vibrio parahaemolyticus

(2015) Yujun Cui et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis

(2015) Lucy A. Weinert et al.   Nature Communications

MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins

(2014) David T. Jones et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Variable recombination dynamics during the emergence, transmission and ‘disarming’ of a multidrug-resistant pneumococcal clone

(2014) Nicholas J Croucher et al.   BMC BIOLOGY

Evidence for Soft Selective Sweeps in the Evolution of Pneumococcal Multidrug Resistance and Vaccine Escape

(2014) Nicholas J. Croucher et al.   Genome Biology and Evolution

Predicting the virulence of MRSA from its genome sequence

(2014) M. Laabei et al.   GENOME RESEARCH

Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences

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Dense genomic sampling identifies highways of pneumococcal recombination

(2014) Claire Chewapreecha et al.   NATURE GENETICS

Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution

(2014) Astrid von Mentzer et al.   NATURE GENETICS

Evolution and transmission of drug-resistant tuberculosis in a Russian population

(2014) Nicola Casali et al.   NATURE GENETICS

CDD: NCBI's conserved domain database

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Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners

(2014) Carlo Baldassi et al.   PLoS One

Evolutionary pathway to increased virulence and epidemic group A Streptococcus disease derived from 3,615 genome sequences

(2014) W. Nasser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns

(2014) Marcin J. Skwark et al.   PLoS Computational Biology

Improving Contact Prediction along Three Dimensions

(2014) Christoph Feinauer et al.   PLoS Computational Biology

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

(2014) Claire Chewapreecha et al.   PLoS Genetics

Interplay of the Serine/Threonine-Kinase StkP and the Paralogs DivIVA and GpsB in Pneumococcal Cell Elongation and Division

(2014) Aurore Fleurie et al.   PLoS Genetics

Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

(2014) Sergey Ovchinnikov et al.   eLife

Phenotypic, genomic, and transcriptional characterization of Streptococcus pneumoniae interacting with human pharyngeal cells

(2013) Sheila Z Kimaro Mlacha et al.   BMC GENOMICS

Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans

(2013) Iñaki Comas et al.   NATURE GENETICS

Population genomics of post-vaccine changes in pneumococcal epidemiology

(2013) Nicholas J Croucher et al.   NATURE GENETICS

Emerging methods in protein co-evolution

(2013) David de Juan et al.   NATURE REVIEWS GENETICS

Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models

(2013) Magnus Ekeberg et al.   PHYSICAL REVIEW E

Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter

(2013) S. K. Sheppard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013) H. Kamisetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Emergence and global spread of epidemic healthcare-associated Clostridium difficile

(2012) Miao He et al.   NATURE GENETICS

Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing

(2012) Simon R Harris et al.   NATURE GENETICS

Growth dynamics and the evolution of cooperation in microbial populations

(2012) Jonas Cremer et al.   Scientific Reports

Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus

(2012) Santiago Castillo-Ramírez et al.   GENOME BIOLOGY

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

(2011) David T. Jones et al.   BIOINFORMATICS

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid Pneumococcal Evolution in Response to Clinical Interventions

(2011) N. J. Croucher et al.   SCIENCE

Prevalence of Epistasis in the Evolution of Influenza A Surface Proteins

(2011) Sergey Kryazhimskiy et al.   PLoS Genetics

High-dimensional Ising model selection using ℓ 1 -regularized logistic regression

(2010) Pradeep Ravikumar et al.   ANNALS OF STATISTICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

PBP Active Site Flexibility as the Key Mechanism for β-Lactam Resistance in Pneumococci

(2009) Carlos Contreras-Martel et al.   JOURNAL OF MOLECULAR BIOLOGY

Bayesian statistical methods for genetic association studies

(2009) Matthew Stephens et al.   NATURE REVIEWS GENETICS

Simpson's Paradox in a Synthetic Microbial System

(2009) J. S. Chuang et al.   SCIENCE

Role of Conjugative Elements in the Evolution of the Multidrug-Resistant Pandemic Clone Streptococcus pneumoniaeSpain23F ST81

(2008) N. J. Croucher et al.   JOURNAL OF BACTERIOLOGY

Identification of direct residue contacts in protein-protein interaction by message passing

(2008) M. Weigt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coordinated evolution of the hepatitis C virus

(2008) D. S. Campo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA