Testing the Role of Genetic Background in Parallel Evolution Using the Comparative Experimental Evolution of Antibiotic Resistance

The cost of antibiotic resistance depends on evolutionary history in Escherichia coli

(2013) Daniel C Angst et al.   BMC EVOLUTIONARY BIOLOGY

Evolution of Escherichia coli rifampicin resistance in an antibiotic-free environment during thermal stress

(2013) Alejandra Rodríguez-Verdugo et al.   BMC EVOLUTIONARY BIOLOGY

Genetic characterization of compensatory evolution in strains carrying rpoB Ser531Leu, the rifampicin resistance mutation most frequently found in clinical isolates

(2013) G. Brandis et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Genotype-by-environment interactions due to antibiotic resistance and adaptation inEscherichia coli

(2013) A. R. Hall   JOURNAL OF EVOLUTIONARY BIOLOGY

Evolutionary biochemistry: revealing the historical and physical causes of protein properties

(2013) Michael J. Harms et al.   NATURE REVIEWS GENETICS

Evolutionary genomics of epidemic and nonepidemic strains of Pseudomonas aeruginosa

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

Putative Compensatory Mutations in the rpoC Gene of Rifampin-Resistant Mycobacterium tuberculosis Are Associated with Ongoing Transmission

(2012) M. de Vos et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Fitness of Escherichia coli strains carrying expressed and partially silent IncN and IncP1 plasmids

(2012) Bruce Humphrey et al.   BMC MICROBIOLOGY

Microevolution of extensively drug-resistant tuberculosis in Russia

(2012) N. Casali et al.   GENOME RESEARCH

The RpoB H481Y Rifampicin Resistance Mutation and an Active Stringent Response Reduce Virulence and Increase Resistance to Innate Immune Responses in Staphylococcus aureus

(2012) Wei Gao et al.   JOURNAL OF INFECTIOUS DISEASES

Fitness-compensatory mutations in rifampicin-resistant RNA polymerase

(2012) Gerrit Brandis et al.   MOLECULAR MICROBIOLOGY

Epistasis as the primary factor in molecular evolution

(2012) Michael S. Breen et al.   NATURE

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Genomics of Adaptation during Experimental Evolution of the Opportunistic Pathogen Pseudomonas aeruginosa

(2012) Alex Wong et al.   PLoS Genetics

MULTIPLE GENETIC PATHWAYS TO SIMILAR FITNESS LIMITS DURING VIRAL ADAPTATION TO A NEW HOST

(2011) Andre H. Nguyen et al.   EVOLUTION

EPISTASIS BUFFERS THE FITNESS EFFECTS OF RIFAMPICIN- RESISTANCE MUTATIONS IN PSEUDOMONAS AERUGINOSA

(2011) Alex R. Hall et al.   EVOLUTION

The Fitness Cost of Rifampicin Resistance in Pseudomonas aeruginosa Depends on Demand for RNA Polymerase

(2011) A. R. Hall et al.   GENETICS

Transfer of an Escherichia coli ST131 multiresistance cassette has created a Klebsiella pneumoniae-specific plasmid associated with a major nosocomial outbreak

(2011) Linus Sandegren et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Defining the Pseudomonas Genus: Where Do We Draw the Line with Azotobacter?

(2011) Asli I. Özen et al.   MICROBIAL ECOLOGY

Parallel evolution and local differentiation in quinolone resistance in Pseudomonas aeruginosa

(2011) A. Wong et al.   MICROBIOLOGY-SGM

Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes

(2011) Tami D Lieberman et al.   NATURE GENETICS

Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes

(2011) Iñaki Comas et al.   NATURE GENETICS

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population

(2011) A. I. Khan et al.   SCIENCE

Evolution in Action: Plants Resistant to Herbicides

(2010) Stephen B. Powles et al.   Annual Review of Plant Biology

SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information

(2010) Gaurav Vaidya et al.   CLADISTICS

Diminishing Returns From Beneficial Mutations and Pervasive Epistasis Shape the Fitness Landscape for Rifampicin Resistance in Pseudomonas aeruginosa

(2010) R. C. MacLean et al.   GENETICS

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Genetic evaluation of relationship between mutations in rpoB and resistance of Mycobacterium tuberculosis to rifampin

(2009) Anna Zaczek et al.   BMC MICROBIOLOGY

Acquisition of High-Level Mupirocin Resistance and Its Fitness Cost among Methicillin-Resistant Staphylococcus aureus Strains with Low-Level Mupirocin Resistance

(2009) K. Mongkolrattanothai et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Phenotypes and gene expression profiles of Saccharopolyspora erythraea rifampicin-resistant (rif) mutants affected in erythromycin production

(2009) Elisabetta Carata et al.   Microbial Cell Factories

Parallel evolution in the major haemoglobin genes of eight species of Andean waterfowl

(2009) K. G. McCRACKEN et al.   MOLECULAR ECOLOGY

Molecular characterization of Rifr mutations in Pseudomonas aeruginosa and Pseudomonas putida

(2009) Tatjana Jatsenko et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Genetic Architecture of Intrinsic Antibiotic Susceptibility

(2009) Hany S. Girgis et al.   PLoS One

The Distribution of Fitness Effects of Beneficial Mutations in Pseudomonas aeruginosa

(2009) R. Craig MacLean et al.   PLoS Genetics

Tuberculosis Drug Resistance Mutation Database

(2009) Andreas Sandgren et al.   PLOS MEDICINE

Parallel Genetic Evolution Within and Between Bacteriophage Species of Varying Degrees of Divergence

(2008) J. P. Bollback et al.   GENETICS

Frequent and Widespread Parallel Evolution of Protein Sequences

(2008) A. Rokas et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Neglected Intrinsic Resistome of Bacterial Pathogens

(2008) Alicia Fajardo et al.   PLoS One

Accumulation of mutants in "aging" bacterial colonies is due to growth under selection, not stress-induced mutagenesis

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

The genetic basis of parallel and divergent phenotypic responses in evolving populations of Escherichia coli

(2007) E. A Ostrowski et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES