Evolutionary Transition from Pathogenicity to Commensalism: Global Regulator Mutations Mediate Fitness Gains through Virulence Attenuation

Microbial pathogenesis and host defense in the nematode C. elegans

(2015) Lianne B Cohen et al.   CURRENT OPINION IN MICROBIOLOGY

Host–Pathogen Coevolution: The Selective Advantage of Bacillus thuringiensis Virulence and Its Cry Toxin Genes

(2015) Leila Masri et al.   PLOS BIOLOGY

The Effect of Immunodeficiency on the Evolution of Virulence: An Experimental Test with the Rodent Malaria Plasmodium chabaudi

(2014) Victoria C. Barclay et al.   AMERICAN NATURALIST

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

(2014) Rasmus Lykke Marvig et al.   NATURE GENETICS

Niche engineering demonstrates a latent capacity for fungal-algal mutualism

(2014) E. F. Y. Hom et al.   SCIENCE

Symbiosis as a General Principle in Eukaryotic Evolution

(2014) A. E. Douglas   Cold Spring Harbor Perspectives in Biology

Sex differences in host defence interfere with parasite-mediated selection for outcrossing during host-parasite coevolution

(2013) Leila Masri et al.   ECOLOGY LETTERS

Evolutionary remodeling of global regulatory networks during long-term bacterial adaptation to human hosts

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

Animals in a bacterial world, a new imperative for the life sciences

(2013) Margaret McFall-Ngai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Immune defense mechanisms in the Caenorhabditis elegans intestinal epithelium

(2012) Read Pukkila-Worley et al.   CURRENT OPINION IN IMMUNOLOGY

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

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

A Symbiotic View of Life: We Have Never Been Individuals

(2012) Scott F. Gilbert et al.   QUARTERLY REVIEW OF BIOLOGY

Experimental evolution

(2012) Tadeusz J. Kawecki et al.   TRENDS IN ECOLOGY & EVOLUTION

Genome-Wide Identification of Pseudomonas aeruginosa Virulence-Related Genes Using a Caenorhabditis elegans Infection Model

(2012) Rhonda L. Feinbaum et al.   PLoS Pathogens

Evolutionary History and Attenuation of Myxoma Virus on Two Continents

(2012) Peter J. Kerr et al.   PLoS Pathogens

A Role for SKN-1/Nrf in Pathogen Resistance and Immunosenescence in Caenorhabditis elegans

(2012) Diána Papp et al.   PLoS Pathogens

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

(2011) A. Abyzov et al.   GENOME RESEARCH

Microbial laboratory evolution in the era of genome-scale science

(2011) T. M. Conrad et al.   Molecular Systems Biology

SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data

(2011) Zhi Wei et al.   NUCLEIC ACIDS RESEARCH

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

(2011) Robert Kofler et al.   PLoS One

Running with the Red Queen: Host-Parasite Coevolution Selects for Biparental Sex

(2011) L. T. Morran et al.   SCIENCE

Ce-Duox1/BLI-3 Generated Reactive Oxygen Species Trigger Protective SKN-1 Activity via p38 MAPK Signaling during Infection in C. elegans

(2011) Ransome van der Hoeven et al.   PLoS Pathogens

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

NOVEL COOPERATION EXPERIMENTALLY EVOLVED BETWEEN SPECIES

(2010) William Harcombe   EVOLUTION

Divergence Involving Global Regulatory Gene Mutations in an Escherichia coli Population Evolving under Phosphate Limitation

(2010) Lei Wang et al.   Genome Biology and Evolution

Rapid evolution of stability and productivity at the origin of a microbial mutualism

(2010) K. L. Hillesland et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiple reciprocal adaptations and rapid genetic change upon experimental coevolution of an animal host and its microbial parasite

(2010) R. D. Schulte et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phenotypic connections in surprising places

(2010) Bolan Linghu et al.   GENOME BIOLOGY

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Increased RNA polymerase availability directs resources towards growth at the expense of maintenance

(2009) Bertil Gummesson et al.   EMBO JOURNAL

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Evolutionary Ecology of Figs and Their Associates: Recent Progress and Outstanding Puzzles

(2008) Edward Allen Herre et al.   Annual Review of Ecology Evolution and Systematics

The great leap forward. Major evolutionary jumps might be caused by changes in gene regulation rather than the emergence of new genes

(2008) Philip Hunter   EMBO REPORTS

Specificity of the innate immune system and diversity of C-type lectin domain (CTLD) proteins in the nematode Caenorhabditis elegans

(2008) Hinrich Schulenburg et al.   IMMUNOBIOLOGY

Pseudomonas aeruginosa lasR mutants are associated with cystic fibrosis lung disease progression

(2008) Lucas R. Hoffman et al.   Journal of Cystic Fibrosis

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Major evolutionary transitions in ant agriculture

(2008) T. R. Schultz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pseudomonas aeruginosa Suppresses Host Immunity by Activating the DAF-2 Insulin-Like Signaling Pathway in Caenorhabditis elegans

(2008) Eric A. Evans et al.   PLoS Pathogens