Strain-level diversity of symbiont communities between individuals and populations of a bioluminescent fish

Museum Genomics Illuminate the High Specificity of a Bioluminescent Symbiosis for a Genus of Reef Fish

(2021) Alison L. Gould et al.   Frontiers in Ecology and Evolution

The impact of LuxF on light intensity in bacterial bioluminescence

(2020) Eveline Brodl et al.   JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY

Strain diversity in the microbiome: Lessons from Bacteroides fragilis

(2020) Hannah C. Carrow et al.   PLoS Pathogens

Symbiont evolution during the free-living phase can improve host colonization

(2019) William Soto et al.   MICROBIOLOGY-SGM

Division of labor in honey bee gut microbiota for plant polysaccharide digestion

(2019) Hao Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Shedding Light on Specificity: Population Genomic Structure of a Symbiosis Between a Coral Reef Fish and Luminous Bacterium

(2019) Alison L. Gould et al.   Frontiers in Microbiology

OUP accepted manuscript

(2018)   BIOINFORMATICS

Fitness variation among host species and the paradox of ineffective rhizobia

(2018) V. J. Pahua et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Phylogeographic patterns in the Philippine archipelago influence symbiont diversity in the bobtail squid-Vibrio mutualism

(2018) Randy L. Coryell et al.   Ecology and Evolution

Achieving a multi-strain symbiosis: strain behavior and infection dynamics

(2018) Clotilde Bongrand et al.   ISME Journal

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

Symbiont strain is the main determinant of variation in Wolbachia -mediated protection against viruses across Drosophila species

(2017) Julien Martinez et al.   MOLECULAR ECOLOGY

Subspecies in the global human gut microbiome

(2017) Paul I Costea et al.   Molecular Systems Biology

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

(2017) Henrique Machado et al.   Frontiers in Microbiology

Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves

(2016) Kathleen Sprouffske et al.   BMC BIOINFORMATICS

Life history of the symbiotically luminous cardinalfishSiphamia tubifer(Perciformes: Apogonidae)

(2016) A. L. Gould et al.   JOURNAL OF FISH BIOLOGY

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

GelJ – a tool for analyzing DNA fingerprint gel images

(2015) Jónathan Heras et al.   BMC BIOINFORMATICS

Xenorhabdus bovienii Strain Diversity Impacts Coevolution and Symbiotic Maintenance with Steinernema spp. Nematode Hosts

(2015) Kristen E. Murfin et al.   mBio

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Diversification of Two Lineages of Symbiotic Photobacterium

(2013) Henryk Urbanczyk et al.   PLoS One

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

(2012) Pablo Cingolani et al.   FLY

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

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

Symbiosis initiation in the bacterially luminous sea urchin cardinalfishSiphamia versicolor

(2012) P. V. Dunlap et al.   JOURNAL OF FISH BIOLOGY

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

Functional morphology of the luminescence system of Siphamia versicolor (Perciformes: Apogonidae), a bacterially luminous coral reef fish

(2011) Paul V. Dunlap et al.   JOURNAL OF MORPHOLOGY

Origins of cheating and loss of symbiosis in wildBradyrhizobium

(2010) J. L. SACHS et al.   JOURNAL OF EVOLUTIONARY BIOLOGY