Microsporidia with Vertical Transmission Were Likely Shaped by Nonadaptive Processes

Predicting the Thermal and Allometric Dependencies of Disease Transmission via the Metabolic Theory of Ecology

(2019) Devin Kirk et al.   AMERICAN NATURALIST

Genomics-Informed Insights into Endosymbiotic Organelle Evolution in Photosynthetic Eukaryotes

(2018) Eva C.M. Nowack et al.   Annual Review of Plant Biology

Patterns of Genomic Variation in the Opportunistic Pathogen Candida glabrata Suggest the Existence of Mating and a Secondary Association with Humans

(2018) Laia Carreté et al.   CURRENT BIOLOGY

Mitogenome phylogeographic analysis of a planktonic crustacean

(2018) Peter D. Fields et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The role of spore morphology in horizontal transmission of a microsporidium of Daphnia

(2018) Hadas Urca et al.   PARASITOLOGY

Microsporidian introns retained against a background of genome reduction: characterization of an unusual set of introns

(2018) T A Whelan et al.   Genome Biology and Evolution

Decay of the glycolytic pathway and adaptation to intranuclear parasitism within Enterocytozoonidae microsporidia

(2017) Dominic Wiredu Boakye et al.   ENVIRONMENTAL MICROBIOLOGY

Coevolution between transposable elements and recombination

(2017) Tyler V. Kent et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Evolution of Bacterial Genome Architecture

(2017) Louis-Marie Bobay et al.   Frontiers in Genetics

A high-density genetic map reveals variation in recombination rate across the genome of Daphnia magna

(2016) Marinela Dukić et al.   BMC GENETICS

The genome of an Encephalitozoon cuniculi type III strain reveals insights into the genetic diversity and mode of reproduction of a ubiquitous vertebrate pathogen

(2016) A Pelin et al.   HEREDITY

EuPathDB: the eukaryotic pathogen genomics database resource

(2016) Cristina Aurrecoechea et al.   NUCLEIC ACIDS RESEARCH

The relationship of recombination rate, genome structure, and patterns of molecular evolution across angiosperms

(2015) George P. Tiley et al.   BMC EVOLUTIONARY BIOLOGY

The Ordospora colligata Genome: Evolution of Extreme Reduction in Microsporidia and Host-To-Parasite Horizontal Gene Transfer

(2015) Jean-François Pombert et al.   mBio

Contrasting host–pathogen interactions and genome evolution in two generalist and specialist microsporidian pathogens of mosquitoes

(2015) Christopher A. Desjardins et al.   Nature Communications

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

The Tiniest Tiny Genomes

(2014) Nancy A. Moran et al.   Annual Review of Microbiology

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Microsporidian Genomes Harbor a Diverse Array of Transposable Elements that Demonstrate an Ancestry of Horizontal Exchange with Metazoans

(2014) Nicolas Parisot et al.   Genome Biology and Evolution

Implications of streamlining theory for microbial ecology

(2014) Stephen J Giovannoni et al.   ISME Journal

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

The expression of virulence for a mixed-mode transmitted parasite in a diapausing host

(2014) ELHAM SHEIKH-JABBARI et al.   PARASITOLOGY

Evolution of a morphological novelty occurred before genome compaction in a lineage of extreme parasites

(2014) K. L. Haag et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Epidemiology and Evolution of Symbionts with Mixed-Mode Transmission

(2013) Dieter Ebert   Annual Review of Ecology Evolution and Systematics

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Shared Signatures of Parasitism and Phylogenomics Unite Cryptomycota and Microsporidia

(2013) Timothy Y. James et al.   CURRENT BIOLOGY

Complete Genome Sequences from Three Genetically Distinct Strains Reveal High Intraspecies Genetic Diversity in the Microsporidian Encephalitozoon cuniculi

(2013) Jean-François Pombert et al.   EUKARYOTIC CELL

Extremely Reduced Levels of Heterozygosity in the Vertebrate Pathogen Encephalitozoon cuniculi

(2013) Mohammed Selman et al.   EUKARYOTIC CELL

Models for the Evolution of GC Content in Asexual Fungi Candida albicans and C. dubliniensis

(2013) Marie-Claude Marsolier-Kergoat   Genome Biology and Evolution

Reduction and Expansion in Microsporidian Genome Evolution: New Insights from Comparative Genomics

(2013) Sirintra Nakjang et al.   Genome Biology and Evolution

Microsatellite and single-nucleotide polymorphisms indicate recurrent transitions to asexuality in a microsporidian parasite

(2013) K. L. Haag et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Local adaptation of sex induction in a facultative sexual crustacean: insights from QTL mapping and natural populations ofDaphnia magna

(2013) Anne C. Roulin et al.   MOLECULAR ECOLOGY

Adaptive phenotypic plasticity and local adaptation for temperature tolerance in freshwater zooplankton

(2013) L. Y. Yampolsky et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Bacterial Adaptation through Loss of Function

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

A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes

(2013) John A. Capra et al.   PLoS Genetics

Web Apollo: a web-based genomic annotation editing platform

(2013) Eduardo Lee et al.   GENOME BIOLOGY

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

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

Single-nucleotide polymorphisms of two closely related microsporidian parasites suggest a clonal population expansion after the last glaciation

(2012) Karen L. Haag et al.   MOLECULAR ECOLOGY

Gain and loss of multiple functionally related, horizontally transferred genes in the reduced genomes of two microsporidian parasites

(2012) J.-F. Pombert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Genome of the Obligate Intracellular Parasite Trachipleistophora hominis: New Insights into Microsporidian Genome Dynamics and Reductive Evolution

(2012) Eva Heinz et al.   PLoS Pathogens

A novel hybrid gene prediction method employing protein multiple sequence alignments

(2011) Oliver Keller et al.   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

The intriguing nature of microsporidian genomes

(2011) N. Corradi et al.   Briefings in Functional Genomics

Extreme genome reduction in symbiotic bacteria

(2011) John P. McCutcheon et al.   NATURE REVIEWS MICROBIOLOGY

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

Extreme reduction and compaction of microsporidian genomes

(2011) Eric Peyretaillade et al.   RESEARCH IN MICROBIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

The Reduced Genome of the Parasitic Microsporidian Enterocytozoon bieneusi Lacks Genes for Core Carbon Metabolism

(2010) Patrick J. Keeling et al.   Genome Biology and Evolution

Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies

(2010) Sébastien Boisvert et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

mlRho - a program for estimating the population mutation and recombination rates from shotgun-sequenced diploid genomes

(2010) BERNHARD HAUBOLD et al.   MOLECULAR ECOLOGY

Cytological and molecular description of Hamiltosporidium tvaerminnensis gen. et sp. nov., a microsporidian parasite of Daphnia magna, and establishment of Hamiltosporidium magnivora comb. nov.

(2010) KAREN LUISA HAAG et al.   PARASITOLOGY

The complete sequence of the smallest known nuclear genome from the microsporidian Encephalitozoon intestinalis

(2010) Nicolas Corradi et al.   Nature Communications

Deletional Bias across the Three Domains of Life

(2009) Chih-Horng Kuo et al.   Genome Biology and Evolution

Draft genome sequence of the Daphnia pathogen Octosporea bayeri: insights into the gene content of a large microsporidian genome and a model for host-parasite interactions

(2009) Nicolas Corradi et al.   GENOME BIOLOGY

Genome sequence surveys of Brachiola algerae and Edhazardia aedis reveal microsporidia with low gene densities

(2008) Bryony AP Williams et al.   BMC GENOMICS

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

(2008) V. Ter-Hovhannisyan et al.   GENOME RESEARCH

Trends in Prokaryotic Evolution Revealed by Comparison of Closely Related Bacterial and Archaeal Genomes

(2008) P. S. Novichkov et al.   JOURNAL OF BACTERIOLOGY