Population Genomics of Paramecium Species

Codon influence on protein expression in E. coli correlates with mRNA levels

(2016) Grégory Boël et al.   NATURE

The Limits of Natural Selection in a Nonequilibrium World

(2016) Yaniv Brandvain et al.   TRENDS IN GENETICS

Genotype-Frequency Estimation from High-Throughput Sequencing Data

(2015) Takahiro Maruki et al.   GENETICS

Inferring Selective Constraint from Population Genomic Data Suggests Recent Regulatory Turnover in the Human Brain

(2015) Daniel R. Schrider et al.   Genome Biology and Evolution

Maintenance and Loss of Duplicated Genes by Dosage Subfunctionalization

(2015) Jean-Francois Gout et al.   MOLECULAR BIOLOGY AND EVOLUTION

The rate of adaptive evolution in animal mitochondria

(2015) Jennifer E. James et al.   MOLECULAR ECOLOGY

Comparative Population Genomics Reveals Strong Divergence and Infrequent Introgression between Asian and African Rice

(2015) Xuehui Huang et al.   Molecular Plant

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Determinants of the rate of protein sequence evolution

(2015) Jianzhi Zhang et al.   NATURE REVIEWS GENETICS

New Paramecium (Ciliophora, Oligohymenophorea) congeners shape our view on its biodiversity

(2015) Sascha Krenek et al.   ORGANISMS DIVERSITY & EVOLUTION

Population genomic structure and adaptation in the zoonotic malaria parasitePlasmodium knowlesi

(2015) Samuel Assefa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The development and characterization of synthetic minimal yeast promoters

(2015) Heidi Redden et al.   Nature Communications

Genotype-Frequency Estimation from High-Throughput Sequencing Data

(2015) Takahiro Maruki et al.   GENETICS

How discordant morphological and molecular evolution among microorganisms can revise our notions of biodiversity on Earth

(2014) Daniel J. G. Lahr et al.   BIOESSAYS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Insights into Three Whole-Genome Duplications Gleaned from the Paramecium caudatum Genome Sequence

(2014) Casey L. McGrath et al.   GENETICS

Differential retention and divergent resolution of duplicate genes following whole-genome duplication

(2014) Casey L. McGrath et al.   GENOME RESEARCH

The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements

(2014) Adrian M. Altenhoff et al.   NUCLEIC ACIDS RESEARCH

Multiple roles of the coding sequence 5′ end in gene expression regulation

(2014) Tamir Tuller et al.   NUCLEIC ACIDS RESEARCH

Population Genomics of the Fission Yeast Schizosaccharomyces pombe

(2014) Jeffrey A. Fawcett et al.   PLoS One

Evolutionary cell biology: Two origins, one objective: Fig. 1.

(2014) Michael Lynch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Eukaryotic Tree of Life from a Global Phylogenomic Perspective

(2014) F. Burki   Cold Spring Harbor Perspectives in Biology

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Molecular hyperdiversity defines populations of the nematode Caenorhabditis brenneri

(2013) A. Dey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A genomic scale map of genetic diversity in Trypanosoma cruzi

(2012) Alejandro A Ackermann et al.   BMC GENOMICS

Genomic Variation in Natural Populations of Drosophila melanogaster

(2012) C. H. Langley et al.   GENETICS

Coding exons function as tissue-specific enhancers of nearby genes

(2012) Ramon Y. Birnbaum et al.   GENOME RESEARCH

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

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

A map of rice genome variation reveals the origin of cultivated rice

(2012) Xuehui Huang et al.   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum

(2012) Daniel E Neafsey et al.   NATURE GENETICS

Maize HapMap2 identifies extant variation from a genome in flux

(2012) Jer-Ming Chia et al.   NATURE GENETICS

Coping with Temperature at the Warm Edge – Patterns of Thermal Adaptation in the Microbial Eukaryote Paramecium caudatum

(2012) Sascha Krenek et al.   PLoS One

Transcriptional Enhancers in Protein-Coding Exons of Vertebrate Developmental Genes

(2012) Deborah I. Ritter et al.   PLoS One

CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms

(2012) Jan Pawlowski et al.   PLOS BIOLOGY

Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?

(2012) Ellen M. Leffler et al.   PLOS BIOLOGY

The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences

(2012) Olivier Arnaiz et al.   PLoS Genetics

DNA Elimination in Ciliates: Transposon Domestication and Genome Surveillance

(2011) Douglas L. Chalker et al.   Annual Review of Genetics

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

The mitochondrial genome sequence of the ciliate Paramecium caudatum reveals a shift in nucleotide composition and codon usage within the genus Paramecium

(2011) Dana Barth et al.   BMC GENOMICS

Thermal performance curves of Paramecium caudatum: A model selection approach

(2011) Sascha Krenek et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

The Oxytricha trifallax Mitochondrial Genome

(2011) Estienne C. Swart et al.   Genome Biology and Evolution

Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance

(2011) T. Downing et al.   GENOME RESEARCH

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

Population genomics and local adaptation in wild isolates of a model microbial eukaryote

(2011) C. E. Ellison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Map of Local Adaptation in Arabidopsis thaliana

(2011) A. Fournier-Level et al.   SCIENCE

De Novo Genesis of Enhancers in Vertebrates

(2011) Michael P. Eichenlaub et al.   PLOS BIOLOGY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Adaptations to Climate-Mediated Selective Pressures in Humans

(2011) Angela M. Hancock et al.   PLoS Genetics

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

(2010) Heng Li et al.   BIOINFORMATICS

New, World-wide Data on the Distribution of Species of the Paramecium aurelia Complex (Ciliophora, Protozoa)

(2010) Ewa Przyboś et al.   FOLIA BIOLOGICA-KRAKOW

Shifts in the intensity of purifying selection: An analysis of genome-wide polymorphism data from two closely related yeast species

(2010) E. Elyashiv et al.   GENOME RESEARCH

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia

(2010) O. Arnaiz et al.   NUCLEIC ACIDS RESEARCH

The Relationship among Gene Expression, the Evolution of Gene Dosage, and the Rate of Protein Evolution

(2010) Jean-François Gout et al.   PLoS Genetics

Parallelized phylogenetic post-analysis on multi-core architectures

(2010) Andre J. Aberer et al.   Journal of Computational Science

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals

(2009) Benoit Nabholz et al.   BMC EVOLUTIONARY BIOLOGY

Estimation of Allele Frequencies From High-Coverage Genome-Sequencing Projects

(2009) M. Lynch   GENETICS

Mitochondrial DNA as a marker of molecular diversity: a reappraisal

(2009) N. GALTIER et al.   MOLECULAR ECOLOGY

Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae

(2009) Joseph Schacherer et al.   NATURE

Population genomics of domestic and wild yeasts

(2009) Gianni Liti et al.   NATURE

Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons

(2009) Xianjun Dong et al.   NUCLEIC ACIDS RESEARCH

Evidence for Variation in the Effective Population Size of Animal Mitochondrial DNA

(2009) Gwenael Piganeau et al.   PLoS One

Coding-Sequence Determinants of Gene Expression in Escherichia coli

(2009) G. Kudla et al.   SCIENCE

Aggressive assembly of pyrosequencing reads with mates

(2008) Jason R. Miller et al.   BIOINFORMATICS

Nucleotide diversity in the mitochondrial and nuclear compartments of Chlamydomonas reinhardtii: investigating the origins of genome architecture

(2008) David R Smith et al.   BMC EVOLUTIONARY BIOLOGY

Genome Annotation in Plants and Fungi: EuGene as a Model Platform

(2008) Sylvain Foissac et al.   Current Bioinformatics

The Paramecium aurelia Species Complex, Frequency and Co-occurrence across Europe

(2008) Ewa Przyboś et al.   FOLIA BIOLOGICA-KRAKOW

Determination of Mitochondrial Genetic Diversity in Mammals

(2008) Benoit Nabholz et al.   GENETICS

Genetic Diversity in the Paramecium aurelia Species Complex

(2008) F. Catania et al.   MOLECULAR BIOLOGY AND EVOLUTION

Translational control of intron splicing in eukaryotes

(2008) Olivier Jaillon et al.   NATURE

Genes mirror geography within Europe

(2008) John Novembre et al.   NATURE

A genome-wide view of the spectrum of spontaneous mutations in yeast

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

Patterns of Codon Usage in two Ciliates that Reassign the Genetic Code: Tetrahymena thermophila and Paramecium tetraurelia

(2008) Hannah M.W. Salim et al.   PROTIST

Variations in Stress Sensitivity and Genomic Expression in Diverse S. cerevisiae Isolates

(2008) Daniel J. Kvitek et al.   PLoS Genetics