NEUROSPORAAND THE DEAD-END HYPOTHESIS: GENOMIC CONSEQUENCES OF SELFING IN THE MODEL GENUS

Evidence for Widespread GC-biased Gene Conversion in Eukaryotes

(2012) Eugénie Pessia et al.   Genome Biology and Evolution

Sex, outcrossing and mating types: unsolved questions in fungi and beyond

(2012) S. BILLIARD et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Efficient Selection of Branch-Specific Models of Sequence Evolution

(2012) Julien Y. Dutheil et al.   MOLECULAR BIOLOGY AND EVOLUTION

Unidirectional Evolutionary Transitions in Fungal Mating Systems and the Role of Transposable Elements

(2012) Anastasia Gioti et al.   MOLECULAR BIOLOGY AND EVOLUTION

Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample

(2012) Chengwei Luo et al.   PLoS One

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Biochemical Diversification through Foreign Gene Expression in Bdelloid Rotifers

(2012) Chiara Boschetti et al.   PLoS Genetics

The relative importance of reproductive assurance and automatic selection as hypotheses for the evolution of self-fertilization

(2011) Jeremiah W. Busch et al.   ANNALS OF BOTANY

Massive Changes in Genome Architecture Accompany the Transition to Self-Fertility in the Filamentous FungusNeurospora tetrasperma

(2011) Christopher E. Ellison et al.   GENETICS

Evolution of Synonymous Codon Usage in Neurospora tetrasperma and Neurospora discreta

(2011) C. A. Whittle et al.   Genome Biology and Evolution

Reduced Efficacy of Natural Selection on Codon Usage Bias in Selfing Arabidopsis and Capsella Species

(2011) Suo Qiu et al.   Genome Biology and Evolution

A comprehensive phylogeny of Neurospora reveals a link between reproductive mode and molecular evolution in fungi

(2011) Kristiina Nygren et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Outcrossing, mitotic recombination, and life-history trade-offs shape genome evolution inSaccharomyces cerevisiae

(2011) Paul M. Magwene et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Direct and indirect consequences of meiotic recombination: implications for genome evolution

(2011) Matthew T. Webster et al.   TRENDS IN GENETICS

Rediscovery by Whole Genome Sequencing: Classical Mutations and Genome Polymorphisms in Neurospora crassa

(2011) Kevin McCluskey et al.   G3-Genes Genomes Genetics

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

The Positive Correlation between dN/dS and dS in Mammals Is Due to Runs of Adjacent Substitutions

(2010) Nina Stoletzki et al.   MOLECULAR BIOLOGY AND EVOLUTION

Patterns of Codon Usage Bias in Silene latifolia

(2010) S. Qiu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Biased Gene Conversion Affects Patterns of Codon Usage and Amino Acid Usage in the Saccharomyces sensu stricto Group of Yeasts

(2010) R. J. Harrison et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Increased Mutagenesis and Unique Mutation Signature Associated with Mitotic Gene Conversion

(2010) W. M. Hicks 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

Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes

(2009) Laurent Duret et al.   Annual Review of Genomics and Human Genetics

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Molecular evolution of synonymous codon usage in Populus

(2009) Pär K Ingvarsson   BMC EVOLUTIONARY BIOLOGY

Nonlinear Dynamics of Nonsynonymous (dN) and Synonymous (dS) Substitution Rates Affects Inference of Selection

(2009) Jochen B. W. Wolf et al.   Genome Biology and Evolution

Phylogenetic and biological species diversity within theNeurospora tetraspermacomplex

(2009) A. MENKIS et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences

(2009) Yujun Han et al.   NUCLEIC ACIDS RESEARCH

Hotspots of Biased Nucleotide Substitutions in Human Genes

(2009) Jonas Berglund et al.   PLOS BIOLOGY

Improved base calling for the Illumina Genome Analyzer using machine learning strategies

(2009) Martin Kircher et al.   GENOME BIOLOGY

Patterns of Molecular Evolution in Caenorhabditis Preclude Ancient Origins of Selfing

(2008) A. D. Cutter et al.   GENETICS

Population frequencies of transposable elements in selfing and outcrossing Caenorhabditis nematodes

(2008) ELIE S. DOLGIN et al.   Genetics Research

Mating system and recombination affect molecular evolution in four Triticeae species

(2008) A. HAUDRY et al.   Genetics Research

Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa

(2008) Z. A. Lewis et al.   GENOME RESEARCH

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

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

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Genomic Consequences of Outcrossing and Selfing in Plants

(2008) Stephen I. Wright et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Sexual Selection and Maintenance of Sex: Evidence from Comparisons of Rates of Genomic Accumulation of Mutations and Divergence of Sex-Related Genes in Sexual and Hermaphroditic Species of Caenorhabditis

(2008) C. G. Artieri et al.   MOLECULAR BIOLOGY AND EVOLUTION

Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes

(2008) Dacheng Tian et al.   NATURE

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

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

Massive Horizontal Gene Transfer in Bdelloid Rotifers

(2008) E. A. Gladyshev et al.   SCIENCE