Contrasting evolutionary genome dynamics between domesticated and wild yeasts

Assemblytics: a web analytics tool for the detection of variants from an assembly

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PRECOG: a tool for automated extraction and visualization of fitness components in microbial growth phenomics

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1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

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Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts

(2016) Brigida Gallone et al.   CELL

Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus

(2016) Nikolaos Vakirlis et al.   GENOME RESEARCH

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Long-read sequence assembly of the gorilla genome

(2016) D. Gordon et al.   SCIENCE

Powerful decomposition of complex traits in a diploid model

(2016) Johan Hallin et al.   Nature Communications

Scan-o-matic: High-Resolution Microbial Phenomics at a Massive Scale

(2016) Martin Zackrisson et al.   G3-Genes Genomes Genetics

Speciation driven by hybridization and chromosomal plasticity in a wild yeast

(2016) Jean-Baptiste Leducq et al.   Nature Microbiology

Genomic Insights into the Saccharomyces sensu stricto Complex

(2015) Anthony R. Borneman et al.   GENETICS

Real-Time Evolution of a Subtelomeric Gene Family in Candida albicans

(2015) Matthew Z. Anderson et al.   GENETICS

The 100-genomes strains, anS. cerevisiaeresource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen

(2015) Pooja K. Strope et al.   GENOME RESEARCH

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

(2015) Sara Goodwin et al.   GENOME RESEARCH

Extensive Horizontal Transfer and Homologous Recombination Generate Highly Chimeric Mitochondrial Genomes in Yeast

(2015) Baojun Wu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary Advantage Conferred by an Eukaryote-to-Eukaryote Gene Transfer Event in Wine Yeasts

(2015) Souhir Marsit et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast Dating Using Least-Squares Criteria and Algorithms

(2015) Thu-Hien To et al.   SYSTEMATIC BIOLOGY

A Dynamic Mobile DNA Family in the Yeast Mitochondrial Genome

(2015) B. Wu et al.   G3-Genes Genomes Genetics

The fascinating and secret wild life of the budding yeast S. cerevisiae

(2015) Gianni Liti   eLife

Genomic Insights into the Saccharomyces sensu stricto Complex

(2015) Anthony R. Borneman et al.   GENETICS

Real-Time Evolution of a Subtelomeric Gene Family in Candida albicans

(2015) Matthew Z. Anderson et al.   GENETICS

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

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

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

(2014) W. Huang et al.   GENOME RESEARCH

A High-Definition View of Functional Genetic Variation from Natural Yeast Genomes

(2014) Anders Bergström et al.   MOLECULAR BIOLOGY AND EVOLUTION

Resolving the complexity of the human genome using single-molecule sequencing

(2014) Mark J. P. Chaisson et al.   NATURE

SynChro: A Fast and Easy Tool to Reconstruct and Visualize Synteny Blocks along Eukaryotic Chromosomes

(2014) Guénola Drillon et al.   PLoS One

Orthology Detection Combining Clustering and Synteny for Very Large Datasets

(2014) Marcus Lechner et al.   PLoS One

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

High-quality genome (re)assembly using chromosomal contact data

(2014) Hervé Marie-Nelly et al.   Nature Communications

Structures of Naturally Evolved CUP1 Tandem Arrays in Yeast Indicate That These Arrays Are Generated by Unequal Nonhomologous Recombination

(2014) Ying Zhao et al.   G3-Genes Genomes Genetics

Long-read, whole-genome shotgun sequence data for five model organisms

(2014) Kristi E Kim et al.   Scientific Data

Chromothripsis and beyond: rapid genome evolution from complex chromosomal rearrangements

(2013) C.-Z. Zhang et al.   GENES & DEVELOPMENT

Mixing of vineyard and oak-tree ecotypes ofSaccharomyces cerevisiaein North American vineyards

(2013) Katie E. Hyma et al.   MOLECULAR ECOLOGY

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Phenotypic impact of genomic structural variation: insights from and for human disease

(2013) Joachim Weischenfeldt et al.   NATURE REVIEWS GENETICS

Inferring Genome-Wide Recombination Landscapes from Advanced Intercross Lines: Application to Yeast Crosses

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A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach

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The Drosophila melanogaster Genetic Reference Panel

(2012) Trudy F. C. Mackay et al.   NATURE

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

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Proteinortho: Detection of (Co-)orthologs in large-scale analysis

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Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development

(2011) Philip J. Stephens et al.   CELL

Revealing the genetic structure of a trait by sequencing a population under selection

(2011) L. Parts et al.   GENOME RESEARCH

Combinatorics of chromosomal rearrangements based on synteny blocks and synteny packs

(2011) G. Drillon et al.   JOURNAL OF LOGIC AND COMPUTATION

Assessing the complex architecture of polygenic traits in diverged yeast populations

(2011) FRANCISCO A. CUBILLOS et al.   MOLECULAR ECOLOGY

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

RATT: Rapid Annotation Transfer Tool

(2011) Thomas D. Otto et al.   NUCLEIC ACIDS RESEARCH

Trait Variation in Yeast Is Defined by Population History

(2011) Jonas Warringer et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Rapid Expansion and Functional Divergence of Subtelomeric Gene Families in Yeasts

(2010) Chris A. Brown et al.   CURRENT BIOLOGY

Gene Duplication and Environmental Adaptation within Yeast Populations

(2010) Ryan M. Ames et al.   Genome Biology and Evolution

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Yeast evolutionary genomics

(2010) Bernard Dujon   NATURE REVIEWS GENETICS

Competitive Repair by Naturally Dispersed Repetitive DNA during Non-Allelic Homologous Recombination

(2010) Margaret L. Hoang et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The Association of yKu With Subtelomeric Core X Sequences Prevents Recombination Involving Telomeric Sequences

(2009) M. E. Marvin et al.   GENETICS

In Saccharomyces cerevisiae, yKu and Subtelomeric Core X Sequences Repress Homologous Recombination Near Telomeres as Part of the Same Pathway

(2009) M. E. Marvin et al.   GENETICS

Population genomics of domestic and wild yeasts

(2009) Gianni Liti et al.   NATURE

Yeast genome analysis identifies chromosomal translocation, gene conversion events and several sites of Ty element insertion

(2009) Yoshiyuki Shibata et al.   NUCLEIC ACIDS RESEARCH

Segregating YKU80 and TLC1 Alleles Underlying Natural Variation in Telomere Properties in Wild Yeast

(2009) Gianni Liti et al.   PLoS Genetics

Molecular Population Genetics of Drosophila Subtelomeric DNA

(2008) Jennifer A. Anderson et al.   GENETICS

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY