Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts

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Widespread Impact of Chromosomal Inversions on Gene Expression Uncovers Robustness via Phenotypic Buffering

(2016) Samina Naseeb et al.   MOLECULAR BIOLOGY AND EVOLUTION

Recombination Rate Evolution and the Origin of Species

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Whole Genome Analysis of 132 Clinical Saccharomyces cerevisiae Strains Reveals Extensive Ploidy Variation

(2016) Yuan O. Zhu et al.   G3-Genes Genomes Genetics

Swi1Timeless Prevents Repeat Instability at Fission Yeast Telomeres

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

Selected Schizosaccharomyces pombe Strains Have Characteristics That Are Beneficial for Winemaking

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An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

The genomic and phenotypic diversity of Schizosaccharomyces pombe

(2015) Daniel C Jeffares et al.   NATURE GENETICS

Copy number variation at the GL7 locus contributes to grain size diversity in rice

(2015) Yuexing Wang et al.   NATURE GENETICS

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(2015) A. Murat Eren et al.   PeerJ

AnGeLi: A Tool for the Analysis of Gene Lists from Fission Yeast

(2015) Danny A. Bitton et al.   Frontiers in Genetics

Chromosomal Rearrangements as a Major Mechanism in the Onset of Reproductive Isolation in Saccharomyces cerevisiae

(2014) Jing Hou et al.   CURRENT BIOLOGY

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

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

Population Genomics of the Fission Yeast Schizosaccharomyces pombe

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LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

NextGenMap: fast and accurate read mapping in highly polymorphic genomes

(2013) Fritz J. Sedlazeck et al.   BIOINFORMATICS

Gene Copy-Number Variation in Haploid and Diploid Strains of the Yeast Saccharomyces cerevisiae

(2013) H. Zhang et al.   GENETICS

CNVs conferring risk of autism or schizophrenia affect cognition in controls

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Dynamic Large-Scale Chromosomal Rearrangements Fuel Rapid Adaptation in Yeast Populations

(2013) Shang-Lin Chang et al.   PLoS Genetics

Improved Heritability Estimation from Genome-wide SNPs

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YAHA: fast and flexible long-read alignment with optimal breakpoint detection

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DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

A comprehensive survey of copy number variation in 18 diverse pig populations and identification of candidate copy number variable genes associated with complex traits

(2012) Congying Chen et al.   BMC GENOMICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

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Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells

(2012) Samuel Marguerat et al.   CELL

REPRODUCTIVE ISOLATION AND LOCAL ADAPTATION QUANTIFIED FOR A CHROMOSOME INVERSION IN A MALARIA MOSQUITO

(2012) Diego Ayala et al.   EVOLUTION

Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments

(2012) B. Dunn et al.   GENOME RESEARCH

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Hierarchical Modularity and the Evolution of Genetic Interactomes across Species

(2012) Colm J. Ryan et al.   MOLECULAR CELL

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

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(2012) Günter Klambauer et al.   NUCLEIC ACIDS RESEARCH

Impact of Chromosomal Inversions on the Yeast DAL Cluster

(2012) Samina Naseeb et al.   PLoS One

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(2011) P. Danecek et al.   BIOINFORMATICS

Effects of Inversions on Within- and Between-Species Recombination and Divergence

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A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Genomic impacts of chromosomal inversions in parapatric Drosophila species

(2011) S. E. McGaugh et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Geographically Diverse Collection of Schizosaccharomyces pombe Isolates Shows Limited Phenotypic Variation but Extensive Karyotypic Diversity

(2011) William R. A. Brown et al.   G3-Genes Genomes Genetics

A Genetic and Structural Study of Genome Rearrangements Mediated by High Copy Repeat Ty1 Elements

(2011) Jason E. Chan et al.   PLoS Genetics

De novo rates and selection of large copy number variation

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Genome-wide mapping of nuclear mitochondrial DNA sequences links DNA replication origins to chromosomal double-strand break formation in Schizosaccharomyces pombe

(2010) S. Lenglez et al.   GENOME RESEARCH

Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe

(2010) Dong-Uk Kim et al.   NATURE BIOTECHNOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

The Baker's Yeast Diploid Genome Is Remarkably Stable in Vegetative Growth and Meiosis

(2010) K. T. Nishant et al.   PLoS Genetics

Copy Number Variation in Human Health, Disease, and Evolution

(2009) Feng Zhang et al.   Annual Review of Genomics and Human Genetics

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Unstable Tandem Repeats in Promoters Confer Transcriptional Evolvability

(2009) M. D. Vinces et al.   SCIENCE

Additions, Losses, and Rearrangements on the Evolutionary Route from a Reconstructed Ancestor to the Modern Saccharomyces cerevisiae Genome

(2009) Jonathan L. Gordon et al.   PLoS Genetics

The Repertoire and Dynamics of Evolutionary Adaptations to Controlled Nutrient-Limited Environments in Yeast

(2008) David Gresham et al.   PLoS Genetics