Integrative Omics Analysis Reveals a Limited Transcriptional Shock After Yeast Interspecies Hybridization

Whole-Genome Sequencing of the Opportunistic Yeast Pathogen Candida inconspicua Uncovers Its Hybrid Origin

(2019) Verónica Mixão et al.   Frontiers in Genetics

Inheritance patterns of the transcriptome in hybrid chickens and their parents revealed by expression analysis

(2019) Hongchang Gu et al.   Scientific Reports

CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies

(2019) Hrant Hovhannisyan et al.   BIOINFORMATICS

Homoeolog expression bias in allopolyploid oleaginous marine diatom Fistulifera solaris

(2018) Tatsuhiro Nomaguchi et al.   BMC GENOMICS

Copy Number Variation in Fungi and Its Implications for Wine Yeast Genetic Diversity and Adaptation

(2018) Jacob L. Steenwyk et al.   Frontiers in Microbiology

Homoeolog expression bias and expression level dominance in resynthesized allopolyploid Brassica napus

(2018) Jian Wu et al.   BMC GENOMICS

Extraordinary Genome Instability and Widespread Chromosome Rearrangements During Vegetative Growth

(2018) Mareike Möller et al.   GENETICS

Evolutionary Dynamics of Regulatory Changes Underlying Gene Expression Divergence among Saccharomyces Species

(2017) Brian P.H. Metzger et al.   Genome Biology and Evolution

Cis-Regulatory Divergence in Gene Expression between Two Thermally Divergent Yeast Species

(2017) Xueying C. Li et al.   Genome Biology and Evolution

Loss of Heterozygosity Drives Adaptation in Hybrid Yeast

(2017) Caiti S. Smukowski Heil et al.   MOLECULAR BIOLOGY AND EVOLUTION

Epichloë hybrida, sp. nov., an emerging model system for investigating fungal allopolyploidy

(2017) Matthew A. Campbell et al.   MYCOLOGIA

Evolution and genome architecture in fungal plant pathogens

(2017) Mareike Möller et al.   NATURE REVIEWS MICROBIOLOGY

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

YEASTRACT: an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae

(2017) Miguel C Teixeira et al.   NUCLEIC ACIDS RESEARCH

Natural variation for gene expression responses to abiotic stress in maize

(2017) Amanda J. Waters et al.   PLANT JOURNAL

Hybridization and emergence of virulence in opportunistic human yeast pathogens

(2017) Verónica Mixão et al.   YEAST

Genome-wide proteomic profiling reveals the role of dominance protein expression in heterosis in immature maize ears

(2017) Xiaojiao Hu et al.   Scientific Reports

Genome Dynamics of Hybrid Saccharomyces cerevisiae During Vegetative and Meiotic Divisions

(2017) Abhishek Dutta et al.   G3-Genes Genomes Genetics

Identification of misexpressed genetic elements in hybrids between Drosophila-related species

(2017) Hélène Lopez-Maestre et al.   Scientific Reports

Novel brewing yeast hybrids: creation and application

(2016) Kristoffer Krogerus et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Transcriptome profiling and comparison of maize ear heterosis during the spikelet and floret differentiation stages

(2016) Xiaojiao Hu et al.   BMC GENOMICS

Interspecific hybridization impacts host range and pathogenicity of filamentous microbes

(2016) Jasper RL Depotter et al.   CURRENT OPINION IN MICROBIOLOGY

Genome evolution in the allotetraploid frog Xenopus laevis

(2016) Adam M. Session et al.   NATURE

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

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species

(2016) Markus S. Schröder et al.   PLoS Genetics

Regulatory Divergence between Parental Alleles Determines Gene Expression Patterns in Hybrids

(2015) Marie-Christine Combes et al.   Genome Biology and Evolution

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions

(2015) Alicia N. Schep et al.   GENOME RESEARCH

Molecular and enological characterization of a natural Saccharomyces uvarum and Saccharomyces cerevisiae hybrid

(2015) Roberto Pérez-Torrado et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

The Genome Sequence ofSaccharomyces eubayanusand the Domestication of Lager-Brewing Yeasts

(2015) EmilyClare Baker et al.   MOLECULAR BIOLOGY AND EVOLUTION

Epigenetic Changes in Hybrids

(2015) Ian K. Greaves et al.   PLANT PHYSIOLOGY

Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage

(2015) Marina Marcet-Houben et al.   PLOS BIOLOGY

The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis

(2015) Leszek P. Pryszcz et al.   PLoS Genetics

Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications

(2014) Eduardo G. Gusmao et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Genome Comparison of Candida orthopsilosis Clinical Strains Reveals the Existence of Hybrids between Two Distinct Subspecies

(2014) Leszek P. Pryszcz et al.   Genome Biology and Evolution

Phenotypic characterisation of Saccharomyces spp. yeast for tolerance to stresses encountered during fermentation of lignocellulosic residues to produce bioethanol

(2014) Tithira T Wimalasena et al.   Microbial Cell Factories

mRNA and Small RNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation of Allopolyploid Heterosis in Nascent Hexaploid Wheat

(2014) A. Li et al.   PLANT CELL

An Interspecific Fungal Hybrid Reveals Cross-Kingdom Rules for Allopolyploid Gene Expression Patterns

(2014) Murray P. Cox et al.   PLoS Genetics

RNA-seq differential expression studies: more sequence or more replication?

(2013) Yuwen Liu et al.   BIOINFORMATICS

Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen

(2013) R. de Jonge et al.   GENOME RESEARCH

Inheritance of Gene Expression Level and Selective Constraints on Trans- and Cis-Regulatory Changes in Yeast

(2013) Bernhard Schaefke et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes

(2013) Pierre Gladieux et al.   MOLECULAR ECOLOGY

Comparative Proteomic Analysis of Embryos between a Maize Hybrid and Its Parental Lines during Early Stages of Seed Germination

(2013) Baojian Guo et al.   PLoS One

Inferring Evolutionary Histories of Pathway Regulation from Transcriptional Profiling Data

(2013) Joshua G. Schraiber et al.   PLoS Computational Biology

Breakage-fusion-bridge Cycles and Large Insertions Contribute to the Rapid Evolution of Accessory Chromosomes in a Fungal Pathogen

(2013) Daniel Croll et al.   PLoS Genetics

Disentangling the Many Layers of Eukaryotic Transcriptional Regulation

(2012) Katherine M. Lelli et al.   Annual Review of Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Homoeolog expression bias and expression level dominance in allopolyploid cotton

(2012) M-J Yoo et al.   HEREDITY

Evolutionary Role of Interspecies Hybridization and Genetic Exchanges in Yeasts

(2012) Lucia Morales et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Allelic Imbalance in Drosophila Hybrid Heads: Exons, Isoforms, and Evolution

(2012) R. M. Graze et al.   MOLECULAR BIOLOGY AND EVOLUTION

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

(2012) Caryn S. Ross-Innes et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Polyploidy in fungi: evolution after whole-genome duplication

(2012) W. Albertin et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Temperature Adaptation Markedly Determines Evolution within the GenusSaccharomyces

(2011) Z. Salvadó et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Transcriptional Regulation inSaccharomyces cerevisiae: Transcription Factor Regulation and Function, Mechanisms of Initiation, and Roles of Activators and Coactivators

(2011) Steven Hahn et al.   GENETICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

Changes in 24-nt siRNA levels in Arabidopsis hybrids suggest an epigenetic contribution to hybrid vigor

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

The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus

(2011) Devin R. Scannell et al.   G3-Genes Genomes Genetics

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

(2010) Heng Li et al.   BIOINFORMATICS

Regulatory divergence in Drosophila revealed by mRNA-seq

(2010) C. J. McManus et al.   GENOME RESEARCH

Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences

(2010) Itay Tirosh et al.   Molecular Systems Biology

Yeast evolutionary genomics

(2010) Bernard Dujon   NATURE REVIEWS GENETICS

Genome-Wide Views of Chromatin Structure

(2009) Oliver J. Rando et al.   Annual Review of Biochemistry

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fungal regulatory evolution: cis and trans in the balance

(2009) Dawn Anne Thompson et al.   FEBS LETTERS

Generation of a large set of genetically tractable haploid and diploidSaccharomyces strains

(2009) Francisco A. Cubillos et al.   FEMS YEAST RESEARCH

Population genomics of domestic and wild yeasts

(2009) Gianni Liti et al.   NATURE

A Yeast Hybrid Provides Insight into the Evolution of Gene Expression Regulation

(2009) I. Tirosh et al.   SCIENCE

Acquisition of Aneuploidy Provides Increased Fitness during the Evolution of Antifungal Drug Resistance

(2009) Anna M. Selmecki et al.   PLoS Genetics

Introduction. Extent, processes and evolutionary impact of interspecific hybridization in animals

(2008) K. Schwenk et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genome-wide allele-specific expression analysis using Massively Parallel Signature Sequencing (MPSS™) Reveals cis- and trans-effects on gene expression in maize hybrid meristem tissue

(2008) Mei Guo et al.   PLANT MOLECULAR BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY