Rapid selection response to ethanol inSaccharomyces eubayanusemulates the domestication process under brewing conditions

The domestication syndrome in vegetatively propagated field crops

(2020) Tim Denham et al.   ANNALS OF BOTANY

MUM&Co: Accurate detection of all SV types through whole genome alignment

(2020) Samuel O’Donnell et al.   BIOINFORMATICS

Postglacial migration shaped the genomic diversity and global distribution of the wild ancestor of lager-brewing hybrids

(2020) Quinn K. Langdon et al.   PLoS Genetics

An Out-of-Patagonia migration explains the worldwide diversity and distribution of Saccharomyces eubayanus lineages

(2020) Roberto F. Nespolo et al.   PLoS Genetics

Volatile Compound Screening Using HS-SPME-GC/MS on Saccharomyces eubayanus Strains under Low-Temperature Pilsner Wort Fermentation

(2020) Kamila Urbina et al.   Microorganisms

Phenotypic characterisation and linkage mapping of domestication syndrome traits in yellow lupin (Lupinus luteus L.)

(2020) Muhammad Munir Iqbal et al.   THEORETICAL AND APPLIED GENETICS

Ethanol exposure increases mutation rate through error-prone polymerases

(2020) Karin Voordeckers et al.   Nature Communications

Performance, genomic rearrangements, and signatures of adaptive evolution: Lessons from fermentative yeasts

(2020) Roberto F. Nespolo et al.   Ecology and Evolution

QTL analysis reveals genomic variants linked to high-temperature fermentation performance in the industrial yeast

(2019) Zhen Wang et al.   Biotechnology for Biofuels

In vivo recombination of Saccharomyces eubayanus maltose-transporter genes yields a chimeric transporter that enables maltotriose fermentation

(2019) Nick Brouwers et al.   PLoS Genetics

Evolution of a novel chimeric maltotriose transporter in Saccharomyces eubayanus from parent proteins unable to perform this function

(2019) EmilyClare P. Baker et al.   PLoS Genetics

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

(2019) Yingyao Zhou et al.   Nature Communications

CiiiDER: A tool for predicting and analysing transcription factor binding sites

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Himalayan Saccharomyces eubayanus Genome Sequences Reveal Genetic Markers Explaining Heterotic Maltotriose Consumption by Saccharomyces pastorianus Hybrids

(2019) Nick Brouwers et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Rapid Phenotypic and Metabolomic Domestication of WildPenicilliumMolds on Cheese

(2019) Ina Bodinaku et al.   mBio

Interspecific hybridization facilitates niche adaptation in beer yeast

(2019) Brigida Gallone et al.   Nature Ecology & Evolution

Fermentation innovation through complex hybridization of wild and domesticated yeasts

(2019) Quinn K. Langdon et al.   Nature Ecology & Evolution

Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

(2019) Alex N. Salazar et al.   BMC GENOMICS

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Origins, evolution, domestication and diversity of Saccharomyces beer yeasts

(2018) Brigida Gallone et al.   CURRENT OPINION IN BIOTECHNOLOGY

Accumulation of intracellular S -adenosylmethionine increases the fermentation rate of bottom-fermenting brewer's yeast during high-gravity brewing

(2018) Mayu Oomuro et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Long-read sequencing data analysis for yeasts

(2018) Jia-Xing Yue et al.   Nature Protocols

Population genomics of bacterial host adaptation

(2018) Samuel K. Sheppard et al.   NATURE REVIEWS GENETICS

The origin and adaptive evolution of domesticated populations of yeast from Far East Asia

(2018) Shou-Fu Duan et al.   Nature Communications

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution

(2018) Bram Van den Bergh et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Structural, Physiological and Regulatory Analysis of Maltose Transporter Genes in Saccharomyces eubayanus CBS 12357T

(2018) Anja Brickwedde et al.   Frontiers in Microbiology

Selection of Pof-Saccharomyces eubayanus Variants for the Construction of S. cerevisiae × S. eubayanus Hybrids With Reduced 4-Vinyl Guaiacol Formation

(2018) Jasper A. Diderich et al.   Frontiers in Microbiology

The Crabtree Effect Shapes the Saccharomyces cerevisiae Lag Phase during the Switch between Different Carbon Sources

(2018) Gemma Perez-Samper et al.   mBio

Clonal Heterogeneity Influences the Fate of New Adaptive Mutations

(2017) Ignacio Vázquez-García et al.   Cell Reports

Rapid evolutionary adaptation to growth on an ‘unfamiliar’ carbon source

(2016) Zvi Tamari et al.   BMC GENOMICS

Distinct Domestication Trajectories in Top-Fermenting Beer Yeasts and Wine Yeasts

(2016) Margarida Gonçalves et al.   CURRENT BIOLOGY

Population genomics of yeasts: towards a comprehensive view across a broad evolutionary scale

(2016) Jackson Peter et al.   YEAST

Cloning and expression of Saccharomyces cerevisiae SUC2 gene in yeast platform and characterization of recombinant enzyme biochemical properties

(2016) Nooshin Mohandesi et al.   3 Biotech

Cloning and expression of Saccharomyces cerevisiae SUC2 gene in yeast platform and characterization of recombinant enzyme biochemical properties

(2016) Nooshin Mohandesi et al.   3 Biotech

Chromosomal Copy Number Variation in Saccharomyces pastorianus Is Evidence for Extensive Genome Dynamics in Industrial Lager Brewing Strains

(2015) M. van den Broek et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

New lager yeast strains generated by interspecific hybridization

(2015) Kristoffer Krogerus et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Comprehensive Temporal Protein Dynamics during the Diauxic Shift inSaccharomyces cerevisiae

(2015) J. Patrick Murphy et al.   MOLECULAR & CELLULAR PROTEOMICS

Rapid evolution of adaptive niche construction in experimental microbial populations

(2014) Benjamin J. Callahan et al.   EVOLUTION

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Iron sensing and regulation in Saccharomyces cerevisiae: Ironing out the mechanistic details

(2013) Caryn E Outten et al.   CURRENT OPINION IN MICROBIOLOGY

The Microbiology of Malting and Brewing

(2013) N. A. Bokulich et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Growth Rates Made Easy

(2013) B. G. Hall et al.   MOLECULAR BIOLOGY AND EVOLUTION

Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast

(2013) G. G. Zampar et al.   Molecular Systems Biology

Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli

(2013) M. Dragosits et al.   Molecular Systems Biology

Impact of Nutrient Imbalance on Wine Alcoholic Fermentations: Nitrogen Excess Enhances Yeast Cell Death in Lipid-Limited Must

(2013) Catherine Tesnière et al.   PLoS One

Yeast “Make-Accumulate-Consume” Life Strategy Evolved as a Multi-Step Process That Predates the Whole Genome Duplication

(2013) Arne Hagman et al.   PLoS One

Mutation Rates, Spectra, and Genome-Wide Distribution of Spontaneous Mutations in Mismatch Repair Deficient Yeast

(2013) Gregory I. Lang et al.   G3-Genes Genomes Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The Evolutionary Imprint of Domestication on Genome Variation and Function of the Filamentous Fungus Aspergillus oryzae

(2012) John G. Gibbons et al.   CURRENT BIOLOGY

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

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

(2011) H. Li   BIOINFORMATICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast

(2011) D. Libkind et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) A. McKenna et al.   GENOME RESEARCH

Characterization of a New Multigene Family Encoding Isomaltases in the YeastSaccharomyces cerevisiae, theIMAFamily

(2010) Marie-Ange Teste et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS