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GC-content normalization for RNA-Seq data

BMC bioinformatics, 2011-12, Vol.12 (1), p.480-480, Article 480

2011

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Reconstruction of the genome origins and evolution of the hybrid lager yeast Saccharomyces pastorianus

Genome Research, 2008-10, Vol.18 (10), p.1610-1623

2008

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Whole genome, whole population sequencing reveals that loss of signaling networks is the major adaptive strategy in a constant environment

PLoS genetics, 2013-11, Vol.9 (11), p.e1003972-e1003972

2013

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Changes in the distribution of fitness effects and adaptive mutational spectra following a single first step towards adaptation

Nature communications, 2021-08, Vol.12 (1), p.5193-5193, Article 5193

2021

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Adaptation is influenced by the complexity of environmental change during evolution in a dynamic environment

PLoS genetics, 2021-01, Vol.17 (1), p.e1009314-e1009314

2021

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An improved algorithm for inferring mutational parameters from bar-seq evolution experiments

BMC genomics, 2023-05, Vol.24 (1), p.246-246, Article 246

2023

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Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape

PLoS genetics, 2011-04, Vol.7 (4), p.e1002056-e1002056

2011

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Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages

Nature communications, 2020-01, Vol.11 (1), p.280-280, Article 280

2020

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Paths to adaptation under fluctuating nitrogen starvation: The spectrum of adaptive mutations in Saccharomyces cerevisiae is shaped by retrotransposons and microhomology-mediated recombination

PLoS genetics, 2023-05, Vol.19 (5), p.e1010747-e1010747

2023

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Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads

BMC genomics, 2010-11, Vol.11 (1), p.663-663, Article 663

2010

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Whole-genome comparison reveals novel genetic elements that characterize the genome of industrial strains of Saccharomyces cerevisiae

PLoS genetics, 2011-02, Vol.7 (2), p.e1001287

2011

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Selection of Candida albicans trisomy during oropharyngeal infection results in a commensal-like phenotype

PLoS genetics, 2019-05, Vol.15 (5), p.e1008137-e1008137

2019

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

PLoS genetics, 2016-11, Vol.12 (11), p.e1006404-e1006404

2016

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

G3 : genes - genomes - genetics, 2016-08, Vol.6 (8), p.2421-2434

2016

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Gene flow contributes to diversification of the major fungal pathogen Candida albicans

Nature communications, 2018-06, Vol.9 (1), p.2253-10, Article 2253

2018

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Ras Signaling Gets Fine-Tuned: Regulation of Multiple Pathogenic Traits of Candida albicans

Eukaryotic Cell, 2013-10, Vol.12 (10), p.1316-1325

2013

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The Prognostic Role of a Gene Signature from Tumorigenic Breast-Cancer Cells

The New England journal of medicine, 2007-01, Vol.356 (3), p.217-226

2007

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Bulk segregant analysis by high-throughput sequencing reveals a novel xylose utilization gene from Saccharomyces cerevisiae

PLoS genetics, 2010-05, Vol.6 (5), p.e1000942-e1000942

2010

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Neural networks enable efficient and accurate simulation-based inference of evolutionary parameters from adaptation dynamics

PLoS biology, 2022-05, Vol.20 (5), p.e3001633-e3001633

2022

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Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae

BMC microbiology, 2013-04, Vol.13 (1), p.91-91, Article 91

2013

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Hunger artists: yeast adapted to carbon limitation show trade-offs under carbon sufficiency

PLoS genetics, 2011-08, Vol.7 (8), p.e1002202-e1002202

2011

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Evolutionary dynamics and structural consequences of de novo beneficial mutations and mutant lineages arising in a constant environment

BMC biology, 2021-02, Vol.19 (1), p.20-20, Article 20

2021

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S. cerevisiae Cells Can Grow without the Pds5 Cohesin Subunit

mBio, 2022-08, Vol.13 (4), p.e0142022-e0142022

2022

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Seeking Goldilocks During Evolution of Drug Resistance

PLoS biology, 2017-02, Vol.15 (2), p.e2001872-e2001872

2017

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A genome-wide analysis reveals no nuclear dobzhansky-muller pairs of determinants of speciation between S. cerevisiae and S. paradoxus, but suggests more complex incompatibilities

PLoS genetics, 2010-07, Vol.6 (7), p.e1001038-e1001038

2010

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GC-content normalization for RNA-Seq data

Reconstruction of the genome origins and evolution of the hybrid lager yeast Saccharomyces pastorianus

Whole genome, whole population sequencing reveals that loss of signaling networks is the major adaptive strategy in a constant environment

Changes in the distribution of fitness effects and adaptive mutational spectra following a single first step towards adaptation

Adaptation is influenced by the complexity of environmental change during evolution in a dynamic environment

An improved algorithm for inferring mutational parameters from bar-seq evolution experiments

Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape

Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages

Paths to adaptation under fluctuating nitrogen starvation: The spectrum of adaptive mutations in Saccharomyces cerevisiae is shaped by retrotransposons and microhomology-mediated recombination

Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads

Whole-genome comparison reveals novel genetic elements that characterize the genome of industrial strains of Saccharomyces cerevisiae

Selection of Candida albicans trisomy during oropharyngeal infection results in a commensal-like phenotype

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

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

Gene flow contributes to diversification of the major fungal pathogen Candida albicans

Ras Signaling Gets Fine-Tuned: Regulation of Multiple Pathogenic Traits of Candida albicans

The Prognostic Role of a Gene Signature from Tumorigenic Breast-Cancer Cells

Bulk segregant analysis by high-throughput sequencing reveals a novel xylose utilization gene from Saccharomyces cerevisiae

Neural networks enable efficient and accurate simulation-based inference of evolutionary parameters from adaptation dynamics

Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae

Hunger artists: yeast adapted to carbon limitation show trade-offs under carbon sufficiency

Evolutionary dynamics and structural consequences of de novo beneficial mutations and mutant lineages arising in a constant environment

S. cerevisiae Cells Can Grow without the Pds5 Cohesin Subunit

Seeking Goldilocks During Evolution of Drug Resistance

A genome-wide analysis reveals no nuclear dobzhansky-muller pairs of determinants of speciation between S. cerevisiae and S. paradoxus, but suggests more complex incompatibilities

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