Intra and Interspecific Variations of Gene Expression Levels in Yeast Are Largely Neutral: (Nei Lecture, SMBE 2016, Gold Coast)

Deciphering the Genic Basis of Yeast Fitness Variation by Simultaneous Forward and Reverse Genetics

(2017) Calum J. Maclean et al.   MOLECULAR BIOLOGY AND EVOLUTION

Massively Parallel Interrogation of the Effects of Gene Expression Levels on Fitness

(2016) Leeat Keren et al.   CELL

Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris

(2016) Jennifer W. Israel et al.   PLOS BIOLOGY

Are Human Translated Pseudogenes Functional?

(2015) Jinrui Xu et al.   MOLECULAR BIOLOGY AND EVOLUTION

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Genomic evidence for adaptation by gene duplication

(2014) Wenfeng Qian et al.   GENOME RESEARCH

Single-cell phenomics reveals intra-species variation of phenotypic noise in yeast

(2013) Gaël Yvert et al.   BMC Systems Biology

Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast

(2013) C. J. McManus et al.   GENOME RESEARCH

Evolution at two levels of gene expression in yeast

(2013) C. G. Artieri et al.   GENOME RESEARCH

Modeling Gene Expression Evolution with an Extended Ornstein–Uhlenbeck Process Accounting for Within-Species Variation

(2013) Rori V. Rohlfs et al.   MOLECULAR BIOLOGY AND EVOLUTION

Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures

(2013) Z. Khan et al.   SCIENCE

Surprisingly diverged populations ofSaccharomyces cerevisiaein natural environments remote from human activity

(2012) Qi-Ming Wang et al.   MOLECULAR ECOLOGY

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

The Genomic Landscape and Evolutionary Resolution of Antagonistic Pleiotropy in Yeast

(2012) Wenfeng Qian et al.   Cell Reports

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Saccharomyces Genome Database: the genomics resource of budding yeast

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

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

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

Trait Variation in Yeast Is Defined by Population History

(2011) Jonas Warringer et al.   PLoS Genetics

Contrasting genetic paths to morphological and physiological evolution

(2010) B.-Y. Liao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evidence for widespread adaptive evolution of gene expression in budding yeast

(2010) H. B. Fraser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polygenic and directional regulatory evolution across pathways in Saccharomyces

(2010) J. H. Bullard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein abundances are more conserved than mRNA abundances across diverse taxa

(2010) Jon M. Laurent et al.   PROTEOMICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Assessing the genomic evidence for conserved transcribed pseudogenes under selection

(2009) Amit N Khachane et al.   BMC GENOMICS

Population genomics of domestic and wild yeasts

(2009) Gianni Liti et al.   NATURE

Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes

(2009) Sabine P Schrimpf et al.   PLOS BIOLOGY

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?

(2008) David L. Stern et al.   EVOLUTION

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

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

(2008) David Gresham et al.   PLoS Genetics