Contrasting Frequencies and Effects ofcis- andtrans-Regulatory Mutations Affecting Gene Expression

Gene Expression Evolves under a House-of-Cards Model of Stabilizing Selection

(2015) Andrea Hodgins-Davis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular Mechanisms and Evolutionary Processes Contributing to Accelerated Divergence of Gene Expression on theDrosophilaX Chromosome

(2015) Joseph D. Coolon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Selection on noise constrains variation in a eukaryotic promoter

(2015) Brian P. H. Metzger et al.   NATURE

The Fitness Consequences of Aneuploidy Are Driven by Condition-Dependent Gene Effects

(2015) Anna B. Sunshine et al.   PLOS BIOLOGY

Ventromedial hypothalamic neurons control a defensive emotion state

(2015) Prabhat S Kunwar et al.   eLife

lawstat: AnRPackage for Law, Public Policy and Biostatistics

(2015) Wallace Hui et al.   Journal of Statistical Software

mixtools: AnRPackage for Analyzing Finite Mixture Models

(2015) Tatiana Benaglia et al.   Journal of Statistical Software

The Nature and Extent of Mutational Pleiotropy in Gene Expression of Male Drosophila serrata

(2014) K. McGuigan et al.   GENETICS

Too Much of a Good Thing: The Unique and Repeated Paths Toward Copper Adaptation

(2014) Aleeza C. Gerstein et al.   GENETICS

Probing the effect of promoters on noise in gene expression using thousands of designed sequences

(2014) Eilon Sharon et al.   GENOME RESEARCH

Tempo and mode of regulatory evolution in Drosophila

(2014) J. D. Coolon et al.   GENOME RESEARCH

Precise estimates of mutation rate and spectrum in yeast

(2014) Y. O. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping Small Effect Mutations in Saccharomyces cerevisiae : Impacts of Experimental Design and Mutational Properties

(2014) Fabien Duveau et al.   G3-Genes Genomes Genetics

Quantitative analysis of mammalian GIRK2 channel regulation by G proteins, the signaling lipid PIP2 and Na+ in a reconstituted system

(2014) Weiwei Wang et al.   eLife

A Novel Test for Selection on cis-Regulatory Elements Reveals Positive and Negative Selection Acting on Mammalian Transcriptional Enhancers

(2013) Justin D. Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Dynamic regulation of transcriptional states by chromatin and transcription factors

(2013) Ty C. Voss et al.   NATURE REVIEWS GENETICS

The Dynamics of Diverse Segmental Amplifications in Populations of Saccharomyces cerevisiae Adapting to Strong Selection

(2013) Celia Payen et al.   G3-Genes Genomes Genetics

Yeast Tdh3 (Glyceraldehyde 3-Phosphate Dehydrogenase) Is a Sir2-Interacting Factor That Regulates Transcriptional Silencing and rDNA Recombination

(2013) Alison E. Ringel et al.   PLoS Genetics

A Test for Selection Employing Quantitative Trait Locus and Mutation Accumulation Data

(2012) D. P. Rice et al.   GENETICS

Noise-mean relationship in mutated promoters

(2012) G. Hornung et al.   GENOME RESEARCH

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression

(2012) A. Goncalves et al.   GENOME RESEARCH

Nonlinear Fitness Consequences of Variation in Expression Level of a Eukaryotic Gene

(2012) J. S. Rest et al.   MOLECULAR BIOLOGY AND EVOLUTION

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Complex effects of nucleotide variants in a mammalian cis-regulatory element

(2012) J. C. Kwasnieski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Contrasting Properties of Gene-Specific Regulatory, Coding, and Copy Number Mutations in Saccharomyces cerevisiae: Frequency, Effects, and Dominance

(2012) Jonathan D. Gruber et al.   PLoS Genetics

Regulatory Variation Within and Between Species

(2011) Wei Zheng et al.   Annual Review of Genomics and Human Genetics

Impact of gene expression noise on organismal fitness and the efficacy of natural selection

(2011) Z. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Heterochronic evolution reveals modular timing changes in budding yeast transcriptomes

(2011) Daniel F Simola et al.   GENOME BIOLOGY

Whole-Genome Profiling of Mutagenesis in Caenorhabditis elegans

(2010) S. Flibotte et al.   GENETICS

Natural selection on cis and trans regulation in yeasts

(2010) J. J. Emerson et al.   GENOME RESEARCH

Annotating non-coding regions of the genome

(2010) Roger P. Alexander et al.   NATURE REVIEWS GENETICS

flowClust: a Bioconductor package for automated gating of flow cytometry data

(2009) Kenneth Lo et al.   BMC BIOINFORMATICS

flowCore: a Bioconductor package for high throughput flow cytometry

(2009) Florian Hahne et al.   BMC BIOINFORMATICS

Polymorphisms in Multiple Genes Contribute to the Spontaneous Mitochondrial Genome Instability of Saccharomyces cerevisiae S288C Strains

(2009) L. N. Dimitrov et al.   GENETICS

Positive selection for elevated gene expression noise in yeast

(2009) Zhihua Zhang et al.   Molecular Systems Biology

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis

(2009) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Is Genetic Evolution Predictable?

(2009) D. L. Stern et al.   SCIENCE

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

(2009) I. Tirosh et al.   SCIENCE

Coding-Sequence Determinants of Gene Expression in Escherichia coli

(2009) G. Kudla et al.   SCIENCE

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

Estimating the Per-Base-Pair Mutation Rate in the Yeast Saccharomyces cerevisiae

(2008) Gregory I. Lang et al.   GENETICS

Regulatory changes underlying expression differences within and between Drosophila species

(2008) Patricia J Wittkopp et al.   NATURE GENETICS

Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae

(2008) Katy C Kao et al.   NATURE GENETICS

Dominance and the evolutionary accumulation of cis- and trans-effects on gene expression

(2008) B. Lemos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Revealing the architecture of gene regulation: the promise of eQTL studies

(2008) Yoav Gilad et al.   TRENDS IN GENETICS