Genomic analysis reveals major determinants ofcis-regulatory variation inCapsella grandiflora

Expression-level support for gene dosage sensitivity in threeGlycinesubgenusGlycinepolyploids and their diploid progenitors

(2016) Jeremy E. Coate et al.   NEW PHYTOLOGIST

Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms

(2016) Zhen Li et al.   PLANT CELL

On the origin and evolutionary consequences of gene body DNA methylation

(2016) Adam J. Bewick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cis-Regulatory Changes Associated with a Recent Mating System Shift and Floral Adaptation inCapsella

(2015) Kim A. Steige et al.   MOLECULAR BIOLOGY AND EVOLUTION

Selection on noise constrains variation in a eukaryotic promoter

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

The role of regulatory variation in complex traits and disease

(2015) Frank W. Albert et al.   NATURE REVIEWS GENETICS

Characteristics of Plant Essential Genes Allow for within- and between-Species Prediction of Lethal Mutant Phenotypes

(2015) John P. Lloyd et al.   PLANT CELL

Association mapping reveals the role of purifying selection in the maintenance of genomic variation in gene expression

(2015) Emily B. Josephs et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation

(2015) Manu J Dubin et al.   eLife

The impact of linked selection on plant genomic variation

(2014) T. Slotte   Briefings in Functional Genomics

Evidence for Widespread Positive and Negative Selection in Coding and Conserved Noncoding Regions of Capsella grandiflora

(2014) Robert J. Williamson et al.   PLoS Genetics

Evolution of DNA Methylation Patterns in the Brassicaceae is Driven by Differences in Genome Organization

(2014) Danelle K. Seymour et al.   PLoS Genetics

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

(2013) Annabelle Haudry et al.   NATURE GENETICS

The Capsella rubella genome and the genomic consequences of rapid mating system evolution

(2013) Tanja Slotte et al.   NATURE GENETICS

Gene body methylation is conserved between plant orthologs and is of evolutionary consequence

(2013) S. Takuno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Frequent adaptation and the McDonald-Kreitman test

(2013) P. W. Messer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Gene balance hypothesis: Connecting issues of dosage sensitivity across biological disciplines

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

Genome-wide approaches to the study of adaptive gene expression evolution

(2011) Hunter B. Fraser   BIOESSAYS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

GENETIC ARCHITECTURE AND ADAPTIVE SIGNIFICANCE OF THE SELFING SYNDROME INCAPSELLA

(2011) Tanja Slotte et al.   EVOLUTION

Genomic Determinants of Protein Evolution and Polymorphism in Arabidopsis

(2011) Tanja Slotte et al.   Genome Biology and Evolution

A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data

(2011) D. A. Skelly et al.   GENOME RESEARCH

Body-Methylated Genes in Arabidopsis thaliana Are Functionally Important and Evolve Slowly

(2011) S. Takuno et al.   MOLECULAR BIOLOGY AND EVOLUTION

Contrasting demographic history and population structure in Capsella rubella and Capsella grandiflora, two closely related species with different mating systems

(2011) KATE R. ST. ONGE et al.   MOLECULAR ECOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence

(2011) Patricia J. Wittkopp et al.   NATURE REVIEWS GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Genome Wide Analyses Reveal Little Evidence for Adaptive Evolution in Many Plant Species

(2010) T. I. Gossmann et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-Wide Evidence for Efficient Positive and Purifying Selection in Capsella grandiflora, a Plant Species with a Large Effective Population Size

(2010) T. Slotte et al.   MOLECULAR BIOLOGY AND EVOLUTION

Lowly Expressed Genes in Arabidopsis thaliana Bear the Signature of Possible Pseudogenization by Promoter Degradation

(2010) L. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Selection at Linked Sites Shapes Heritable Phenotypic Variation in C. elegans

(2010) M. V. Rockman et al.   SCIENCE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Estimating the Rate of Adaptive Molecular Evolution in the Presence of Slightly Deleterious Mutations and Population Size Change

(2009) A. Eyre-Walker et al.   MOLECULAR BIOLOGY AND EVOLUTION

Recent speciation associated with the evolution of selfing in Capsella

(2009) J. P. Foxe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2008) Sean B. Carroll   CELL

Selection to minimise noise in living systems and its implications for the evolution of gene expression

(2008) Ben Lehner   Molecular Systems Biology

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS