Recent mating-system evolution inEichhorniais accompanied bycis-regulatory divergence

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

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

Strong Maternal Effects on Gene Expression inArabidopsis lyrataHybrids

(2015) Elin Videvall et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Enhancer Runaway and the Evolution of Diploid Gene Expression

(2015) Frédéric Fyon et al.   PLoS Genetics

The Evolution of Selfing Is Accompanied by Reduced Efficacy of Selection and Purging of Deleterious Mutations

(2015) R. Arunkumar et al.   GENETICS

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

A flexible Bayesian method for detecting allelic imbalance in RNA-seq data

(2014) Luis G León-Novelo et al.   BMC GENOMICS

Mating system shifts and transposable element evolution in the plant genus Capsella

(2014) J Ågren et al.   BMC GENOMICS

The genetic architecture of traits associated with the evolution of self-pollination inMimulus

(2014) Lila Fishman et al.   NEW PHYTOLOGIST

The demography and population genomics of evolutionary transitions to self-fertilization in plants

(2014) S. C. H. Barrett et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Role of cis Regulatory Evolution in Maize Domestication

(2014) Zachary H. Lemmon et al.   PLoS Genetics

Sources of bias in measures of allele-specific expression derived from RNA-seq data aligned to a single reference genome

(2013) Kraig R Stevenson et al.   BMC GENOMICS

RNA-Seq Analysis of Allele-Specific Expression, Hybrid Effects, and Regulatory Divergence in Hybrids Compared with Their Parents from Natural Populations

(2013) Graeme D.M. Bell et al.   Genome Biology and Evolution

Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly

(2013) C. Park et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic Imprinting in the Arabidopsis Embryo Is Partly Regulated by PRC2

(2013) Michael T. Raissig et al.   PLoS Genetics

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

Genomic consequences of transitions from cross- to self-fertilization on the efficacy of selection in three independently derived selfing plants

(2012) Rob W Ness et al.   BMC GENOMICS

Genome-wide Analysis of Cis-regulatory Divergence between Species in the Arabidopsis Genus

(2012) Fei He et al.   MOLECULAR BIOLOGY AND EVOLUTION

Maternal and paternal genomes contribute equally to the transcriptome of early plant embryos

(2012) Michael D. Nodine et al.   NATURE

Protein misinteraction avoidance causes highly expressed proteins to evolve slowly

(2012) J.-R. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The selfing syndrome: a model for studying the genetic and evolutionary basis of morphological adaptation in plants

(2011) Adrien Sicard et al.   ANNALS OF BOTANY

GENETIC ARCHITECTURE AND ADAPTIVE SIGNIFICANCE OF THE SELFING SYNDROME INCAPSELLA

(2011) Tanja Slotte et al.   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

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

(2011) Mark A DePristo et al.   NATURE GENETICS

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Genetics, Evolution, and Adaptive Significance of the Selfing Syndrome in the GenusCapsella

(2011) Adrien Sicard et al.   PLANT CELL

Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata

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

Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners

(2011) Peter L Chang et al.   GENOME BIOLOGY

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

Genome-wide allele-specific analysis: insights into regulatory variation

(2010) Tomi Pastinen   NATURE REVIEWS GENETICS

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

The genetic basis of evolutionary change in gene expression levels

(2010) J. J. Emerson et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

(2009) Jacob F. Degner et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Mating-System Variation, Demographic History and Patterns of Nucleotide Diversity in the Tristylous Plant Eichhornia paniculata

(2009) R. W. Ness et al.   GENETICS

Mechanisms and evolution of genomic imprinting in plants

(2009) C Köhler et al.   HEREDITY

Evolutionary pathways to self-fertilization in a tristylous plant species

(2009) Spencer C. H. Barrett et al.   NEW PHYTOLOGIST

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution

(2008) D. Allan Drummond et al.   CELL

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Genomic Consequences of Outcrossing and Selfing in Plants

(2008) Stephen I. Wright et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Positive and Negative Selection on Noncoding DNA in Drosophila simulans

(2008) P. R. Haddrill et al.   MOLECULAR BIOLOGY AND EVOLUTION