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

Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression

(2011) Zhao Lai et al.   AMERICAN JOURNAL OF BOTANY

Genetic and Molecular Bases of Rice Yield

(2010) Yongzhong Xing et al.   Annual Review of Plant Biology

EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics

(2010) Michael S. Barker et al.   Evolutionary Bioinformatics

Regulatory divergence in Drosophila revealed by mRNA-seq

(2010) C. J. McManus et al.   GENOME RESEARCH

Natural selection on cis and trans regulation in yeasts

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

Key considerations for measuring allelic expression on a genomic scale using high-throughput sequencing

(2010) PIERRE FONTANILLAS et al.   MOLECULAR ECOLOGY

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

Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids

(2010) G. He et al.   PLANT CELL

Heterosis

(2010) J. A. Birchler et al.   PLANT CELL

Hybrid fitness across time and habitats

(2010) Michael L. Arnold et al.   TRENDS IN ECOLOGY & EVOLUTION

Molecular mechanisms of polyploidy and hybrid vigor

(2010) Z. Jeffrey Chen   TRENDS IN PLANT SCIENCE

TagDust--a program to eliminate artifacts from next generation sequencing data

(2009) T. Lassmann et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Regulatory Divergence in Drosophila melanogaster and D. simulans, a Genomewide Analysis of Allele-Specific Expression

(2009) R. M. Graze et al.   GENETICS

Cis-regulatory Changes at FLOWERING LOCUS T Mediate Natural Variation in Flowering Responses of Arabidopsis thaliana

(2009) C. Schwartz et al.   GENETICS

Global Analysis of Allele-Specific Expression in Arabidopsis thaliana

(2009) Xu Zhang et al.   GENETICS

Roles of Trans and Cis Variation in Yeast Intraspecies Evolution of Gene Expression

(2009) Huang-Mo Sung et al.   MOLECULAR BIOLOGY AND EVOLUTION

The gene balance hypothesis: implications for gene regulation, quantitative traits and evolution

(2009) James A. Birchler et al.   NEW PHYTOLOGIST

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

(2009) I. Tirosh et al.   SCIENCE

Evolution of Weediness and Invasiveness: Charting the Course for Weed Genomics

(2009) C. Neal Stewart et al.   WEED SCIENCE

AmiGO: online access to ontology and annotation data

(2008) Seth Carbon et al.   BIOINFORMATICS

THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?

(2008) David L. Stern et al.   EVOLUTION

Cis-regulatory Variation Is Typically Polyallelic in Drosophila

(2008) J. D. Gruber et al.   GENETICS

Independent Effects of cis- and trans-regulatory Variation on Gene Expression in Drosophila melanogaster

(2008) P. J. Wittkopp et al.   GENETICS

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Roles of cis- and trans-Changes in the Regulatory Evolution of Genes in the Gluconeogenic Pathway in Yeast

(2008) Y.-W. Chang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Regulatory changes underlying expression differences within and between Drosophila species

(2008) Patricia J Wittkopp et al.   NATURE GENETICS

Whole-genome sequencing and variant discovery in C. elegans

(2008) LaDeana W Hillier et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Genome-wide allele-specific expression analysis using Massively Parallel Signature Sequencing (MPSS™) Reveals cis- and trans-effects on gene expression in maize hybrid meristem tissue

(2008) Mei Guo et al.   PLANT MOLECULAR BIOLOGY

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

Adaptive evolution in invasive species

(2008) Peter J. Prentis et al.   TRENDS IN PLANT SCIENCE

Differential Allelic Expression in the Human Genome: A Robust Approach To Identify Genetic and Epigenetic Cis-Acting Mechanisms Regulating Gene Expression

(2008) David Serre et al.   PLoS Genetics

Transcriptome content and dynamics at single-nucleotide resolution

(2008) Nicole Cloonan et al.   GENOME BIOLOGY

Founding events in species invasions: genetic variation, adaptive evolution, and the role of multiple introductions

(2007) K. M. DLUGOSCH et al.   MOLECULAR ECOLOGY