Widespread and Adaptive Alterations in Genome-Wide Gene Expression Associated with Ecological Divergence of TwoOryzaSpecies

Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (Oryza glaberrima)

(2014) Benoit Nabholz et al.   MOLECULAR ECOLOGY

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

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

Ecogeographic Variation in the Morphology of Two Asian Wild Rice Species, Oryza nivara and Oryza rufipogon

(2013) Maria Celeste N. Banaticla-Hilario et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Extending the Arabidopsis flowering paradigm to a mass flowering phenomenon in the tropics

(2013) David J. Weston et al.   MOLECULAR ECOLOGY

Targeted sequence capture and resequencing implies a predominant role of regulatory regions in the divergence of a sympatric lake whitefish species pair (Coregonus clupeaformis)

(2013) Francois Olivier Hebert et al.   MOLECULAR ECOLOGY

QST–FST comparisons: evolutionary and ecological insights from genomic heterogeneity

(2013) Tuomas Leinonen et al.   NATURE REVIEWS GENETICS

Organ Evolution in Angiosperms Driven by Correlated Divergences of Gene Sequences and Expression Patterns

(2013) Ruolin Yang et al.   PLANT CELL

Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato

(2013) D. Koenig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic islands of divergence are not affected by geography of speciation in sunflowers

(2013) S. Renaut et al.   Nature Communications

Hard Selective Sweep and Ectopic Gene Conversion in a Gene Cluster Affording Environmental Adaptation

(2013) Marc Hanikenne et al.   PLoS Genetics

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Comparative studies of gene expression and the evolution of gene regulation

(2012) Irene Gallego Romero et al.   NATURE REVIEWS GENETICS

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

A Selection Index for Gene Expression Evolution and Its Application to the Divergence between Humans and Chimpanzees

(2012) Maria Warnefors et al.   PLoS One

Evaluation of Different Reference Based Annotation Strategies Using RNA-Seq – A Case Study in Drososphila pseudoobscura

(2012) Nicola Palmieri et al.   PLoS One

Mutation in CSA creates a new photoperiod-sensitive genic male sterile line applicable for hybrid rice seed production

(2012) H. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reshaping of the maize transcriptome by domestication

(2012) R. Swanson-Wagner 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

Widespread Interspecific Divergence in Cis-Regulation of Transposable Elements in the Arabidopsis Genus

(2011) F. He et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

Heading date gene, dth3 controlled late flowering in O. Glaberrima Steud. by down-regulating Ehd1

(2011) X. F. Bian et al.   PLANT CELL REPORTS

Evolution of the PEBP Gene Family in Plants: Functional Diversification in Seed Plant Evolution

(2011) A. Karlgren et al.   PLANT PHYSIOLOGY

Comparative Functional Genomics of the Fission Yeasts

(2011) N. Rhind et al.   SCIENCE

The role of gene expression in ecological speciation

(2010) Scott A. Pavey et al.   Annals of the New York Academy of Sciences

Insights into the role of differential gene expression on the ecological adaptation of the snail Littorina saxatilis

(2010) Mónica Martínez-Fernández et al.   BMC EVOLUTIONARY BIOLOGY

Regulatory divergence in Drosophila revealed by mRNA-seq

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

Ecological divergence in the presence of gene flow in two closely related Oryza species (Oryza rufipogon and O. nivara)

(2010) XIAO-MING ZHENG et al.   MOLECULAR ECOLOGY

The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing

(2010) JULIE JEUKENS et al.   MOLECULAR ECOLOGY

Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow

(2010) JOCHEN B. W. WOLF et al.   MOLECULAR ECOLOGY

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species

(2010) Song Liu et al.   NUCLEIC ACIDS RESEARCH

Speciation genetics: current status and evolving approaches

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

Digital Gene Expression Signatures for Maize Development

(2010) A. L. Eveland et al.   PLANT PHYSIOLOGY

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

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

GENETIC ARCHITECTURE FOR THE ADAPTIVE ORIGIN OF ANNUAL WILD RICE,ORYZA NIVARA

(2009) Michael A. Grillo et al.   EVOLUTION

A TEST OF THE NEUTRAL MODEL OF EXPRESSION CHANGE IN NATURAL POPULATIONS OF HOUSE MOUSE SUBSPECIES

(2009) Fabian Staubach et al.   EVOLUTION

Sex-specific and lineage-specific alternative splicing in primates

(2009) R. Blekhman et al.   GENOME RESEARCH

Next-generation tag sequencing for cancer gene expression profiling

(2009) A. S. Morrissy et al.   GENOME RESEARCH

Geographical genomics of human leukocyte gene expression variation in southern Morocco

(2009) Youssef Idaghdour et al.   NATURE GENETICS

Natural selection in action during speciation

(2009) S. Via   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional neoteny in the human brain

(2009) M. Somel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

(2009) Y. F. Chan et al.   SCIENCE

Evidence for Ecological Speciation and Its Alternative

(2009) D. Schluter   SCIENCE

The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species

(2009)   PLoS Computational Biology

Comparative expression profiling in grape (Vitis vinifera) berries derived from frequency analysis of ESTs and MPSS signatures

(2008) Alberto Iandolino et al.   BMC PLANT BIOLOGY

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

(2008) Sean B. Carroll   CELL

ENVIRONMENTAL FACTORS PREDICT ADAPTIVE PHENOTYPIC DIFFERENTIATION WITHIN AND BETWEEN TWO WILD ANDEAN TOMATOES

(2008) Takuya Nakazato et al.   EVOLUTION

The Phenomics and Expression Quantitative Trait Locus Mapping of Brain Transcriptomes Regulating Adaptive Divergence in Lake Whitefish Species Pairs (Coregonus sp.)

(2008) A. R. Whiteley et al.   GENETICS

Natural Variation in Gene Expression Between Wild and Weedy Populations of Helianthus annuus

(2008) Z. Lai et al.   GENETICS

Pervasive Sex-Linked Effects on Transcription Regulation As Revealed by Expression Quantitative Trait Loci Mapping in Lake Whitefish Species Pairs (Coregonus sp., Salmonidae)

(2008) N. Derome et al.   GENETICS

The genetic mosaic suggests a new role for hitchhiking in ecological speciation

(2008) SARA VIA et al.   MOLECULAR ECOLOGY

The transcriptomics of life-history trade-offs in whitefish species pairs (Coregonussp.)

(2008) J. ST-CYR et al.   MOLECULAR ECOLOGY

Regulatory changes underlying expression differences within and between Drosophila species

(2008) Patricia J Wittkopp et al.   NATURE GENETICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures

(2008) Ran Blekhman et al.   PLoS Genetics