Population transcriptomics reveals a potentially positive role of expression diversity in adaptation

Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the Common Bean

(2014) E. Bellucci et al.   PLANT CELL

Genotype-by-Environment Interaction and Plasticity: Exploring Genomic Responses of Plants to the Abiotic Environment

(2013) David L. Des Marais et al.   Annual Review of Ecology Evolution and Systematics

RNA-seq differential expression studies: more sequence or more replication?

(2013) Yuwen Liu et al.   BIOINFORMATICS

Nuclear DNA content variation of three Miscanthus species in China

(2013) Xi Li et al.   Genes & Genomics

Gene expression drives local adaptation in humans

(2013) H. B. Fraser   GENOME RESEARCH

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

Mendelian and Non-Mendelian Regulation of Gene Expression in Maize

(2013) Lin Li et al.   PLoS Genetics

Yield potential of Miscanthus energy crops in the Loess Plateau of China

(2012) Wei Liu et al.   Global Change Biology Bioenergy

Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus)

(2012) MORTEN T. LIMBORG et al.   MOLECULAR ECOLOGY

Population transcriptomics of cactus host shifts inDrosophila mojavensis

(2012) LUCIANO M. MATZKIN   MOLECULAR ECOLOGY

Comparative population genomics of maize domestication and improvement

(2012) Matthew B Hufford et al.   NATURE GENETICS

Comparative studies of gene expression and the evolution of gene regulation

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

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

Phenotypic Plasticity of the Drosophila Transcriptome

(2012) Shanshan Zhou et al.   PLoS Genetics

Epigenetic contribution to stress adaptation in plants

(2011) Marie Mirouze et al.   CURRENT OPINION IN PLANT BIOLOGY

Variability and adaptability of Miscanthus species evaluated for energy crop domestication

(2011) JUAN YAN et al.   Global Change Biology Bioenergy

Gene Space Dynamics During the Evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor Genomes

(2011) A. N. Massa et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

(2011) Xiangchao Gan et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

A taxonomic revision of Miscanthus s.l. (Poaceae) from China

(2010) QIAN SUN et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Genome-Wide Survey and Expression Analysis Suggest Diverse Roles of Glutaredoxin Gene Family Members During Development and Response to Various Stimuli in Rice

(2010) R. Garg et al.   DNA RESEARCH

China's bioenergy potential

(2010) TAO SANG et al.   Global Change Biology Bioenergy

Optimization of de novo transcriptome assembly from next-generation sequencing data

(2010) Y. Surget-Groba et al.   GENOME RESEARCH

Molecular Mechanisms Regulating Rapid Stress Signaling Networks inArabidopsis

(2010) Justin W. Walley et al.   Journal of Integrative Plant Biology

Toward the Domestication of Lignocellulosic Energy Crops: Learning from Food Crop DomesticationFree Access

(2010) Tao Sang   Journal of Integrative Plant Biology

Marginal Land-based Biomass Energy Production in China

(2010) Ya Tang et al.   Journal of Integrative Plant Biology

Genome-wide Expansion and Expression Divergence of the Basic Leucine Zipper Transcription Factors in Higher Plants with an Emphasis on SorghumF

(2010) Jizhou Wang et al.   Journal of Integrative Plant Biology

Genetic Engineering of Energy Crops: A Strategy for Biofuel Production in ChinaFree Access

(2010) Guosheng Xie et al.   Journal of Integrative Plant Biology

Survey of Genomics Approaches to Improve Bioenergy Traits in Maize, Sorghum and SugarcaneFree Access

(2010) Wilfred Vermerris   Journal of Integrative Plant Biology

Whole-Genome Expression Plasticity across Tropical and Temperate Drosophila melanogaster Populations from Eastern Australia

(2010) M. T. Levine et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

WAVY LEAF1, an Ortholog of Arabidopsis HEN1, Regulates Shoot Development by Maintaining MicroRNA and Trans-Acting Small Interfering RNA Accumulation in Rice

(2010) M. Abe 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

Phenotypic plasticity's impacts on diversification and speciation

(2010) David W. Pfennig et al.   TRENDS IN ECOLOGY & EVOLUTION

WRKY transcription factors

(2010) Paul J. Rushton et al.   TRENDS IN PLANT SCIENCE

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

(2009) Likun Wang et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Epigenetic regulation of stress responses in plants

(2009) Viswanathan Chinnusamy et al.   CURRENT OPINION IN PLANT BIOLOGY

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

Transcript Profiling Provides Evidence of Functional Divergence and Expression Networks among Ribosomal Protein Gene Paralogs in Brassica napus

(2009) C. A. Whittle et al.   PLANT CELL

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Evolving gene expression: from G to E to G×E

(2009) Andrea Hodgins-Davis et al.   TRENDS IN ECOLOGY & EVOLUTION

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

The environmental contribution to gene expression profiles

(2008) Greg Gibson   NATURE REVIEWS GENETICS

Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation

(2008) Luis López-Maury et al.   NATURE REVIEWS GENETICS

Gene expression variation in African and European populations of Drosophila melanogaster

(2008) Stephan Hutter et al.   GENOME BIOLOGY