Population transcriptomic characterization of the genetic and expression variation of a candidate progenitor of Miscanthus energy crops

Transcriptomic characterization of candidate genes responsive to salt tolerance of Miscanthus energy crops

(2017) Zhihong Song et al.   Global Change Biology Bioenergy

Transcriptomic responses to conspecific and congeneric competition in co-occurring Trifolium

(2017) Alan W. Bowsher et al.   JOURNAL OF ECOLOGY

Population transcriptomes reveal synergistic responses of DNA polymorphism and RNA expression to extreme environments on the Qinghai-Tibetan Plateau in a predatory bird

(2017) Shengkai Pan et al.   MOLECULAR ECOLOGY

missMDA: A Package for Handling Missing Values in Multivariate Data Analysis

(2016) Julie Josse et al.   Journal of Statistical Software

Genetic variation and bidirectional gene flow in the riparian plantMiscanthus lutarioriparius, across its endemic range: implications for adaptive potential

(2015) Juan Yan et al.   Global Change Biology Bioenergy

Genetic structure ofMiscanthus sinensisandMiscanthus sacchariflorusin Japan indicates a gradient of bidirectional but asymmetric introgression

(2015) Lindsay V. Clark et al.   JOURNAL OF EXPERIMENTAL BOTANY

Transcriptome-wide characterization of candidate genes for improving the water use efficiency of energy crops grown on semiarid land

(2015) Yangyang Fan et al.   JOURNAL OF EXPERIMENTAL BOTANY

Ten years of transcriptomics in wild populations: what have we learned about their ecology and evolution?

(2015) Mariano Alvarez et al.   MOLECULAR ECOLOGY

A footprint of past climate change on the diversity and population structure of Miscanthus sinensis

(2014) Lindsay V. Clark et al.   ANNALS OF BOTANY

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

(2014) S. Anders et al.   BIOINFORMATICS

Long-term water balance and sustainable production of Miscanthus energy crops in the Loess Plateau of China

(2014) Wei Liu et al.   BIOMASS & BIOENERGY

High photosynthetic rate and water use efficiency ofMiscanthus lutarioripariuscharacterize an energy crop in the semiarid temperate region

(2014) Juan Yan et al.   Global Change Biology Bioenergy

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

(2014) Qin Xu et al.   Journal of Integrative Plant Biology

The Evolution and Adaptive Potential of Transcriptional Variation in Sticklebacks—Signatures of Selection and Widespread Heritability

(2014) Erica H. Leder et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2014) Benoit Nabholz et al.   MOLECULAR ECOLOGY

Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations

(2014) Stephen E. Harris et al.   Molecular Ecology Resources

Miscanthus: a case study for the utilization of natural genetic variation

(2014) T. R. Hodkinson et al.   Plant Genetic Resources-Characterization and Utilization

Carbon sequestration by Miscanthus energy crops plantations in a broad range semi-arid marginal land in China

(2014) Jia Mi et al.   SCIENCE OF THE TOTAL ENVIRONMENT

European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation

(2014) Mbaye Tine et al.   Nature Communications

Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets

(2013) Xiao Xu et al.   BMC BIOINFORMATICS

Potential productivity of theMiscanthusenergy crop in the Loess Plateau of China under climate change

(2013) Wei Liu et al.   Environmental Research Letters

SNP development from RNA-seq data in a nonmodel fish: how many individuals are needed for accurate allele frequency prediction?

(2013) C. Schunter et al.   Molecular Ecology Resources

Transcriptome divergence between introduced and native populations of Canada thistle,Cirsium arvense

(2013) Alessia Guggisberg et al.   NEW PHYTOLOGIST

Reference-Free Population Genomics from Next-Generation Transcriptome Data and the Vertebrate–Invertebrate Gap

(2013) Philippe Gayral et al.   PLoS Genetics

Impact of Natural Genetic Variation on Gene Expression Dynamics

(2013) Marit Ackermann et al.   PLoS Genetics

De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments

(2012) Parul Gahlan et al.   BMC GENOMICS

Next generation sequencing and de novo transcriptome analysis of Costus pictus D. Don, a non-model plant with potent anti-diabetic properties

(2012) Ramasamy S Annadurai et al.   BMC GENOMICS

Molecular mechanisms of robustness in plants

(2012) Janne Lempe et al.   CURRENT OPINION IN PLANT BIOLOGY

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

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

Disrupted fine-scale population processes in fragmented landscapes despite large-scale genetic connectivity for a widespread and common cooperative breeder: the superb fairy-wren (Malurus cyaneus)

(2012) Katherine A. Harrisson et al.   JOURNAL OF ANIMAL ECOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring

(2012) S. Lamichhaney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Teosinte as a model system for population and ecological genomics

(2012) Matthew B. Hufford et al.   TRENDS IN GENETICS

Unraveling the Regulatory Mechanisms Underlying Tissue-Dependent Genetic Variation of Gene Expression

(2012) Jingyuan Fu et al.   PLoS Genetics

Variability and adaptability of Miscanthus species evaluated for energy crop domestication

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

Evolutionary History of Pearl Millet (Pennisetum glaucum [L.] R. Br.) and Selection on Flowering Genes since Its Domestication

(2011) J. Clotault et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Population genomics and local adaptation in wild isolates of a model microbial eukaryote

(2011) C. E. Ellison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic and physiological footprint of the Deepwater Horizon oil spill on resident marsh fishes

(2011) A. Whitehead et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The evolution of gene expression and the transcriptome–phenotype relationship

(2011) Peter W. Harrison et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method

(2011) Dent A. Earl et al.   Conservation Genetics Resources

Discovery of natural Miscanthus (Poaceae) triploid plants in sympatric populations of Miscanthus sacchariflorus and Miscanthus sinensis in southern Japan

(2010) A. Nishiwaki et al.   AMERICAN JOURNAL OF BOTANY

Invasiveness potential of Miscanthus sinensis: implications for bioenergy production in the United States

(2010) LAUREN D. QUINN et al.   Global Change Biology Bioenergy

China's bioenergy potential

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

Applications of next generation sequencing in molecular ecology of non-model organisms

(2010) R Ekblom et al.   HEREDITY

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

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

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

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

(2010) LAURENT EXCOFFIER et al.   Molecular Ecology Resources

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Feedstocks for Lignocellulosic Biofuels

(2010) C. Somerville et al.   SCIENCE

Adaptation genomics: the next generation

(2010) Jessica Stapley et al.   TRENDS IN ECOLOGY & EVOLUTION

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The effect of genetic and environmental variation on metabolic gene expression

(2009) CINDA P. SCOTT et al.   MOLECULAR ECOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells

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

Transcriptomic variation and plasticity in rufous-collared sparrows (Zonotrichia capensis) along an altitudinal gradient

(2008) ZACHARY A. CHEVIRON et al.   MOLECULAR ECOLOGY

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Interpreting principal component analyses of spatial population genetic variation

(2008) John Novembre et al.   NATURE GENETICS

The environmental contribution to gene expression profiles

(2008) Greg Gibson   NATURE REVIEWS GENETICS

Adaptation from standing genetic variation

(2007) R BARRETT et al.   TRENDS IN ECOLOGY & EVOLUTION