Ecological speciation in sympatric palms: 1. Gene expression, selection and pleiotropy

The Diversity, Biogenesis, and Activities of Endogenous Silencing Small RNAs inArabidopsis

(2014) Nicolas G. Bologna et al.   Annual Review of Plant Biology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Rapid genetic adaptation precedes the spread of an exotic plant species

(2014) Katrien Vandepitte et al.   MOLECULAR ECOLOGY

Evaluation of genetic isolation within an island flora reveals unusually widespread local adaptation and supports sympatric speciation

(2014) A. S. T. Papadopulos et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Overproduction of an Arabidopsis aldo–keto reductase increases barley tolerance to oxidative and cadmium stress by an in vivo reactive aldehyde detoxification

(2014) Csaba Éva et al.   PLANT GROWTH REGULATION

Global Analysis of Gene Expression Profiles in Physic Nut (Jatropha curcas L.) Seedlings Exposed to Salt Stress

(2014) Lin Zhang et al.   PLoS One

Expression Profiling of FLOWERING LOCUS T-Like Gene in Alternate Bearing ‘Hass' Avocado Trees Suggests a Role for PaFT in Avocado Flower Induction

(2014) Dafna Ziv et al.   PLoS One

A Single Gene Affects Both Ecological Divergence and Mate Choice in Drosophila

(2014) H. Chung et al.   SCIENCE

4P: fast computing of population genetics statistics from large DNA polymorphism panels

(2014) Andrea Benazzo et al.   Ecology and Evolution

Divergence in Gene Expression Is Uncoupled from Divergence in Coding Sequence in a Secondarily Woody Sunflower

(2013) Brook T. Moyers et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

A comparative analysis of the mechanisms underlying speciation on Lord Howe Island

(2013) A. S. T. Papadopulos et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Genomic Divergence during Speciation Driven by Adaptation to Altitude

(2013) Mark A. Chapman et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Indirect Evolution of Hybrid Lethality Due to Linkage with Selected Locus in Mimulus guttatus

(2013) Kevin M. Wright et al.   PLOS BIOLOGY

Fulcrum: condensing redundant reads from high-throughput sequencing studies

(2012) Matthew S. Burriesci et al.   BIOINFORMATICS

MicroRNAs play critical roles during plant development and in response to abiotic stresses

(2012) Júlio César de Lima et al.   GENETICS AND MOLECULAR BIOLOGY

The simple fool's guide to population genomics via RNA-Seq: an introduction to high-throughput sequencing data analysis

(2012) Pierre De Wit et al.   Molecular Ecology Resources

Identification and removal of ribosomal RNA sequences from metatranscriptomes

(2011) Robert Schmieder et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Transcriptome profile analysis of flowering molecular processes of early flowering trifoliate orange mutant and the wild-type [Poncirus trifoliata (L.) Raf.] by massively parallel signature sequencing

(2011) Jin-Zhi Zhang et al.   BMC GENOMICS

Regulation of flowering time: all roads lead to Rome

(2011) Anusha Srikanth et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Accelerated and Adaptive Evolution of Yeast Sexual Adhesins

(2011) X. Xie et al.   MOLECULAR BIOLOGY AND EVOLUTION

A framework for comparing processes of speciation in the presence of gene flow

(2011) CAROLE M. SMADJA et al.   MOLECULAR ECOLOGY

Control of flowering and storage organ formation in potato by FLOWERING LOCUS T

(2011) Cristina Navarro et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

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

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

A Nucleotide Metabolite Controls Stress-Responsive Gene Expression and Plant Development

(2011) Hao Chen et al.   PLoS One

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

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

The role of gene expression in ecological speciation

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

Conservation between higher plants and the moss Physcomitrella patens in response to the phytohormone abscisic acid: a proteomics analysis

(2010) Xiaoqin Wang et al.   BMC PLANT BIOLOGY

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

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

Characterization of Two Novel Aldo–Keto Reductases from Arabidopsis: Expression Patterns, Broad Substrate Specificity, and an Open Active-Site Structure Suggest a Role in Toxicant Metabolism Following Stress

(2009) Paul J. Simpson et al.   JOURNAL OF MOLECULAR BIOLOGY

Isolation with Migration Models for More Than Two Populations

(2009) Jody Hey   MOLECULAR BIOLOGY AND EVOLUTION

How sympatric is speciation in theHoweapalms of Lord Howe Island?

(2009) WIESŁAW BABIK et al.   MOLECULAR ECOLOGY

How relevant are flavonoids as antioxidants in plants?

(2009) Iker Hernández et al.   TRENDS IN PLANT SCIENCE

A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective

(2008) M. Foll et al.   GENETICS

What, if anything, is sympatric speciation?

(2008) B. M. FITZPATRICK et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

The nucleotidase/phosphatase SAL1 is a negative regulator of drought tolerance in Arabidopsis

(2008) Pip B. Wilson et al.   PLANT JOURNAL