Convergent evolution of gene expression in two high-toothed stickleback populations

Different contributions of local- and distant-regulatory changes to transcriptome divergence between stickleback ecotypes

(2017) Asano Ishikawa et al.   EVOLUTION

Gene expression plasticity in response to salinity acclimation in threespine stickleback ecotypes from different salinity habitats

(2017) Taylor C. Gibbons et al.   MOLECULAR ECOLOGY

Promoter shape varies across populations and affects promoter evolution and expression noise

(2017) Ignacio E Schor et al.   NATURE GENETICS

Evolving New Skeletal Traits by cis -Regulatory Changes in Bone Morphogenetic Proteins

(2016) Vahan B. Indjeian et al.   CELL

Partially repeatable genetic basis of benthic adaptation in threespine sticklebacks

(2016) Priscilla A. Erickson et al.   EVOLUTION

Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks

(2016) Yun Huang et al.   MOLECULAR ECOLOGY

Receptors rather than signals change in expression in four physiological regulatory networks during evolutionary divergence in threespine stickleback

(2016) Carole Di Poi et al.   MOLECULAR ECOLOGY

The genetic and molecular architecture of phenotypic diversity in sticklebacks

(2016) Catherine L. Peichel et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Sox2+ progenitors in sharks link taste development with the evolution of regenerative teeth from denticles

(2016) Kyle J. Martin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulatory Architecture of Gene Expression Variation in the Threespine Stickleback Gasterosteus aculeatus

(2016) Victoria L. Pritchard et al.   G3-Genes Genomes Genetics

Heads, Shoulders, Elbows, Knees, and Toes: Modular Gdf5 Enhancers Control Different Joints in the Vertebrate Skeleton

(2016) Hao Chen et al.   PLoS Genetics

Distinct developmental genetic mechanisms underlie convergently evolved tooth gain in sticklebacks

(2015) N. A. Ellis et al.   DEVELOPMENT

Coevolutionary patterning of teeth and taste buds

(2015) Ryan F. Bloomquist et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tempo and mode of regulatory evolution in Drosophila

(2014) J. D. Coolon et al.   GENOME RESEARCH

Hybrid Mice Reveal Parent-of-Origin and Cis- and Trans-Regulatory Effects in the Retina

(2014) Susan Q. Shen et al.   PLoS One

Evolved tooth gain in sticklebacks is associated with a cis-regulatory allele of Bmp6

(2014) P. A. Cleves et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

The Role of cis Regulatory Evolution in Maize Domestication

(2014) Zachary H. Lemmon et al.   PLoS Genetics

Common developmental pathways link tooth shape to regeneration

(2013) Gareth J. Fraser et al.   DEVELOPMENTAL BIOLOGY

Competitive balance of intrabulge BMP/Wnt signaling reveals a robust gene network ruling stem cell homeostasis and cyclic activation

(2013) Eve Kandyba et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tooth shape formation and tooth renewal: evolving with the same signals

(2012) J. Jernvall et al.   DEVELOPMENT

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression

(2012) A. Goncalves et al.   GENOME RESEARCH

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

(2012) David Bryant et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Transcriptional Enhancers in Protein-Coding Exons of Vertebrate Developmental Genes

(2012) Deborah I. Ritter et al.   PLoS One

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

The Developmental Role of Agouti in Color Pattern Evolution

(2011) M. Manceau et al.   SCIENCE

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

Regulatory divergence in Drosophila revealed by mRNA-seq

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

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Gene set enrichment analysis made simple

(2010) Rafael A Irizarry et al.   STATISTICAL METHODS IN MEDICAL RESEARCH

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

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

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

(2009) Y. F. Chan et al.   SCIENCE

An Ancient Gene Network Is Co-opted for Teeth on Old and New Jaws

(2009) Gareth J Fraser et al.   PLOS BIOLOGY

Regulatory changes underlying expression differences within and between Drosophila species

(2008) Patricia J Wittkopp et al.   NATURE GENETICS