Gene regulatory network architecture in different developmental contexts influences the genetic basis of morphological evolution

Comprehensive Analysis of a cis -Regulatory Region Reveals Pleiotropy in Enhancer Function

(2018) Ella Preger-Ben Noon et al.   Cell Reports

Taxon-restricted genes at the origin of a novel trait allowing access to a new environment

(2017) M. Emília Santos et al.   SCIENCE

Perspectives on Gene Regulatory Network Evolution

(2017) Marc S. Halfon   TRENDS IN GENETICS

MicroRNA-92a is a circadian modulator of neuronal excitability in Drosophila

(2017) Xiao Chen et al.   Nature Communications

Evolved Repression Overcomes Enhancer Robustness

(2016) Ella Preger-Ben Noon et al.   DEVELOPMENTAL CELL

FlyBase at 25: looking to the future

(2016) L. Sian Gramates et al.   NUCLEIC ACIDS RESEARCH

Reorganisation of Hoxd regulatory landscapes during the evolution of a snake-like body plan

(2016) Isabel Guerreiro et al.   eLife

Low Affinity Binding Site Clusters Confer Hox Specificity and Regulatory Robustness

(2015) Justin Crocker et al.   CELL

Co-option of an Ancestral Hox-Regulated Network Underlies a Recently Evolved Morphological Novelty

(2015) William J. Glassford et al.   DEVELOPMENTAL CELL

Fromshavenbabyto the naked valley: trichome formation as a model for evolutionary developmental biology

(2015) Saad Arif et al.   EVOLUTION & DEVELOPMENT

Pri sORF peptides induce selective proteasome-mediated protein processing

(2015) J. Zanet et al.   SCIENCE

Downregulation of the Host Gene jigr1 by miR-92 Is Essential for Neuroblast Self-Renewal in Drosophila

(2015) Yeliz Yuva-Aydemir et al.   PLoS Genetics

Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures

(2014) D. H. Phanstiel et al.   BIOINFORMATICS

Systematic Study of Drosophila MicroRNA Functions Using a Collection of Targeted Knockout Mutations

(2014) Ya-Wen Chen et al.   DEVELOPMENTAL CELL

Genome-scale functional characterization of Drosophila developmental enhancers in vivo

(2014) Evgeny Z. Kvon et al.   NATURE

Pri peptides are mediators of ecdysone for the temporal control of development

(2014) Hélène Chanut-Delalande et al.   NATURE CELL BIOLOGY

Multiple recent co-options of Optix associated with novel traits in adaptive butterfly wing radiations

(2014) Arnaud Martin et al.   EvoDevo

Evolution of mir-92a Underlies Natural Morphological Variation in Drosophila melanogaster

(2013) Saad Arif et al.   CURRENT BIOLOGY

A Perspective on Micro-Evo-Devo: Progress and Potential

(2013) Maria D. S. Nunes et al.   GENETICS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

The genetic causes of convergent evolution

(2013) David L. Stern   NATURE REVIEWS GENETICS

The structure and evolution ofcis-regulatory regions: theshavenbabystory

(2013) David L. Stern et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Emergence and Diversification of Fly Pigmentation Through Evolution of a Gene Regulatory Module

(2013) L. Arnoult et al.   SCIENCE

Genome-wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization

(2013) Delphine Menoret et al.   GENOME BIOLOGY

Functional Characterization of Drosophila microRNAs by a Novel in Vivo Library

(2012) Claus Schertel et al.   GENETICS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Cole Trapnell et al.   Nature Protocols

Conserved regulatory architecture underlies parallel genetic changes and convergent phenotypic evolution

(2012) N. Frankel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutations in the neverland Gene Turned Drosophila pachea into an Obligate Specialist Species

(2012) M. Lang et al.   SCIENCE

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Dry under water: Comparative morphology and functional aspects of air-retaining insect surfaces

(2011) Alexander Balmert et al.   JOURNAL OF MORPHOLOGY

Morphological evolution caused by many subtle-effect substitutions in regulatory DNA

(2011) Nicolás Frankel et al.   NATURE

optix Drives the Repeated Convergent Evolution of Butterfly Wing Pattern Mimicry

(2011) R. D. Reed et al.   SCIENCE

Superhydrophobic surfaces of the water bugNotonecta glauca: a model for friction reduction and air retention

(2011) Petra Ditsche-Kuru et al.   Beilstein Journal of Nanotechnology

Genome-level identification of targets of Hox protein Ultrabithorax in Drosophila: novel mechanisms for target selection

(2011) Pavan Agrawal et al.   Scientific Reports

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

(2010) Nicolás Frankel et al.   NATURE

Small Peptides Switch the Transcriptional Activity of Shavenbaby During Drosophila Embryogenesis

(2010) T. Kondo et al.   SCIENCE

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

METAMODELS AND PHYLOGENETIC REPLICATION: A SYSTEMATIC APPROACH TO THE EVOLUTION OF DEVELOPMENTAL PATHWAYS

(2009) Artyom Kopp   EVOLUTION

Use of microRNA sponges to explore tissue-specific microRNA functions in vivo

(2009) Stephen M Cohen   NATURE METHODS

Is Genetic Evolution Predictable?

(2009) D. L. Stern et al.   SCIENCE

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

(2009) Y. F. Chan et al.   SCIENCE

Moulding technique demonstrates the contribution of surface geometry to the super-hydrophobic properties of the surface of a water strider

(2008) Pablo Perez Goodwyn et al.   Acta Biomaterialia

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

(2008) Sean B. Carroll   CELL

The 11-aminoacid long Tarsal-less peptides trigger a cell signal in Drosophila leg development

(2008) Jose Ignacio Pueyo et al.   DEVELOPMENTAL BIOLOGY

THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?

(2008) David L. Stern et al.   EVOLUTION

Skating and diving: Changes in functional morphology of the setal and microtrichial cover during ontogenesis inAquarius paludum fabricius (Heteroptera, Gerridae)

(2008) P.J. Perez Goodwyn et al.   JOURNAL OF MORPHOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY