Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia

GATAe regulates intestinal stem cell maintenance and differentiation in Drosophila adult midgut

(2016) Takashi Okumura et al.   DEVELOPMENTAL BIOLOGY

Mammalian Heat Shock Response and Mechanisms Underlying Its Genome-wide Transcriptional Regulation

(2016) Dig B. Mahat et al.   MOLECULAR CELL

The power and promise of RNA-seq in ecology and evolution

(2016) Erica V. Todd et al.   MOLECULAR ECOLOGY

A beak size locus in Darwins finches facilitated character displacement during a drought

(2016) S. Lamichhaney et al.   SCIENCE

Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors

(2016) Luisa Orsini et al.   Scientific Data

NMDA receptor activation upstream of methyl farnesoate signaling for short day-induced male offspring production in the water flea, Daphnia pulex

(2015) Kenji Toyota et al.   BMC GENOMICS

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

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

(2015) Saad Arif et al.   EVOLUTION & DEVELOPMENT

Transcriptional profiling of predator-induced phenotypic plasticity in Daphnia pulex

(2015) Andrey Rozenberg et al.   Frontiers in Zoology

The power of next-generation sequencing as illustrated by the neuropeptidome of the crayfish Procambarus clarkii

(2015) Jan A. Veenstra   GENERAL AND COMPARATIVE ENDOCRINOLOGY

Allatotropin inhibits juvenile hormone biosynthesis by the corpora allata of adult Bombyx mori

(2015) Yu Kaneko et al.   JOURNAL OF INSECT PHYSIOLOGY

The pleiotropic allatoregulatory neuropeptides and their receptors: A mini-review

(2015) Heleen Verlinden et al.   JOURNAL OF INSECT PHYSIOLOGY

Tequila Regulates Insulin-Like Signaling and Extends Life Span inDrosophila melanogaster

(2015) Cheng-Wen Huang et al.   JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES

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

(2015) Mariano Alvarez et al.   MOLECULAR ECOLOGY

Evolution of vertebrates as viewed from the crest

(2015) Stephen A. Green et al.   NATURE

i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly

(2015) Hana Imrichová et al.   NUCLEIC ACIDS RESEARCH

FlyBase: establishing a Gene Group resource forDrosophila melanogaster

(2015) Helen Attrill et al.   NUCLEIC ACIDS RESEARCH

Towards the identification of the loci of adaptive evolution

(2015) Carolina Pardo-Diaz et al.   Methods in Ecology and Evolution

Suppressive effects of dRYamides on feeding behavior of the blowfly, Phormia regina

(2015) Toru Maeda et al.   Zoological Letters

A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data

(2014) Ngoc Tam L Tran et al.   Biology Direct

Deciphering the genetic basis of microcystin tolerance

(2014) Anke Schwarzenberger et al.   BMC GENOMICS

An SNP-based second-generation genetic map of Daphnia magna and its application to QTL analysis of phenotypic traits

(2014) Jarkko Routtu et al.   BMC GENOMICS

Genomic data integration for ecological and evolutionary traits in non-model organisms

(2014) Denis Tagu et al.   BMC GENOMICS

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Genome-Wide Transcription Profiles Reveal Genotype-Dependent Responses of Biological Pathways and Gene-Families in Daphnia Exposed to Single and Mixed Stressors

(2014) Dieter I. M. De Coninck et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Roles of ecdysteroids for progression of reproductive cycle in the fresh water crustacean Daphnia magna

(2014) Eri Sumiya et al.   Frontiers in Zoology

Quantitative Neuropeptidomics Study of the Effects of Temperature Change in the Crab Cancer borealis

(2014) Ruibing Chen et al.   JOURNAL OF PROTEOME RESEARCH

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

Juvenile hormone regulates body size and perturbs insulin signaling in Drosophila

(2014) C. K. Mirth et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Promiscuous Intermediate Underlies the Evolution of LEAFY DNA Binding Specificity

(2014) C. Sayou et al.   SCIENCE

iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections

(2014) Rekin's Janky et al.   PLoS Computational Biology

dusky-like is required to maintain the integrity and planar cell polarity of hairs during the development of the Drosophila wing

(2013) Paul N. Adler et al.   DEVELOPMENTAL BIOLOGY

Gene Coexpression Networks Reveal Key Drivers of Phenotypic Divergence in Lake Whitefish

(2013) Marie Filteau et al.   MOLECULAR BIOLOGY AND EVOLUTION

Annotated genes and nonannotated genomes: cross-species use of Gene Ontology in ecology and evolution research

(2013) C. R. Primmer et al.   MOLECULAR ECOLOGY

A road map for molecular ecology

(2013) Rose L. Andrew et al.   MOLECULAR ECOLOGY

Interspecific Differences between D. pulex and D. magna in Tolerance to Cyanobacteria with Protease Inhibitors

(2013) Christian J. Kuster et al.   PLoS One

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

(2013) Delphine Menoret et al.   GENOME BIOLOGY

The developmental control of size in insects

(2013) H. Frederik Nijhout et al.   Wiley Interdisciplinary Reviews-Developmental Biology

The Juvenile Hormone Signaling Pathway in Insect Development

(2012) Marek Jindra et al.   Annual Review of Entomology

Ecdysone Control of Developmental Transitions: Lessons from Drosophila Research

(2012) Naoki Yamanaka et al.   Annual Review of Entomology

Identification of Pathways, Gene Networks, and Paralogous Gene Families in Daphnia pulex Responding to Exposure to the Toxic Cyanobacterium Microcystis aeruginosa

(2012) Jana Asselman et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Empirically determining the sample size for large-scale gene network inference algorithms

(2012) G. Altay   IET Systems Biology

The transcription factor Grainy head and the steroid hormone ecdysone cooperate during differentiation of the skin of Drosophila melanogaster

(2012) U. Gangishetti et al.   INSECT MOLECULAR BIOLOGY

Insulin signalling in mushroom body neurons regulates feeding behaviour in Drosophila larvae

(2012) X. L. Zhao et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Molecular mechanisms of tolerance to cyanobacterial protease inhibitors revealed by clonal differences inDaphnia magna

(2012) Anke Schwarzenberger et al.   MOLECULAR ECOLOGY

Genomic approaches towards finding cis-regulatory modules in animals

(2012) Ross C. Hardison et al.   NATURE REVIEWS GENETICS

i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules

(2012) Carl Herrmann et al.   NUCLEIC ACIDS RESEARCH

Comparing Statistical Methods for Constructing Large Scale Gene Networks

(2012) Jeffrey D. Allen et al.   PLoS One

Linking genes to communities and ecosystems: Daphnia as an ecogenomic model

(2012) B. E. Miner et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

What is needed for next-generation ecological and evolutionary genomics?

(2012) Scott A. Pavey et al.   TRENDS IN ECOLOGY & EVOLUTION

Deciphering the transcriptional cis-regulatory code

(2012) J. Omar Yáñez-Cuna et al.   TRENDS IN GENETICS

Identification of the novel bioactive peptides dRYamide-1 and dRYamide-2, ligands for a neuropeptide Y-like receptor in Drosophila

(2011) Takanori Ida et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Regulation of crustacean molting: A review and our perspectives

(2011) Ernest S. Chang et al.   GENERAL AND COMPARATIVE ENDOCRINOLOGY

Peptidomics and Peptide Hormone Processing in theDrosophilaMidgut

(2011) Wencke Reiher et al.   JOURNAL OF PROTEOME RESEARCH

Genomics, Transcriptomics, and Peptidomics ofDaphnia pulexNeuropeptides and Protein Hormones

(2011) Heinrich Dircksen et al.   JOURNAL OF PROTEOME RESEARCH

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets

(2011) Morgane Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Whole-Genome Analysis Reveals That Active Heat Shock Factor Binding Sites Are Mostly Associated with Non-Heat Shock Genes in Drosophila melanogaster

(2011) Sarah E. Gonsalves et al.   PLoS One

Extensive DNA-binding specificity divergence of a conserved transcription regulator

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

The Ecoresponsive Genome of Daphnia pulex

(2011) J. K. Colbourne et al.   SCIENCE

The Developmental Role of Agouti in Color Pattern Evolution

(2011) M. Manceau et al.   SCIENCE

Towards a System Level Understanding of Non-Model Organisms Sampled from the Environment: A Network Biology Approach

(2011) Tim D. Williams et al.   PLoS Computational Biology

Two Frizzled Planar Cell Polarity Signals in the Drosophila Wing Are Differentially Organized by the Fat/Dachsous Pathway

(2011) Justin Hogan et al.   PLoS Genetics

Zona Pellucida Domain Proteins Remodel the Apical Compartment for Localized Cell Shape Changes

(2010) Isabelle Fernandes et al.   DEVELOPMENTAL CELL

Nutritional constraints at the cyanobacteria-Daphnia magnainterface: The role of sterols

(2010) Dominik Martin-Creuzburg et al.   LIMNOLOGY AND OCEANOGRAPHY

Genome-wide analysis of a long-term evolution experiment with Drosophila

(2010) Molly K. Burke et al.   NATURE

Conflicting processes in the evolution of body size and development time

(2010) H. F. Nijhout et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Bombyx prothoracicostatic peptides activate the sex peptide receptor to regulate ecdysteroid biosynthesis

(2010) N. Yamanaka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small Peptides Switch the Transcriptional Activity of Shavenbaby During Drosophila Embryogenesis

(2010) T. Kondo et al.   SCIENCE

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same

(2010) Matthew T. Weirauch et al.   TRENDS IN GENETICS

Robust Target Gene Discovery through Transcriptome Perturbations and Genome-Wide Enhancer Predictions in Drosophila Uncovers a Regulatory Basis for Sensory Specification

(2010) Stein Aerts et al.   PLOS BIOLOGY

Evidence that Adaptation in Drosophila Is Not Limited by Mutation at Single Sites

(2010) Talia Karasov et al.   PLoS Genetics

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Can metal stress induce transferable changes in gene transcription in Daphnia magna?

(2009) Michiel B. Vandegehuchte et al.   AQUATIC TOXICOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder

(2009) A. A. Sharov et al.   DNA RESEARCH

Genomic mapping of binding regions for the Ecdysone receptor protein complex

(2009) Z. Gauhar et al.   GENOME RESEARCH

Influence of Daphnia infochemicals on functional traits of Microcystis strains (Cyanobacteria)

(2009) Ineke van Gremberghe et al.   HYDROBIOLOGIA

Expression and ecdysteroid responsiveness of the nuclear receptors HR3 and E75 in the crustacean Daphnia magna

(2009) Bethany R. Hannas et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Linking genotypes to phenotypes and fitness: how mechanistic biology can inform molecular ecology

(2009) ANNE C. DALZIEL et al.   MOLECULAR ECOLOGY

Border-cell migration requires integration of spatial and temporal signals by the BTB protein Abrupt

(2009) Anna C.-C. Jang et al.   NATURE CELL BIOLOGY

Connecting Genes, Coexpression Modules, and Molecular Signatures to Environmental Stress Phenotypes in Plants

(2008) David J Weston et al.   BMC Systems Biology

Regulatory peptides in fruit fly midgut

(2008) Jan A. Veenstra et al.   CELL AND TISSUE RESEARCH

Opposing Effects of Dietary Protein and Sugar Regulate a Transcriptional Target of Drosophila Insulin-like Peptide Signaling

(2008) Susanne Buch et al.   Cell Metabolism

Expression of theDrosophilasecreted cuticle protein 73 (dsc73) requires shavenbaby

(2008) Deborah J. Andrew et al.   DEVELOPMENTAL DYNAMICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

From Genotype to Phenotype: Systems Biology Meets Natural Variation

(2008) P. N. Benfey et al.   SCIENCE

ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?

(2008) Peter Van Loo et al.   GENOME BIOLOGY

Systems biology meets stress ecology: linking molecular and organismal stress responses in Daphnia magna

(2008) Lars-Henrik Heckmann et al.   GENOME BIOLOGY