Developmental Progression in the CoralAcropora digitiferaIs Controlled by Differential Expression of Distinct Regulatory Gene Networks

Snake venoms are integrated systems, but abundant venom proteins evolve more rapidly

(2015) Steven D. Aird et al.   BMC GENOMICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

MYC proteins promote neuronal differentiation by controlling the mode of progenitor cell division

(2014) N. Zinin et al.   EMBO REPORTS

Gene Co-expression Modules Underlying Polymorphic and Monomorphic Zooids in the Colonial Hydrozoan, Hydractinia symbiolongicarpus

(2014) D. C. Plachetzki et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

BMP signaling requires retromer-dependent recycling of the type I receptor

(2014) R. J. Gleason et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential Responses to Wnt and PCP Disruption Predict Expression and Developmental Function of Conserved and Novel Genes in a Cnidarian

(2014) Pascal Lapébie et al.   PLoS Genetics

KEGG orthology-based annotation of the predicted proteome of Acropora digitifera: ZoophyteBase - an open access and searchable database of a coral genome

(2013) Walter C Dunlap et al.   BMC GENOMICS

Comparison of RNA- or LNA-hybrid oligonucleotides in template-switching reactions for high-speed sequencing library preparation

(2013) Matthias Harbers et al.   BMC GENOMICS

Characterization of differential transcript abundance through time during Nematostella vectensis development

(2013) Rebecca Helm et al.   BMC GENOMICS

Quantitative high-throughput profiling of snake venom gland transcriptomes and proteomes (Ovophis okinavensis and Protobothrops flavoviridis)

(2013) Steven D Aird et al.   BMC GENOMICS

Fold change and p-value cutoffs significantly alter microarray interpretations

(2012) Mark R Dalman et al.   BMC BIOINFORMATICS

Coral Comparative Genomics Reveal Expanded Hox Cluster in the Cnidarian-Bilaterian Ancestor

(2012) T. Q. DuBuc et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Whole Transcriptome Analysis of the CoralAcropora milleporaReveals Complex Responses to CO2-driven Acidification during the Initiation of Calcification

(2012) A. MOYA et al.   MOLECULAR ECOLOGY

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

(2012) Cole Trapnell et al.   Nature Protocols

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Hymyc1 Downregulation Promotes Stem Cell Proliferation in Hydra vulgaris

(2012) Alfredo Ambrosone et al.   PLoS One

The Neuronal Calcium Sensor Protein Acrocalcin: A Potential Target of Calmodulin Regulation during Development in the Coral Acropora millepora

(2012) Alejandro Reyes-Bermudez et al.   PLoS One

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Chromatin Connections to Pluripotency and Cellular Reprogramming

(2011) Stuart H. Orkin et al.   CELL

Cell Fate Plug and Play: Direct Reprogramming and Induced Pluripotency

(2011) Stuart M. Chambers et al.   CELL

Pluripotency Factors in Embryonic Stem Cells Regulate Differentiation into Germ Layers

(2011) Matt Thomson et al.   CELL

Induced stem cell neoplasia in a cnidarian by ectopic expression of a POU domain transcription factor

(2011) R. C. Millane et al.   DEVELOPMENT

The biology of coral metamorphosis: Molecular responses of larvae to inducers of settlement and metamorphosis

(2011) L.C. Grasso et al.   DEVELOPMENTAL BIOLOGY

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

Using the Acropora digitifera genome to understand coral responses to environmental change

(2011) Chuya Shinzato et al.   NATURE

Mechanisms and functions of Hedgehog signalling across the metazoa

(2011) Philip W. Ingham et al.   NATURE REVIEWS GENETICS

Multiple Sox genes are expressed in stem cells or in differentiating neuro-sensory cells in the hydrozoan Clytia hemisphaerica

(2011) Muriel Jager et al.   EvoDevo

The role of FGF/Erk signaling in pluripotent cells

(2010) F. Lanner et al.   DEVELOPMENT

Dishevelled-associated activator of morphogenesis 1 (Daam1) is required for heart morphogenesis

(2010) D. Li et al.   DEVELOPMENT

Mammalian Krüppel-Like Factors in Health and Diseases

(2010) Beth B. McConnell et al.   PHYSIOLOGICAL REVIEWS

A genomic view of 500 million years of cnidarian evolution

(2010) Robert E. Steele et al.   TRENDS IN GENETICS

Hydra and the evolution of stem cells

(2009) Thomas C. G. Bosch   BIOESSAYS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

In vitro culture of cells derived from larvae of the staghorn coral Acropora millepora

(2009) A. Reyes-Bermudez et al.   CORAL REEFS

The transcriptional foundation of pluripotency

(2009) I. Chambers et al.   DEVELOPMENT

The cyclic gene Hes1 contributes to diverse differentiation responses of embryonic stem cells

(2009) T. Kobayashi et al.   GENES & DEVELOPMENT

Gene expression microarray analysis encompassing metamorphosis and the onset of calcification in the scleractinian coral Montastraea faveolata

(2009) Alejandro Reyes-Bermudez et al.   Marine Genomics

Deep homology and the origins of evolutionary novelty

(2009) Neil Shubin et al.   NATURE

The evolution of Fox genes and their role in development and disease

(2009) Sridhar Hannenhalli et al.   NATURE REVIEWS GENETICS

Long non-coding RNAs: insights into functions

(2009) Tim R. Mercer et al.   NATURE REVIEWS GENETICS

Axial Patterning in Hydra

(2009) H. R. Bode   Cold Spring Harbor Perspectives in Biology

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Microarray analysis identifies candidate genes for key roles in coral development

(2008) Lauretta C Grasso et al.   BMC GENOMICS

Carbonic Anhydrase in the Scleractinian CoralStylophora pistillata

(2008) Aurélie Moya et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Specific Expression of BMP2/4 Ortholog in Biomineralizing Tissues of Corals and Action on Mouse BMP Receptor

(2008) Didier Zoccola et al.   MARINE BIOTECHNOLOGY

The Groucho/TLE/Grg family of transcriptional co-repressors

(2008) Barbara H Jennings et al.   GENOME BIOLOGY