Global identification of Smad2 and Eomesodermin targets in zebrafish identifies a conserved transcriptional network in mesendoderm and a novel role for Eomesodermin in repression of ectodermal gene expression

Maternal Eomesodermin regulates zygotic nodal gene expression for mesendoderm induction in zebrafish embryos

(2014) Pengfei Xu et al.   Journal of Molecular Cell Biology

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

In Vivo T-Box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuromesodermal Bipotency

(2013) George E. Gentsch et al.   Cell Reports

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

A zebrafish Notum homolog specifically blocks the Wnt/ -catenin signaling pathway

(2012) G. P. Flowers et al.   DEVELOPMENT

An essential and highly conserved role for Zic3 in left–right patterning, gastrulation and convergent extension morphogenesis

(2012) Ashley E. Cast et al.   DEVELOPMENTAL BIOLOGY

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

Multilayered chromatin analysis reveals E2f, Smad and Zfx as transcriptional regulators of histones

(2012) David Gokhman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Stress-Response Gene redd1 Regulates Dorsoventral Patterning by Antagonizing Wnt/β-catenin Activity in Zebrafish

(2012) Qiang Feng et al.   PLoS One

Chromatin and transcriptional signatures for Nodal signaling during endoderm formation in hESCs

(2011) Si Wan Kim et al.   DEVELOPMENTAL BIOLOGY

Differential regulation of epiboly initiation and progression by zebrafish Eomesodermin A

(2011) Susan Du et al.   DEVELOPMENTAL BIOLOGY

Pluripotency factors regulate definitive endoderm specification through eomesodermin

(2011) A. K. K. Teo et al.   GENES & DEVELOPMENT

HEB and E2A function as SMAD/FOXH1 cofactors

(2011) S.-J. Yoon et al.   GENES & DEVELOPMENT

Global Identification of SMAD2 Target Genes Reveals a Role for Multiple Co-regulatory Factors in Zebrafish Early Gastrulas

(2011) Zhaoting Liu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The T-box transcription factor Eomesodermin acts upstream of Mesp1 to specify cardiac mesoderm during mouse gastrulation

(2011) Ita Costello et al.   NATURE CELL BIOLOGY

Nodal-Dependent Mesendoderm Specification Requires the Combinatorial Activities of FoxH1 and Eomesodermin

(2011) Christopher E. Slagle et al.   PLoS Genetics

Graded Nodal/Activin Signaling Titrates Conversion of Quantitative Phospho-Smad2 Levels into Qualitative Embryonic Stem Cell Fate Decisions

(2011) Kian Leong Lee et al.   PLoS Genetics

Manipulation of FASTQ data with Galaxy

(2010) D. Blankenberg et al.   BIOINFORMATICS

The tbx/bHLH transcription factor mga regulates gata4 and organogenesis

(2010) Amir Rikin et al.   DEVELOPMENTAL DYNAMICS

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

A gene regulatory network directed by zebrafish No tail accounts for its roles in mesoderm formation

(2009) R. H. Morley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nodal Morphogens

(2009) A. F. Schier   Cold Spring Harbor Perspectives in Biology

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Pivotal roles for eomesodermin during axis formation, epithelium-to-mesenchyme transition and endoderm specification in the mouse

(2008) S. J. Arnold et al.   DEVELOPMENT

Genome-Wide Identification of Smad/Foxh1 Targets Reveals a Role for Foxh1 in Retinoic Acid Regulation and Forebrain Development

(2008) Cristoforo Silvestri et al.   DEVELOPMENTAL CELL

Prdm1- and Sox6-mediated transcriptional repression specifies muscle fibre type in the zebrafish embryo

(2008) Jonas von Hofsten et al.   EMBO REPORTS

The T-box transcription factor Eomes/Tbr2 regulates neurogenesis in the cortical subventricular zone

(2008) S. J. Arnold et al.   GENES & DEVELOPMENT

Eomesodermin Requires Transforming Growth Factor-β/Activin Signaling and Binds Smad2 to Activate Mesodermal Genes

(2008) Paola Picozzi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY