Genome-wide strategies identify downstream target genes of chick connective tissue-associated transcription factors

Floor-plate-derived netrin-1 is dispensable for commissural axon guidance

(2017) Chloé Dominici et al.   NATURE

Odd skipped-related 1 identifies a population of embryonic fibro-adipogenic progenitors regulating myogenesis during limb development

(2017) Pedro Vallecillo-García et al.   Nature Communications

A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken model

(2017) Mickael Orgeur et al.   Biology Open

The chemokines CXCL12 and CXCL14 differentially regulate connective tissue markers during limb development

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TGF-β/SMAD Pathway and Its Regulation in Hepatic Fibrosis

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Notch in fibrosis and as a target of anti-fibrotic therapy

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Architectural and Functional Commonalities between Enhancers and Promoters

(2015) Tae-Kyung Kim et al.   CELL

Molecular regulation of tendon cell fate during development

(2015) Alice H. Huang et al.   JOURNAL OF ORTHOPAEDIC RESEARCH

The selection and function of cell type-specific enhancers

(2015) Sven Heinz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Translational regulation of inhibin βA by TGFβ via the RNA-binding protein hnRNP E1 enhances the invasiveness of epithelial-to-mesenchymal transitioned cells

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Efficient Test and Visualization of Multi-Set Intersections

(2015) Minghui Wang et al.   Scientific Reports

Tendon development and diseases

(2015) Ludovic Gaut et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Distinct contextual roles for Notch signalling in skeletal muscle stem cells

(2014) Philippos Mourikis et al.   BMC DEVELOPMENTAL BIOLOGY

Transcriptomic analysis of mouse limb tendon cells during development

(2014) E. Havis et al.   DEVELOPMENT

ADAMTS-18: A metalloproteinase with multiple functions

(2014) Jianlu Wei   Frontiers in Bioscience-Landmark

Egr1 Protein Acts Downstream of Estrogen-Leukemia Inhibitory Factor (LIF)-STAT3 Pathway and Plays a Role during Implantation through Targeting Wnt4

(2014) Xiao-Huan Liang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Physical influences of the extracellular environment on cell migration

(2014) Guillaume Charras et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Extracellular matrix assembly: a multiscale deconstruction

(2014) Janna K. Mouw et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Defining functional DNA elements in the human genome

(2014) M. Kellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tendon proper- and peritenon-derived progenitor cells have unique tenogenic properties

(2014) Michael J Mienaltowski et al.   Stem Cell Research & Therapy

Mechanobiology and Developmental Control

(2013) Tadanori Mammoto et al.   Annual Review of Cell and Developmental Biology

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Molecular basis of organ fibrosis: Potential therapeutic approaches

(2013) Asish K Ghosh et al.   EXPERIMENTAL BIOLOGY AND MEDICINE

Distinct global shifts in genomic binding profiles of limb malformation-associated HOXD13 mutations

(2013) D. M. Ibrahim et al.   GENOME RESEARCH

Transcription factor EGR1 directs tendon differentiation and promotes tendon repair

(2013) Marie-Justine Guerquin et al.   JOURNAL OF CLINICAL INVESTIGATION

Wnt4/ -Catenin Signaling in Medullary Kidney Myofibroblasts

(2013) D. P. DiRocco et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Topology of mammalian developmental enhancers and their regulatory landscapes

(2013) Wouter de Laat et al.   NATURE

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

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

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

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Cell Fate Potential of Human Pluripotent Stem Cells Is Encoded by Histone Modifications

(2011) Seok-Ho Hong et al.   Cell Stem Cell

The extracellular matrix dimension of skeletal muscle development

(2011) Sólveig Thorsteinsdóttir et al.   DEVELOPMENTAL BIOLOGY

The zinc finger transcription factors Osr1 and Osr2 control synovial joint formation

(2011) Yang Gao et al.   DEVELOPMENTAL BIOLOGY

ERK5 Regulates Muscle Cell Fusion through Klf Transcription Factors

(2011) Kazunori Sunadome et al.   DEVELOPMENTAL CELL

“Soft” tissue patterning: Muscles and tendons of the limb take their form

(2011) Peleg Hasson   DEVELOPMENTAL DYNAMICS

Transcriptional mechanisms regulating skeletal muscle differentiation, growth and homeostasis

(2011) Thomas Braun et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Odd-Skipped Related Genes Regulate Differentiation of Embryonic Limb Mesenchyme and Bone Marrow Mesenchymal Stromal Cells

(2011) Sigmar Stricker et al.   STEM CELLS AND DEVELOPMENT

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Wnt/frizzled signalling modulates the migration and differentiation of immortalized cardiac fibroblasts

(2010) Hilde Laeremans et al.   CARDIOVASCULAR RESEARCH

Connective tissue fibroblasts and Tcf4 regulate myogenesis

(2010) S. J. Mathew et al.   DEVELOPMENT

Tbx4 and Tbx5 Acting in Connective Tissue Are Required for Limb Muscle and Tendon Patterning

(2010) Peleg Hasson et al.   DEVELOPMENTAL CELL

Bmp Signaling at the Tips of Skeletal Muscles Regulates the Number of Fetal Muscle Progenitors and Satellite Cells during Development

(2010) Hui Wang et al.   DEVELOPMENTAL CELL

Embryonic expression of the chicken krüppel-like (KLF) transcription factor gene family

(2010) Parker B. Antin et al.   DEVELOPMENTAL DYNAMICS

EGR1 and EGR2 Involvement in Vertebrate Tendon Differentiation

(2010) Véronique Lejard et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Netrin 1 provides a chemoattractive cue for the ventral migration of GnRH neurons in the chick forebrain

(2010) Shizuko Murakami et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Mutations of the FHL1 Gene Cause Emery-Dreifuss Muscular Dystrophy

(2009) Lucie Gueneau et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

The extracellular matrix in development and morphogenesis: A dynamic view

(2009) Tania Rozario et al.   DEVELOPMENTAL BIOLOGY

A Disintegrin-like and Metalloprotease (Reprolysin-type) with Thrombospondin Type 1 Motif (ADAMTS) Superfamily: Functions and Mechanisms

(2009) Suneel S. Apte   JOURNAL OF BIOLOGICAL CHEMISTRY

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium

(2009) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

WNT11 acts as a directional cue to organize the elongation of early muscle fibres

(2008) Jérôme Gros et al.   NATURE

A core Klf circuitry regulates self-renewal of embryonic stem cells

(2008) Jianming Jiang et al.   NATURE CELL BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY