Computational prediction and experimental validation of novel Hedgehog-responsive enhancers linked to genes of the Hedgehog pathway

Roles for Hedgehog signaling in adult organ homeostasis and repair

(2014) R. Petrova et al.   DEVELOPMENT

Scube2 enhances proteolytic Shh processing from the surface of Shh-producing cells

(2014) P. Jakobs et al.   JOURNAL OF CELL SCIENCE

Absence of a simple code: how transcription factors read the genome

(2014) Matthew Slattery et al.   TRENDS IN BIOCHEMICAL SCIENCES

Essential role for ligand-dependent feedback antagonism of vertebrate hedgehog signaling by PTCH1, PTCH2 and HHIP1 during neural patterning

(2013) A. M. Holtz et al.   DEVELOPMENT

The mechanisms of Hedgehog signalling and its roles in development and disease

(2013) James Briscoe et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets

(2013) Christopher Fletez-Brant et al.   NUCLEIC ACIDS RESEARCH

Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning

(2012) K. A. Peterson et al.   GENES & DEVELOPMENT

Scube/You activity mediates release of dually lipid-modified Hedgehog signal in soluble form

(2012) A. Creanga et al.   GENES & DEVELOPMENT

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Inferring direct DNA binding from ChIP-seq

(2012) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

Boc and Gas1 Each Form Distinct Shh Receptor Complexes with Ptch1 and Are Required for Shh-Mediated Cell Proliferation

(2011) Luisa Izzi et al.   DEVELOPMENTAL CELL

Overlapping Roles and Collective Requirement for the Coreceptors GAS1, CDO, and BOC in SHH Pathway Function

(2011) Benjamin L. Allen et al.   DEVELOPMENTAL CELL

Discriminative prediction of mammalian enhancers from DNA sequence

(2011) D. Lee et al.   GENOME RESEARCH

A High-Resolution Anatomical Atlas of the Transcriptome in the Mouse Embryo

(2011) Graciana Diez-Roux et al.   PLOS BIOLOGY

Non-consensus GLI binding sites in Hedgehog target gene regulation

(2010) Martina Winklmayr et al.   BMC MOLECULAR BIOLOGY

Interactions between Hedgehog proteins and their binding partners come into view

(2010) P. A. Beachy et al.   GENES & DEVELOPMENT

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

The primary cilium: a signalling centre during vertebrate development

(2010) Sarah C. Goetz et al.   NATURE REVIEWS GENETICS

Hedgehog pathway-regulated gene networks in cerebellum development and tumorigenesis

(2010) E. Y. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mouse Kif7/Costal2 is a cilia-associated protein that regulates Sonic hedgehog signaling

(2009) K. F. Liem et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gli2 trafficking links Hedgehog-dependent activation of Smoothened in the primary cilium to transcriptional activation in the nucleus

(2009) J. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hedgehog Signaling in Development and Cancer

(2008) Jin Jiang et al.   DEVELOPMENTAL CELL

Building it up and taking it down: The regulation of vertebrate ciliogenesis

(2008) Nicole Santos et al.   DEVELOPMENTAL DYNAMICS

A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog-mediated patterning of the mammalian limb

(2008) S. A. Vokes et al.   GENES & DEVELOPMENT

Hedgehog: functions and mechanisms

(2008) M. Varjosalo et al.   GENES & DEVELOPMENT