CTCF-dependent co-localization of canonical Smad signaling factors at architectural protein binding sites inD. melanogaster

Functional and topological characteristics of mammalian regulatory domains

(2014) O. Symmons et al.   GENOME RESEARCH

Strategies for exploring TGF-β signaling in Drosophila

(2014) Aidan J. Peterson et al.   METHODS

Transforming Growth Factor β/Activin Signaling Functions as a Sugar-Sensing Feedback Loop to Regulate Digestive Enzyme Expression

(2014) Wen-bin Alfred Chng et al.   Cell Reports

Insulator function and topological domain border strength scale with architectural protein occupancy

(2014) Kevin Van Bortle et al.   GENOME BIOLOGY

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

Activin receptor inhibition by Smad2 regulates Drosophila wing disc patterning through BMP-response elements

(2013) A. J. Peterson et al.   DEVELOPMENT

Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments

(2013) V. C. Seitan et al.   GENOME RESEARCH

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

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

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains

(2012) K. Van Bortle et al.   GENOME RESEARCH

Transforming Growth Factor   Inhibits Bone Morphogenetic Protein-Induced Transcription through Novel Phosphorylated Smad1/5-Smad3 Complexes

(2012) E. Gronroos et al.   MOLECULAR AND CELLULAR BIOLOGY

Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains

(2012) Chunhui Hou et al.   MOLECULAR CELL

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

R-Smad Competition Controls Activin Receptor Output in Drosophila

(2012) Aidan J. Peterson et al.   PLoS One

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

(2012) Zhen Shao et al.   GENOME BIOLOGY

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

Master Transcription Factors Determine Cell-Type-Specific Responses to TGF-β Signaling

(2011) Alan C. Mullen et al.   CELL

A Poised Chromatin Platform for TGF-β Access to Master Regulators

(2011) Qiaoran Xi et al.   CELL

Lineage Regulators Direct BMP and Wnt Pathways to Cell-Specific Programs during Differentiation and Regeneration

(2011) Eirini Trompouki et al.   CELL

Neuroendocrine regulation of Drosophila metamorphosis requires TGF /Activin signaling

(2011) Y. Y. Gibbens et al.   DEVELOPMENT

Regulation of Chromatin Organization and Inducible Gene Expression by a Drosophila Insulator

(2011) Ashley M. Wood et al.   MOLECULAR CELL

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

Glia instruct developmental neuronal remodeling through TGF-β signaling

(2011) Takeshi Awasaki et al.   NATURE NEUROSCIENCE

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Transforming Growth Factor β Promotes Complexes between Smad Proteins and the CCCTC-binding Factor on theH19Imprinting Control Region Chromatin

(2010) Rosita Bergström et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

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

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

Three subclasses of a Drosophila insulator show distinct and cell type-specific genomic distributions

(2009) A. M. Bushey et al.   GENES & DEVELOPMENT

The Drosophila Activin-like ligand Dawdle signals preferentially through one isoform of the Type-I receptor Baboon

(2009) Philip A. Jensen et al.   MECHANISMS OF DEVELOPMENT

A conserved activation element in BMP signaling during Drosophila development

(2009) Alexander Weiss et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

(2009) Stewart MacArthur et al.   GENOME BIOLOGY

Multiple modular promoter elements drive graded brinker expression in response to the Dpp morphogen gradient

(2008) L.-C. Yao et al.   DEVELOPMENT

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

How the Smads regulate transcription

(2007) Sarah Ross et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY