Rfx2 Stabilizes Foxj1 Binding at Chromatin Loops to Enable Multiciliated Cell Gene Expression

Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis

(2016) Luis Luna-Zurita et al.   CELL

3D Chromosome Regulatory Landscape of Human Pluripotent Cells

(2016) Xiong Ji et al.   Cell Stem Cell

Genome evolution in the allotetraploid frog Xenopus laevis

(2016) Adam M. Session et al.   NATURE

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

(2015) Zhonghui Tang et al.   CELL

Tree of Life Reveals Clock-Like Speciation and Diversification

(2015) S. Blair Hedges et al.   MOLECULAR BIOLOGY AND EVOLUTION

Human Promoters Are Intrinsically Directional

(2015) Sascha H.C. Duttke et al.   MOLECULAR CELL

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

The selection and function of cell type-specific enhancers

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

A new transcription factor for mitosis: inSchizosaccharomyces pombe, the RFX transcription factor Sak1 works with forkhead factors to regulate mitotic expression

(2015) Angad Garg et al.   NUCLEIC ACIDS RESEARCH

RFX transcription factors are essential for hearing in mice

(2015) Ran Elkon et al.   Nature Communications

Inferring regulatory element landscapes and transcription factor networks from cancer methylomes

(2015) Lijing Yao et al.   GENOME BIOLOGY

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes

(2014) Jill M. Dowen et al.   CELL

Multiciliated Cells

(2014) Eric R. Brooks et al.   CURRENT BIOLOGY

Switching on cilia: transcriptional networks regulating ciliogenesis

(2014) S. P. Choksi et al.   DEVELOPMENT

Systematic discovery of novel ciliary genes through functional genomics in the zebrafish

(2014) S. P. Choksi et al.   DEVELOPMENT

Evolutionary conservation of the eumetazoan gene regulatory landscape

(2014) M. Schwaiger et al.   GENOME RESEARCH

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Myb promotes centriole amplification and later steps of the multiciliogenesis program

(2013) F. E. Tan et al.   DEVELOPMENT

Cohesin-mediated interactions organize chromosomal domain architecture

(2013) Sevil Sofueva et al.   EMBO JOURNAL

Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types

(2013) J. Ernst et al.   GENOME RESEARCH

Topology of mammalian developmental enhancers and their regulatory landscapes

(2013) Wouter de Laat et al.   NATURE

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

(2013) Simon Anders et al.   Nature Protocols

Transcriptional Program of Ciliated Epithelial Cells Reveals New Cilium and Centrosome Components and Links to Human Disease

(2013) Ramona A. Hoh et al.   PLoS One

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

(2013) J. Zuin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RFX3 Modulation of FOXJ1 regulation of cilia genes in the human airway epithelium

(2013) Lukas Didon et al.   RESPIRATORY RESEARCH

A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs

(2013) G. Andrey et al.   SCIENCE

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

Regulation of the Boundaries of Accessible Chromatin

(2013) Xiaoran Chai et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

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

Forkhead Transcription Factor Fd3F Cooperates with Rfx to Regulate a Gene Expression Program for Mechanosensory Cilia Specialization

(2012) Fay G. Newton et al.   DEVELOPMENTAL CELL

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Multicilin promotes centriole assembly and ciliogenesis during multiciliate cell differentiation

(2012) J. L. Stubbs et al.   NATURE CELL BIOLOGY

Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate

(2012) Yin C Lin et al.   NATURE IMMUNOLOGY

Streaming fragment assignment for real-time analysis of sequencing experiments

(2012) Adam Roberts et al.   NATURE METHODS

Evolutionarily Ancient Association of the FoxJ1 Transcription Factor with the Motile Ciliogenic Program

(2012) Shubha Vij et al.   PLoS Genetics

Specification of ion transport cells in the Xenopus larval skin

(2011) I. K. Quigley et al.   DEVELOPMENT

RFX2 is broadly required for ciliogenesis during vertebrate development

(2011) Mei-I Chung et al.   DEVELOPMENTAL BIOLOGY

Nucleotide composition-linked divergence of vertebrate core promoter architecture

(2011) S. J. van Heeringen et al.   GENOME RESEARCH

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

AnimalTFDB: a comprehensive animal transcription factor database

(2011) H.-M. Zhang et al.   NUCLEIC ACIDS RESEARCH

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

Gene expression studies in cells from primary ciliary dyskinesia patients identify 208 potential ciliary genes

(2010) Maciej Geremek et al.   HUMAN GENETICS

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

Regulatory Factor X (RFX)-mediated transcriptional rewiring of ciliary genes in animals

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Identification and characterization of novel human tissue-specific RFX transcription factors

(2008) Syed Aftab et al.   BMC EVOLUTIONARY BIOLOGY

FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription

(2008) Mathieu Lupien et al.   CELL

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

The forkhead protein Foxj1 specifies node-like cilia in Xenopus and zebrafish embryos

(2008) Jennifer L Stubbs et al.   NATURE GENETICS