Pioneer and repressive functions of p63 during zebrafish embryonic ectoderm specification

TFAP2C- and p63-Dependent Networks Sequentially Rearrange Chromatin Landscapes to Drive Human Epidermal Lineage Commitment

(2019) Lingjie Li et al.   Cell Stem Cell

Pioneer transcription factors shape the epigenetic landscape

(2018) Alexandre Mayran et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

(2018) Jeffrey A. Farrell et al.   SCIENCE

Single Cell and Open Chromatin Analysis Reveals Molecular Origin of Epidermal Cells of the Skin

(2018) Xiying Fan et al.   DEVELOPMENTAL CELL

Co-activation of super-enhancer-driven CCAT1 by TP63 and SOX2 promotes squamous cancer progression

(2018) Yuan Jiang et al.   Nature Communications

Amphioxus functional genomics and the origins of vertebrate gene regulation

(2018) Ferdinand Marlétaz et al.   NATURE

Functional Equivalence of the SOX2 and SOX3 Transcription Factors in the Developing Mouse Brain and Testes

(2017) Fatwa Adikusuma et al.   GENETICS

Functional Equivalence of the SOX2 and SOX3 Transcription Factors in the Developing Mouse Brain and Testes

(2017) Fatwa Adikusuma et al.   GENETICS

Dnmt3a and Dnmt3b Associate with Enhancers to Regulate Human Epidermal Stem Cell Homeostasis

(2016) Lorenzo Rinaldi et al.   Cell Stem Cell

Pioneer transcription factors, chromatin dynamics, and cell fate control

(2016) Kenneth S Zaret et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Active DNA demethylation at enhancers during the vertebrate phylotypic period

(2016) Ozren Bogdanović et al.   NATURE GENETICS

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Cbx4 maintains the epithelial lineage identity and cell proliferation in the developing stratified epithelium

(2015) Andrei N. Mardaryev et al.   JOURNAL OF CELL BIOLOGY

CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo

(2015) Miguel A Moreno-Mateos et al.   NATURE METHODS

ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors

(2015) Christian Schmidl et al.   NATURE METHODS

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Role of chromatin and transcriptional co-regulators in mediating p63-genome interactions in keratinocytes

(2014) Isha Sethi et al.   BMC GENOMICS

p63 and Brg1 control developmentally regulated higher-order chromatin remodelling at the epidermal differentiation complex locus in epidermal progenitor cells

(2014) A. N. Mardaryev et al.   DEVELOPMENT

TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity

(2014) Morgan A. Sammons et al.   GENOME RESEARCH

SOX2 and p63 colocalize at genetic loci in squamous cell carcinomas

(2014) Hideo Watanabe et al.   JOURNAL OF CLINICAL INVESTIGATION

Deep conservation of wrist and digit enhancers in fish

(2014) Andrew R. Gehrke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis

(2012) O. Bogdanovic et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Yap1 Acts Downstream of α-Catenin to Control Epidermal Proliferation

(2011) Karin Schlegelmilch et al.   CELL

ΔNp63is regulated by BMP4 signaling and is required for early epidermal development inXenopus

(2011) Celeste Tríbulo et al.   DEVELOPMENTAL DYNAMICS

p63 regulatesSatb1to control tissue-specific chromatin remodeling during development of the epidermis

(2011) Michael Y. Fessing et al.   JOURNAL OF CELL BIOLOGY

Yes-associated protein (YAP) transcriptional coactivator functions in balancing growth and differentiation in skin

(2011) H. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pioneer factors: directing transcriptional regulators within the chromatin environment

(2011) Luca Magnani et al.   TRENDS IN GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

ΔNp63 is an ectodermal gatekeeper of epidermal morphogenesis

(2010) R Shalom-Feuerstein et al.   CELL DEATH AND DIFFERENTIATION

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

seqMINER: an integrated ChIP-seq data interpretation platform

(2010) Tao Ye et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

p63 Suppresses Non-epidermal Lineage Markers in a Bone Morphogenetic Protein-dependent Manner via Repression of Smad7

(2009) Laura De Rosa et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2009) Da Wei Huang et al.   Nature Protocols

Sox3 regulates both neural fate and differentiation in the zebrafish ectoderm

(2008) Chris T. Dee et al.   DEVELOPMENTAL BIOLOGY

Xenopus Sox3 activates sox2 and geminin and indirectly represses Xvent2 expression to induce neural progenitor formation at the expense of non-neural ectodermal derivatives

(2008) Crystal D. Rogers et al.   MECHANISMS OF DEVELOPMENT

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY