Time-dependent Pax3-mediated chromatin remodeling and cooperation with Six4 and Tead2 specify the skeletal myogenic lineage in developing mesoderm

Pioneer factor Pax7 deploys a stable enhancer repertoire for specification of cell fate

(2018) Alexandre Mayran et al.   NATURE GENETICS

Genetic determinants and epigenetic effects of pioneer-factor occupancy

(2018) Julie Donaghey et al.   NATURE GENETICS

Direct Reprogramming of Mouse Fibroblasts into Functional Skeletal Muscle Progenitors

(2018) Ori Bar-Nur et al.   Stem Cell Reports

Pax7 remodels the chromatin landscape in skeletal muscle stem cells

(2017) Karin C. Lilja et al.   PLoS One

Myogenic progenitor specification from pluripotent stem cells

(2017) Alessandro Magli et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Direct reprogramming of fibroblasts into skeletal muscle progenitor cells by transcription factors enriched in undifferentiated subpopulation of satellite cells

(2017) Naoki Ito et al.   Scientific Reports

TEAD transcription factors are required for normal primary myoblast differentiation in vitro and muscle regeneration in vivo

(2017) Shilpy Joshi et al.   PLoS Genetics

Pioneer transcription factors, chromatin dynamics, and cell fate control

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

Mitotic binding of Esrrb marks key regulatory regions of the pluripotency network

(2016) Nicola Festuccia et al.   NATURE CELL BIOLOGY

MyoD reprogramming requires Six1 and Six4 homeoproteins: genome-widecis-regulatory module analysis

(2016) Marc Santolini et al.   NUCLEIC ACIDS RESEARCH

DUX4 recruits p300/CBP through its C-terminus and induces global H3K27 acetylation changes

(2016) Si Ho Choi et al.   NUCLEIC ACIDS RESEARCH

Epigenetic balance of gene expression by Polycomb and COMPASS families

(2016) Andrea Piunti et al.   SCIENCE

A dynamic mode of mitotic bookmarking by transcription factors

(2016) Sheila S Teves et al.   eLife

Development of Bipotent Cardiac/Skeletal Myogenic Progenitors from MESP1+ Mesoderm

(2016) Sunny Sun-Kin Chan et al.   Stem Cell Reports

Tbx6, Mesp-b and Ripply1 regulate the onset of skeletal myogenesis in zebrafish

(2015) S. E. Windner et al.   DEVELOPMENT

Genome-wide association between Six4, MyoD, and the histone demethylase Utx during myogenesis

(2015) Imane Chakroun et al.   FASEB JOURNAL

A cost-effective RNA sequencing protocol for large-scale gene expression studies

(2015) Zhonggang Hou et al.   Scientific Reports

Runx1 Transcription Factor Is Required for Myoblasts Proliferation during Muscle Regeneration

(2015) Kfir Baruch Umansky et al.   PLoS Genetics

Fine-tuning the onset of myogenesis by homeobox proteins that interact with the Myf5 limb enhancer

(2015) P. Daubas et al.   Biology Open

Distinct contextual roles for Notch signalling in skeletal muscle stem cells

(2014) Philippos Mourikis et al.   BMC DEVELOPMENTAL BIOLOGY

Looping Back to Leap Forward: Transcription Enters a New Era

(2014) Michael Levine et al.   CELL

Mesogenin 1 is a master regulator of paraxial presomitic mesoderm differentiation

(2014) R. B. Chalamalasetty et al.   DEVELOPMENT

Gene Regulatory Networks and Transcriptional Mechanisms that Control Myogenesis

(2014) Margaret Buckingham et al.   DEVELOPMENTAL CELL

Genome-wide identification and characterization of functional neuronal activity–dependent enhancers

(2014) Athar N Malik et al.   NATURE NEUROSCIENCE

Pax3 and Tbx5 Specify Whether PDGFRα+ Cells Assume Skeletal or Cardiac Muscle Fate in Differentiating Embryonic Stem Cells

(2014) Alessandro Magli et al.   STEM CELLS

PAVIS: a tool for Peak Annotation and Visualization

(2013) Weichun Huang et al.   BIOINFORMATICS

Mesp1 Patterns Mesoderm into Cardiac, Hematopoietic, or Skeletal Myogenic Progenitors in a Context-Dependent Manner

(2013) Sunny Sun-Kin Chan et al.   Cell Stem Cell

Direct molecular regulation of the myogenic determination gene Myf5 by Pax3, with modulation by Six1/4 factors, is exemplified by the −111kb-Myf5 enhancer

(2013) Philippe Daubas et al.   DEVELOPMENTAL BIOLOGY

Modification of Enhancer Chromatin: What, How, and Why?

(2013) Eliezer Calo et al.   MOLECULAR CELL

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

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

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

Tissue-Specific Mitotic Bookmarking by Hematopoietic Transcription Factor GATA1

(2012) Stephan Kadauke et al.   CELL

Carm1 Regulates Pax7 Transcriptional Activity through MLL1/2 Recruitment during Asymmetric Satellite Stem Cell Divisions

(2012) Yoh-ichi Kawabe et al.   Cell Stem Cell

Human ES- and iPS-Derived Myogenic Progenitors Restore DYSTROPHIN and Improve Contractility upon Transplantation in Dystrophic Mice

(2012) Radbod Darabi et al.   Cell Stem Cell

Transcriptional Dominance of Pax7 in Adult Myogenesis Is Due to High-Affinity Recognition of Homeodomain Motifs

(2012) Vahab D. Soleimani et al.   DEVELOPMENTAL CELL

Colonization of the Satellite Cell Niche by Skeletal Muscle Progenitor Cells Depends on Notch Signals

(2012) Dominique Bröhl et al.   DEVELOPMENTAL CELL

The selector gene Pax7 dictates alternate pituitary cell fates through its pioneer action on chromatin remodeling

(2012) L. Budry et al.   GENES & DEVELOPMENT

Genome-wide identification of enhancers in skeletal muscle: the role of MyoD1

(2012) R. Blum et al.   GENES & DEVELOPMENT

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Picking ChIP-seq peak detectors for analyzing chromatin modification experiments

(2012) Mariann Micsinai et al.   NUCLEIC ACIDS RESEARCH

Functional Dissection of Pax3 in Paraxial Mesoderm Development and Myogenesis

(2012) Alessandro Magli et al.   STEM CELLS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Cooperative activity of noggin and gremlin 1 in axial skeleton development

(2011) D. A. Stafford et al.   DEVELOPMENT

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

The transcription factor Pax5 regulates its target genes by recruiting chromatin-modifying proteins in committed B cells

(2011) Shane McManus et al.   EMBO JOURNAL

Inducible Cassette Exchange: A Rapid and Efficient System Enabling Conditional Gene Expression in Embryonic Stem and Primary Cells

(2011) Michelina Iacovino et al.   STEM CELLS

Cistrome: an integrative platform for transcriptional regulation studies

(2011) Tao Liu et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Transcriptome analyses based on genetic screens for Pax3 myogenic targets in the mouse embryo

(2010) Mounia Lagha et al.   BMC GENOMICS

Neural crest migration requires the activity of the extracellular sulphatases XtSulf1 and XtSulf2

(2010) Emily C. Guiral et al.   DEVELOPMENTAL BIOLOGY

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

A molecular network for de novo generation of the apical surface and lumen

(2010) David M. Bryant et al.   NATURE CELL BIOLOGY

Cooperation between myogenic regulatory factors and SIX family transcription factors is important for myoblast differentiation

(2010) Yubing Liu et al.   NUCLEIC ACIDS RESEARCH

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

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

(2009) Da Wei Huang et al.   Nature Protocols

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Pax3 activation promotes the differentiation of mesenchymal stem cells toward the myogenic lineage

(2008) Eun Ji Gang et al.   EXPERIMENTAL CELL RESEARCH

Upstream stimulatory factors, USF1 and USF2 are differentially expressed during Xenopus embryonic development

(2008) Takahiko J. Fujimi et al.   GENE EXPRESSION PATTERNS

Pax3 regulation of FGF signaling affects the progression of embryonic progenitor cells into the myogenic program

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

A Cdo–Bnip-2–Cdc42 signaling pathway regulates p38α/β MAPK activity and myogenic differentiation

(2008) Jong-Sun Kang et al.   JOURNAL OF CELL BIOLOGY

Functional skeletal muscle regeneration from differentiating embryonic stem cells

(2008) Radbod Darabi et al.   NATURE MEDICINE

The genetics of vertebrate myogenesis

(2008) Robert J. Bryson-Richardson et al.   NATURE REVIEWS GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY