The landscape of chromatin accessibility in skeletal muscle during embryonic development in pigs

CASZ1 induces skeletal muscle and rhabdomyosarcoma differentiation through a feed-forward loop with MYOD and MYOG

(2020) Zhihui Liu et al.   Nature Communications

Dynamics of the Transcriptome and Accessible Chromatin Landscapes During Early Goose Ovarian Development

(2020) Shenqiang Hu et al.   Frontiers in Cell and Developmental Biology

A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues

(2020) Michelle M. Halstead et al.   BMC GENOMICS

Fine-mapping cis-regulatory variants in diverse human populations

(2019) Ashley Tehranchi et al.   eLife

Combined analysis of dissimilar promoter accessibility and gene expression profiles identifies tissue-specific genes and actively repressed networks

(2019) Rebekah R. Starks et al.   Epigenetics & Chromatin

Multi-species annotation of transcriptome and chromatin structure in domesticated animals

(2019) Sylvain Foissac et al.   BMC BIOLOGY

Ectonucleotide pyrophosphatase 2 (ENPP2) plays a crucial role in myogenic differentiation through the regulation by WNT/β-Catenin signaling

(2019) Jay Prakash Sah et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

CTCF inhibits endoplasmic reticulum stress and apoptosis in cardiomyocytes by upregulating RYR2 via inhibiting S100A1

(2019) Zhu Zeng et al.   LIFE SCIENCES

Identification of chromatin-accessible domains in non-alcoholic steatohepatitis-derived hepatocellular carcinoma

(2018) Mekonnen L. Dechassa et al.   MOLECULAR CARCINOGENESIS

ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration

(2018) Jie Wang et al.   Nature Communications

Loss of MyoD and Myf5 in Skeletal Muscle Stem Cells Results in Altered Myogenic Programming and Failed Regeneration

(2018) Masakazu Yamamoto et al.   Stem Cell Reports

The interaction landscape between transcription factors and the nucleosome

(2018) Fangjie Zhu et al.   NATURE

High-throughput chromatin accessibility profiling at single-cell resolution

(2018) Anja Mezger et al.   Nature Communications

Age Alters Chromatin Structure and Expression of SUMO Proteins under Stress Conditions in Human Adipose-Derived Stem Cells

(2018) Xiaoyin Shan et al.   Scientific Reports

Chromatin accessibility landscape of articular knee cartilage reveals aberrant enhancer regulation in osteoarthritis

(2018) Ye Liu et al.   Scientific Reports

Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons

(2018) Sarah A. McClymont et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A rapid and robust method for single cell chromatin accessibility profiling

(2018) Xi Chen et al.   Nature Communications

Mef2 and the skeletal muscle differentiation program

(2017) Michael V. Taylor et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

DNA methylation and chromatin accessibility profiling of mouse and human fetal germ cells

(2016) Hongshan Guo et al.   CELL RESEARCH

Mechanisms of DNA-binding specificity and functional gene regulation by transcription factors

(2016) Ngaio C Smith et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Identification of Regulatory DNA Elements Using Genome-wide Mapping of DNase I Hypersensitive Sites during Tomato Fruit Development

(2016) Zhengkun Qiu et al.   Molecular Plant

The landscape of accessible chromatin in mammalian preimplantation embryos

(2016) Jingyi Wu et al.   NATURE

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes

(2016) Amanda M. Ackermann et al.   Molecular Metabolism

Temporal activation of XRCC1-mediated DNA repair is essential for muscle differentiation

(2016) Mohammad H Al-Khalaf et al.   Cell Discovery

InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams

(2015) Henry Heberle et al.   BMC BIOINFORMATICS

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

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

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Chromatin accessibility: a window into the genome

(2014) Maria Tsompana et al.   Epigenetics & Chromatin

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

OTX2 Represses Myogenic and Neuronal Differentiation in Medulloblastoma Cells

(2012) R.-Y. Bai et al.   CANCER RESEARCH

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Comprehensive Identification and Annotation of Cell Type-Specific and Ubiquitous CTCF-Binding Sites in the Human Genome

(2012) Hebing Chen et al.   PLoS One

Building Muscle: Molecular Regulation of Myogenesis

(2012) C. F. Bentzinger et al.   Cold Spring Harbor Perspectives in Biology

Skeletal muscle proteomics in livestock production

(2011) B. Picard et al.   Briefings in Functional Genomics

The pig: a model for human infectious diseases

(2011) François Meurens et al.   TRENDS IN MICROBIOLOGY

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

Epigenetic control of skeletal muscle fibre type

(2010) K. Baar   Acta Physiologica

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

(2010) Andrew Adey et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The myocardin-related transcription factor, MASTR, cooperates with MyoD to activate skeletal muscle gene expression

(2008) S. M. Meadows et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

Consequences of pig domestication for skeletal muscle growth and cellularity

(2007) C. Rehfeldt et al.   Livestock Science