Transcriptional states and chromatin accessibility during bovine myoblasts proliferation and myogenic differentiation

Integration of selection signatures and multi-trait GWAS reveals polygenic genetic architecture of carcass traits in beef cattle

(2021) Qunhao Niu et al.   GENOMICS

KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis

(2021) Dechao Bu et al.   NUCLEIC ACIDS RESEARCH

Integrated Small RNA Sequencing, Transcriptome and GWAS Data Reveal microRNA Regulation in Response to Milk Protein Traits in Chinese Holstein Cattle

(2021) Wentao Cai et al.   Frontiers in Genetics

Comparative Enhancer Map of Cattle Muscle Genome Annotated by ATAC-Seq

(2021) Xiukai Cao et al.   Frontiers in Veterinary Science

Hox genes maintain critical roles in the adult skeleton

(2020) Jane Y. Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification and validation of a novel candidate gene regulating net meat weight in Simmental beef cattle based on imputed next‐generation sequencing

(2020) Farhad Bordbar et al.   CELL PROLIFERATION

LncRNAs are regulated by chromatin states and affect the skeletal muscle cell differentiation

(2020) Xiaolong Qi et al.   CELL PROLIFERATION

Farm animals for studying muscle development and metabolism: dual purposes for animal production and human health

(2019) Liang Zhao et al.   Animal Frontiers

Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits

(2019) Ruidong Xiang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic enhancers control skeletal muscle identity and reprogramming

(2019) Krithika Ramachandran et al.   PLOS BIOLOGY

MLL1 promotes myogenesis by epigenetically regulating Myf5

(2019) Shufang Cai et al.   CELL PROLIFERATION

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

(2018) Annalisa Buniello et al.   NUCLEIC ACIDS RESEARCH

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

Function of the myogenic regulatory factors Myf5, MyoD, Myogenin and MRF4 in skeletal muscle, satellite cells and regenerative myogenesis

(2017) Peter S. Zammit   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

The myogenic regulatory factors, determinants of muscle development, cell identity and regeneration

(2017) J. Manuel Hernández-Hernández et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

bta-miR-23a involves in adipogenesis of progenitor cells derived from fetal bovine skeletal muscle

(2017) Long Guan 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

Gene activation by metazoan enhancers: Diverse mechanisms stimulate distinct steps of transcription

(2016) Robert A. Beagrie et al.   BIOESSAYS

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

The landscape of accessible chromatin in mammalian preimplantation embryos

(2016) Jingyi Wu et al.   NATURE

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

(2016) M Ryan Corces et al.   NATURE GENETICS

Data-driven hypothesis weighting increases detection power in genome-scale multiple testing

(2016) Nikolaos Ignatiadis et al.   NATURE METHODS

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

FGF13regulates proliferation and differentiation of skeletal muscle by down-regulatingSpry1

(2015) Hongzhao Lu et al.   CELL PROLIFERATION

Mechanisms of myoblast fusion during muscle development

(2015) Ji Hoon Kim et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The many faces of cell adhesion during Drosophila muscle development

(2015) Aidan P. Maartens et al.   DEVELOPMENTAL BIOLOGY

The BioMart community portal: an innovative alternative to large, centralized data repositories

(2015) Damian Smedley et al.   NUCLEIC ACIDS RESEARCH

Cellular Cholesterol Regulates Ubiquitination and Degradation of the Cholesterol Export Proteins ABCA1 and ABCG1

(2014) Victar Hsieh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Advantages and pitfalls in the application of mixed-model association methods

(2014) Jian Yang et al.   NATURE GENETICS

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

ATP-binding cassette transporters and cholesterol translocation

(2013) Ge Li et al.   IUBMB LIFE

Adhesion Proteins - An Impact on Skeletal Myoblast Differentiation

(2013) Marta Przewoźniak et al.   PLoS One

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Metazoan promoters: emerging characteristics and insights into transcriptional regulation

(2012) Boris Lenhard et al.   NATURE REVIEWS GENETICS

Functional and Mechanistic Diversity of Distal Transcription Enhancers

(2011) Michael Bulger et al.   CELL

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence

(2011) Patricia J. Wittkopp et al.   NATURE REVIEWS GENETICS

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Jun and JunD-dependent functions in cell proliferation and stress response

(2010) A Meixner et al.   CELL DEATH AND DIFFERENTIATION

Transcriptional Enhancers in Animal Development and Evolution

(2010) Mike Levine   CURRENT BIOLOGY

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

Role of HDL, ABCA1, and ABCG1 Transporters in Cholesterol Efflux and Immune Responses

(2009) Laurent Yvan-Charvet et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

Finding distal regulatory elements in the human genome

(2009) Nathaniel D Heintzman et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

(2009) Da Wei Huang et al.   Nature Protocols

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH