Transcriptional reprogramming of skeletal muscle stem cells by the niche environment

FOS licenses early events in stem cell activation driving skeletal muscle regeneration

(2021) Albert E. Almada et al.   Cell Reports

Preprocessing choices affect RNA velocity results for droplet scRNA-seq data

(2021) Charlotte Soneson et al.   PLoS Computational Biology

Macrophages provide a transient muscle stem cell niche via NAMPT secretion

(2021) Dhanushika Ratnayake et al.   NATURE

Human muscle stem cells are refractory to aging

(2021) James S. Novak et al.   AGING CELL

JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles

(2021) Jaime A Castro-Mondragon et al.   NUCLEIC ACIDS RESEARCH

Aging induces aberrant state transition kinetics in murine muscle stem cells

(2020) Jacob C. Kimmel et al.   DEVELOPMENT

Skeletal Muscle Extracellular Matrix – What Do We Know About Its Composition, Regulation, and Physiological Roles? A Narrative Review

(2020) Robert Csapo et al.   Frontiers in Physiology

Dissecting Murine Muscle Stem Cell Aging through Regeneration Using Integrative Genomic Analysis

(2020) Anna Shcherbina et al.   Cell Reports

ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation

(2020) Mette Bentsen et al.   Nature Communications

Aging Disrupts Muscle Stem Cell Function by Impairing Matricellular WISP1 Secretion from Fibro-Adipogenic Progenitors

(2019) Laura Lukjanenko et al.   Cell Stem Cell

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

Skewed macrophage polarization in aging skeletal muscle

(2019) Chang‐Yi Cui et al.   AGING CELL

Adipogenic progenitors keep muscle stem cells young

(2019) Sara Ancel et al.   Aging-US

hypeR: an R package for geneset enrichment workflows

(2019) Anthony Federico et al.   BIOINFORMATICS

Enhancer DNA methylation: implications for gene regulation

(2019) Allegra Angeloni et al.   Essays in Biochemistry

Fibro–Adipogenic Progenitors Cross-Talk in Skeletal Muscle: The Social Network

(2019) Beatrice Biferali et al.   Frontiers in Physiology

Muscle‐secreted granulocyte colony‐stimulating factor functions as metabolic niche factor ameliorating loss of muscle stem cells in aged mice

(2019) Hu Li et al.   EMBO JOURNAL

High-Resolution Genome-Wide Expression Analysis of Single Myofibers Using SMART-Seq

(2019) Darren M Blackburn et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Ageing affects DNA methylation drift and transcriptional cell-to-cell variability in mouse muscle stem cells

(2019) Irene Hernando-Herraez et al.   Nature Communications

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

GWAS4D: multidimensional analysis of context-specific regulatory variant for human complex diseases and traits

(2018) Dandan Huang et al.   NUCLEIC ACIDS RESEARCH

Implication of SPARC in the modulation of the extracellular matrix and mitochondrial function in muscle cells

(2018) Aicha Melouane et al.   PLoS One

Induction of muscle stem cell quiescence by the secreted niche factor Oncostatin M

(2018) Srinath C. Sampath et al.   Nature Communications

A general and flexible method for signal extraction from single-cell RNA-seq data

(2018) Davide Risso et al.   Nature Communications

Macrophage Polarization in Chronic Inflammatory Diseases: Killers or Builders?

(2018) Luca Parisi et al.   Journal of Immunology Research

OUP accepted manuscript

(2018)   AGE AND AGEING

Reciprocal signalling by Notch–Collagen V–CALCR retains muscle stem cells in their niche

(2018) Meryem B. Baghdadi et al.   NATURE

Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences

(2018) Anqi Zhu et al.   BIOINFORMATICS

Muscle Satellite Cell Cross-Talk with a Vascular Niche Maintains Quiescence via VEGF and Notch Signaling

(2018) Mayank Verma et al.   Cell Stem Cell

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Delta-Like 4 Activates Notch 3 to Regulate Self-Renewal in Skeletal Muscle Stem Cells

(2017) SiewHui Low et al.   STEM CELLS

Selenoprotein MsrB1 promotes anti-inflammatory cytokine gene expression in macrophages and controls immune response in vivo

(2017) Byung Cheon Lee et al.   Scientific Reports

Age-associated NF-κB signaling in myofibers alters the satellite cell niche and re-strains muscle stem cell function

(2016) Juhyun Oh et al.   Aging-US

In Vivo Amelioration of Age-Associated Hallmarks by Partial Reprogramming

(2016) Alejandro Ocampo et al.   CELL

Phosphorylation of eIF2α Is a Translational Control Mechanism Regulating Muscle Stem Cell Quiescence and Self-Renewal

(2016) Victoria Zismanov et al.   Cell Stem Cell

Influence of exercise and aging on extracellular matrix composition in the skeletal muscle stem cell niche

(2016) Koyal Garg et al.   JOURNAL OF APPLIED PHYSIOLOGY

Loss of fibronectin from the aged stem cell niche affects the regenerative capacity of skeletal muscle in mice

(2016) Laura Lukjanenko et al.   NATURE MEDICINE

Satellite Cell Heterogeneity in Skeletal Muscle Homeostasis

(2016) Matthew T. Tierney et al.   TRENDS IN CELL BIOLOGY

Different expression and subcellular localization of Phosphoinositide-specific Phospholipase C enzymes in differently polarized macrophages

(2016) Tania Di Raimo et al.   Journal of Cell Communication and Signaling

Increases of M2a macrophages and fibrosis in aging muscle are influenced by bone marrow aging and negatively regulated by muscle-derived nitric oxide

(2015) Ying Wang et al.   AGING CELL

Interactions between muscle stem cells, mesenchymal-derived cells and immune cells in muscle homeostasis, regeneration and disease

(2015) J Farup et al.   Cell Death & Disease

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

(2014) Simone Picelli et al.   GENOME RESEARCH

Continuity and Innovation in the Data Collection Protocols of the Second Wave of the National Social Life, Health, and Aging Project

(2014) A. Jaszczak et al.   JOURNALS OF GERONTOLOGY SERIES B-PSYCHOLOGICAL SCIENCES AND SOCIAL SCIENCES

Inhibition of JAK-STAT signaling stimulates adult satellite cell function

(2014) Feodor D Price et al.   NATURE MEDICINE

Stem cell aging: mechanisms, regulators and therapeutic opportunities

(2014) Juhyun Oh et al.   NATURE MEDICINE

p38 MAPK signaling underlies a cell-autonomous loss of stem cell self-renewal in skeletal muscle of aged mice

(2014) Jennifer D Bernet et al.   NATURE MEDICINE

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Isolation, characterization, and molecular regulation of muscle stem cells

(2013) So-ichiro Fukada et al.   Frontiers in Physiology

A Subpopulation of Adult Skeletal Muscle Stem Cells Retains All Template DNA Strands after Cell Division

(2012) Pierre Rocheteau et al.   CELL

Glutathione peroxidase 3, a new retinoid target gene, is crucial for human skeletal muscle precursor cell survival

(2012) M. El Haddad et al.   JOURNAL OF CELL SCIENCE

The aged niche disrupts muscle stem cell quiescence

(2012) Joe V. Chakkalakal et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

The ageing systemic milieu negatively regulates neurogenesis and cognitive function

(2011) Saul A. Villeda et al.   NATURE

A Critical Requirement for Notch Signaling in Maintenance of the Quiescent Skeletal Muscle Stem Cell State

(2011) Philippos Mourikis et al.   STEM CELLS

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Muscle injury activates resident fibro/adipogenic progenitors that facilitate myogenesis

(2010) Aaron W. B. Joe et al.   NATURE CELL BIOLOGY

Substrate Elasticity Regulates Skeletal Muscle Stem Cell Self-Renewal in Culture

(2010) P. M. Gilbert et al.   SCIENCE

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

(2010) Andrew Adey et al.   GENOME BIOLOGY

Distinct Regulatory Cascades Govern Extraocular and Pharyngeal Arch Muscle Progenitor Cell Fates

(2009) Ramkumar Sambasivan et al.   DEVELOPMENTAL CELL

A systematic review of human antioxidant genes

(2009) Daniel et al.   Frontiers in Bioscience-Landmark

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY