Tissue damage induces a conserved stress response that initiates quiescent muscle stem cell activation

Interstitial Cell Remodeling Promotes Aberrant Adipogenesis in Dystrophic Muscles

(2020) Jordi Camps et al.   Cell Reports

Single-Cell Analysis of the Muscle Stem Cell Hierarchy Identifies Heterotypic Communication Signals Involved in Skeletal Muscle Regeneration

(2020) Andrea J. De Micheli et al.   Cell Reports

Tissue Stem Cells: Architects of Their Niches

(2020) Elaine Fuchs et al.   Cell Stem Cell

Single-nucleus RNA-seq and FISH identify coordinated transcriptional activity in mammalian myofibers

(2020) Matthieu Dos Santos et al.   Nature Communications

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

High-Dimensional Single-Cell Cartography Reveals Novel Skeletal Muscle-Resident Cell Populations

(2019) Lorenzo Giordani et al.   MOLECULAR CELL

Single-cell analysis of adult skeletal muscle stem cells in homeostatic and regenerative conditions

(2019) Stefania Dell'Orso et al.   DEVELOPMENT

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Cross-talk between TGF-β and PDGFRα signaling pathways regulates the fate of stromal fibro–adipogenic progenitors

(2019) Osvaldo Contreras et al.   JOURNAL OF CELL SCIENCE

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

p110α of PI3K is necessary and sufficient for quiescence exit in adult muscle satellite cells

(2018) Gang Wang et al.   EMBO JOURNAL

Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy

(2018) Guiping Wang et al.   Scientific Reports

Advantages of Single-Nucleus over Single-Cell RNA Sequencing of Adult Kidney: Rare Cell Types and Novel Cell States Revealed in Fibrosis

(2018) Haojia Wu et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

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

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Single-nucleus and single-cell transcriptomes compared in matched cortical cell types

(2018) Trygve E. Bakken et al.   PLoS One

eIF5A Functions Globally in Translation Elongation and Termination

(2017) Anthony P. Schuller et al.   MOLECULAR CELL

Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations

(2017) Susanne C van den Brink et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Detecting Activated Cell Populations Using Single-Cell RNA-Seq

(2017) Ye Emily Wu et al.   NEURON

In Situ Fixation Redefines Quiescence and Early Activation of Skeletal Muscle Stem Cells

(2017) Léo Machado et al.   Cell Reports

Transcriptional Profiling of Quiescent Muscle Stem Cells In Vivo

(2017) Cindy T.J. van Velthoven et al.   Cell Reports

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Nuclear RNA-seq of single neurons reveals molecular signatures of activation

(2016) Benjamin Lacar et al.   Nature Communications

The Role of Cell Plasticity in Tissue Repair: Adaptive Cellular Reprogramming

(2015) Kristjan R. Jessen et al.   DEVELOPMENTAL CELL

Fixed single-cell transcriptomic characterization of human radial glial diversity

(2015) Elliot R Thomsen et al.   NATURE METHODS

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

(2015) Iain C Macaulay et al.   NATURE METHODS

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

Calcitonin Receptor Signaling Inhibits Muscle Stem Cells from Escaping the Quiescent State and the Niche

(2015) Masahiko Yamaguchi et al.   Cell Reports

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

(2014) S. Anders et al.   BIOINFORMATICS

Distinct contextual roles for Notch signalling in skeletal muscle stem cells

(2014) Philippos Mourikis et al.   BMC DEVELOPMENTAL BIOLOGY

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

(2014) Simone Picelli et al.   Nature Protocols

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

(2013) Y. Liao et al.   BIOINFORMATICS

Depletion of cellular polyamines, spermidine and spermine, causes a total arrest in translation and growth in mammalian cells

(2013) S. Mandal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The aged niche disrupts muscle stem cell quiescence

(2012) Joe V. Chakkalakal et al.   NATURE

Regulation of endothelial cell plasticity by TGF-β

(2011) Laurens A. van Meeteren et al.   CELL AND TISSUE RESEARCH

Hepatocyte growth factor/c-metsignaling is required for stem-cell-mediated liver regeneration in mice

(2011) Tsuyoshi Ishikawa et al.   HEPATOLOGY

New concepts in liver regeneration

(2011) Kimberly J Riehle et al.   JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY

Transient Regenerative Potential of the Neonatal Mouse Heart

(2011) E. R. Porrello et al.   SCIENCE

Beneficial paracrine effects of cannabinoid receptor 2 on liver injury and regeneration

(2010) Fatima Teixeira-Clerc et al.   HEPATOLOGY

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

(2009) Ramkumar Sambasivan et al.   DEVELOPMENTAL CELL