Differentiation reveals latent features of aging and an energy barrier in murine myogenesis

Semi-supervised adversarial neural networks for single-cell classification

(2021) Jacob C. Kimmel et al.   GENOME RESEARCH

Aging induces aberrant state transition kinetics in murine muscle stem cells

(2020) Jacob C. Kimmel et al.   DEVELOPMENT

Transient non-integrative expression of nuclear reprogramming factors promotes multifaceted amelioration of aging in human cells

(2020) Tapash Jay Sarkar et al.   Nature Communications

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

A single-cell transcriptomic atlas characterizes ageing tissues in the mouse

(2020)   NATURE

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Solo: Doublet Identification in Single-Cell RNA-Seq via Semi-Supervised Deep Learning

(2020) Nicholas J. Bernstein et al.   Cell Systems

An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics

(2019) Ilias Angelidis et al.   Nature Communications

The barcode, UMI, set format and BUStools

(2019) Páll Melsted et al.   BIOINFORMATICS

Lineage Tracing Reveals a Subset of Reserve Muscle Stem Cells Capable of Clonal Expansion under Stress

(2019) Annarita Scaramozza et al.   Cell Stem Cell

Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species

(2019) Genevieve L. Stein-O’Brien et al.   Cell Systems

Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq

(2019) Dylan Kotliar et al.   eLife

Supervised classification enables rapid annotation of cell atlases

(2019) Hannah A. Pliner et al.   NATURE METHODS

Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging

(2019) Jacob C. Kimmel et al.   GENOME RESEARCH

A Muscle Stem Cell Support Group: Coordinated Cellular Responses in Muscle Regeneration

(2018) Michael N. Wosczyna et al.   DEVELOPMENTAL CELL

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

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Inferring cell state by quantitative motility analysis reveals a dynamic state system and broken detailed balance

(2018) Jacob C. Kimmel et al.   PLoS Computational Biology

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Enter the Matrix: Factorization Uncovers Knowledge from Omics

(2018) Genevieve L. Stein-O’Brien et al.   TRENDS IN GENETICS

Aligning Single-Cell Developmental and Reprogramming Trajectories Identifies Molecular Determinants of Myogenic Reprogramming Outcome

(2018) Davide Cacchiarelli et al.   Cell Systems

Orienting Muscle Stem Cells for Regeneration in Homeostasis, Aging, and Disease

(2018) Peter Feige 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

Deep generative modeling for single-cell transcriptomics

(2018) Romain Lopez et al.   NATURE METHODS

Stem cells: Aging and transcriptional fingerprints

(2017) Brice E. Keyes et al.   JOURNAL OF CELL BIOLOGY

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Aging increases cell-to-cell transcriptional variability upon immune stimulation

(2017) Celia Pilar Martinez-Jimenez et al.   SCIENCE

Clonal reversal of ageing-associated stem cell lineage bias via a pluripotent intermediate

(2017) Martin Wahlestedt et al.   Nature Communications

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

HGFA Is an Injury-Regulated Systemic Factor that Induces the Transition of Stem Cells into G Alert

(2017) Joseph T. Rodgers et al.   Cell Reports

Association of Omics Features with Histopathology Patterns in Lung Adenocarcinoma

(2017) Kun-Hsing Yu et al.   Cell Systems

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

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

The NAD+-Dependent SIRT1 Deacetylase Translates a Metabolic Switch into Regulatory Epigenetics in Skeletal Muscle Stem Cells

(2015) James G. Ryall et al.   Cell Stem Cell

Directly Reprogrammed Human Neurons Retain Aging-Associated Transcriptomic Signatures and Reveal Age-Related Nucleocytoplasmic Defects

(2015) Jerome Mertens et al.   Cell Stem Cell

Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells

(2015) Monika S. Kowalczyk et al.   GENOME RESEARCH

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

Single Mammalian Cells Compensate for Differences in Cellular Volume and DNA Copy Number through Independent Global Transcriptional Mechanisms

(2015) Olivia Padovan-Merhar et al.   MOLECULAR CELL

Nilotinib reduces muscle fibrosis in chronic muscle injury by promoting TNF-mediated apoptosis of fibro/adipogenic progenitors

(2015) Dario R Lemos et al.   NATURE MEDICINE

The central role of muscle stem cells in regenerative failure with aging

(2015) Helen M Blau et al.   NATURE MEDICINE

mTORC1 controls the adaptive transition of quiescent stem cells from G0 to GAlert

(2014) Joseph T. Rodgers et al.   NATURE

Geriatric muscle stem cells switch reversible quiescence into senescence

(2014) Pedro Sousa-Victor et al.   NATURE

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Rejuvenation of the muscle stem cell population restores strength to injured aged muscles

(2014) Benjamin D Cosgrove 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

ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software

(2014) Mathieu Jacomy et al.   PLoS One

Sox4-mediated caldesmon expression facilitates differentiation of skeletal myoblasts

(2013) S.-M. Jang et al.   JOURNAL OF CELL SCIENCE

Chromatin Modifications as Determinants of Muscle Stem Cell Quiescence and Chronological Aging

(2013) Ling Liu et al.   Cell Reports

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Tissue-Specific Stem Cells: Lessons from the Skeletal Muscle Satellite Cell

(2012) Andrew S. Brack et al.   Cell Stem Cell

Snail Regulates MyoD Binding-Site Occupancy to Direct Enhancer Switching and Differentiation-Specific Transcription in Myogenesis

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

The aged niche disrupts muscle stem cell quiescence

(2012) Joe V. Chakkalakal et al.   NATURE

Rejuvenating senescent and centenarian human cells by reprogramming through the pluripotent state

(2011) L. Lapasset et al.   GENES & DEVELOPMENT

Sprouty1 Regulates Reversible Quiescence of a Self-Renewing Adult Muscle Stem Cell Pool during Regeneration

(2010) Kelly L. Shea et al.   Cell Stem Cell

Muscle injury activates resident fibro/adipogenic progenitors that facilitate myogenesis

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

The first long-lived mutants: discovery of the insulin/IGF-1 pathway for ageing

(2010) C. Kenyon   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Functionally distinct hematopoietic stem cells modulate hematopoietic lineage potential during aging by a mechanism of clonal expansion

(2010) I. Beerman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) P. M. Gilbert et al.   SCIENCE