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

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

(2019) Ilias Angelidis et al.   Nature Communications

Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses

(2019) Bérénice A. Benayoun et al.   GENOME RESEARCH

Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming

(2019) Geoffrey Schiebinger et al.   CELL

Age Mosaicism across Multiple Scales in Adult Tissues

(2019) Rafael Arrojo e Drigo et al.   Cell Metabolism

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

(2019) Dylan Kotliar et al.   eLife

A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain

(2018) Kristofer Davie et al.   CELL

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

Tissue aging: the integration of collective and variant responses of cells to entropic forces over time

(2018) Michael E Todhunter et al.   CURRENT OPINION IN CELL BIOLOGY

scmap: projection of single-cell RNA-seq data across data sets

(2018) Vladimir Yu Kiselev et al.   NATURE METHODS

Windowed Granger causal inference strategy improves discovery of gene regulatory networks

(2018) Justin D. Finkle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease

(2018) Jihwan Park et al.   SCIENCE

Age-Related Decline in Primary CD8 + T Cell Responses Is Associated with the Development of Senescence in Virtual Memory CD8 + T Cells

(2018) Kylie M. Quinn et al.   Cell Reports

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

A new experimental platform facilitates assessment of the transcriptional and chromatin landscapes of aging yeast

(2018) David G Hendrickson et al.   eLife

Stem cells: Aging and transcriptional fingerprints

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

Report: NIA Workshop on Measures of Physiologic Resiliencies in Human Aging

(2017) Evan C Hadley et al.   JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES

Senescent cells: an emerging target for diseases of ageing

(2017) Bennett G. Childs et al.   NATURE REVIEWS DRUG DISCOVERY

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

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

Proliferation Drives Aging-Related Functional Decline in a Subpopulation of the Hematopoietic Stem Cell Compartment

(2017) Kristina Kirschner et al.   Cell Reports

Canonical Wnt Signaling Ameliorates Aging of Intestinal Stem Cells

(2017) Kodandaramireddy Nalapareddy et al.   Cell Reports

Robust classification of single-cell transcriptome data by nonnegative matrix factorization

(2016) Chunxuan Shao et al.   BIOINFORMATICS

The EMT regulator ZEB2 is a novel dependency of human and murine acute myeloid leukemia

(2016) Hubo Li et al.   BLOOD

Hematopoietic Stem Cells Count and Remember Self-Renewal Divisions

(2016) Jeffrey M. Bernitz et al.   CELL

Impaired Epidermal to Dendritic T Cell Signaling Slows Wound Repair in Aged Skin

(2016) Brice E. Keyes et al.   CELL

A Ribosomal Perspective on Proteostasis and Aging

(2016) Kristan K. Steffen et al.   Cell Metabolism

Resilience in Aging Mice

(2016) James L. Kirkland et al.   JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES

Naturally occurring p16Ink4a-positive cells shorten healthy lifespan

(2016) Darren J. Baker et al.   NATURE

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Heightened self-reactivity associated with selective survival, but not expansion, of naïve virus-specific CD8+T cells in aged mice

(2016) Kylie M. Quinn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2016) I. Tirosh et al.   SCIENCE

Tissue-Specific Suppression of Thyroid Hormone Signaling in Various Mouse Models of Aging

(2016) W. Edward Visser et al.   PLoS One

Comprehensive transcriptional landscape of aging mouse liver

(2015) Ryan R. White et al.   BMC GENOMICS

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

(2015) Aleksandra A. Kolodziejczyk 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

Naive T Cell Maintenance and Function in Human Aging

(2015) Jörg J. Goronzy et al.   JOURNAL OF IMMUNOLOGY

Age-Associated Failure To Adjust Type I IFN Receptor Signaling Thresholds after T Cell Activation

(2015) Guangjin Li et al.   JOURNAL OF IMMUNOLOGY

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

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

(2015) Helen M Blau et al.   NATURE MEDICINE

A nested parallel experiment demonstrates differences in intensity-dependence between RNA-seq and microarrays

(2015) David G. Robinson et al.   NUCLEIC ACIDS RESEARCH

The Inflammatory Transcription Factors NFκB, STAT1 and STAT3 Drive Age-Associated Transcriptional Changes in the Human Kidney

(2015) Zach K. O’Brown et al.   PLoS Genetics

A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging

(2015) Jing Su et al.   Skeletal Muscle

The ins and outs of muscle stem cell aging

(2015) Andrew S. Brack et al.   Skeletal Muscle

Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats

(2015) Alessandro Ori et al.   Cell Systems

The Four Layers of Aging

(2015) Ran Zhang et al.   Cell Systems

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

UsingC. elegansfor aging research

(2014) Heidi A. Tissenbaum   INVERTEBRATE REPRODUCTION & DEVELOPMENT

Replication stress is a potent driver of functional decline in ageing haematopoietic stem cells

(2014) Johanna Flach et al.   NATURE

Geriatric muscle stem cells switch reversible quiescence into senescence

(2014) Pedro Sousa-Victor et al.   NATURE

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

(2014) Benjamin D Cosgrove et al.   NATURE MEDICINE

Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling

(2014) M. J. Wawer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A circadian gene expression atlas in mammals: Implications for biology and medicine

(2014) Ray Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plac8 Links Oncogenic Mutations to Regulation of Autophagy and Is Critical to Pancreatic Cancer Progression

(2014) Conan Kinsey et al.   Cell Reports

Life spanning murine gene expression profiles in relation to chronological and pathological aging in multiple organs

(2013) Martijs J. Jonker et al.   AGING CELL

The Hallmarks of Aging

(2013) Carlos López-Otín et al.   CELL

Nfatc1 orchestrates aging in hair follicle stem cells

(2013) B. E. Keyes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The origin of aging: imperfectness-driven non-random damage defines the aging process and control of lifespan

(2013) Vadim N. Gladyshev   TRENDS IN GENETICS

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

(2013) Ling Liu et al.   Cell Reports

DNA methylation age of human tissues and cell types

(2013) Steve Horvath   GENOME BIOLOGY

Replicative and Chronological Aging in Saccharomyces cerevisiae

(2012) Valter D. Longo et al.   Cell Metabolism

Defective CD8 T Cell Responses in Aged Mice Are Due to Quantitative and Qualitative Changes in Virus-Specific Precursors

(2012) V. Decman et al.   JOURNAL OF IMMUNOLOGY

The aged niche disrupts muscle stem cell quiescence

(2012) Joe V. Chakkalakal et al.   NATURE

Studying and modelling dynamic biological processes using time-series gene expression data

(2012) Ziv Bar-Joseph et al.   NATURE REVIEWS GENETICS

Pathobiology of Aging Mice and GEM

(2012) C. F. Brayton et al.   VETERINARY PATHOLOGY

Aging Is Associated with an Increase in T Cells and Inflammatory Macrophages in Visceral Adipose Tissue

(2011) C. N. Lumeng et al.   JOURNAL OF IMMUNOLOGY

Molecular basis of fosmidomycin's action on the human malaria parasite Plasmodium falciparum

(2011) Tomonobu Umeda et al.   Scientific Reports

Cellular Heterogeneity: Do Differences Make a Difference?

(2010) Steven J. Altschuler et al.   CELL

Aging of the innate immune system

(2010) Albert C Shaw et al.   CURRENT OPINION IN IMMUNOLOGY

The genetics of ageing

(2010) Cynthia J. Kenyon   NATURE

Experimental evolution of bet hedging

(2009) Hubertus J. E. Beaumont et al.   NATURE

The Clinical Significance of Subclinical Thyroid Dysfunction

(2008) Bernadette Biondi et al.   ENDOCRINE REVIEWS

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Delayed and Accelerated Aging Share Common Longevity Assurance Mechanisms

(2008) Björn Schumacher et al.   PLoS Genetics