Decoding Aging Hallmarks at the Single-Cell Level

Hallmarks of aging: An expanding universe

(2023) Carlos López-Otín et al.   CELL

Resurrection of endogenous retroviruses during aging reinforces senescence

(2023) Xiaoqian Liu et al.   CELL

scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning

(2022) Yingxin Lin et al.   NATURE BIOTECHNOLOGY

Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO

(2022) Britta Velten et al.   NATURE METHODS

Spatial transcriptomic analysis reveals inflammatory foci defined by senescent cells in the white matter, hippocampi and cortical grey matter in the aged mouse brain

(2022) Tamas Kiss et al.   GeroScience

Heterochronic parabiosis induces stem cell revitalization and systemic rejuvenation across aged tissues

(2022) Shuai Ma et al.   Cell Stem Cell

Single-cell analysis of human testis aging and correlation with elevated body mass index

(2022) Xichen Nie et al.   DEVELOPMENTAL CELL

Large-scale chromatin reorganization reactivates placenta-specific genes that drive cellular aging

(2022) Zunpeng Liu et al.   DEVELOPMENTAL CELL

Somatic mutation rates scale with lifespan across mammals

(2022) Alex Cagan et al.   NATURE

Molecular hallmarks of heterochronic parabiosis at single-cell resolution

(2022) Róbert Pálovics et al.   NATURE

Multi-omics single-cell data integration and regulatory inference with graph-linked embedding

(2022) Zhi-Jie Cao et al.   NATURE BIOTECHNOLOGY

Mapping the developing human immune system across organs

(2022) Chenqu Suo et al.   SCIENCE

Cross-tissue immune cell analysis reveals tissue-specific features in humans

(2022) C. Domínguez Conde et al.   SCIENCE

Hyperexcitable arousal circuits drive sleep instability during aging

(2022) Shi-Bin Li et al.   SCIENCE

Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function

(2022) Gökcen Eraslan et al.   SCIENCE

Mapping cell types across human tissues

(2022) Zedao Liu et al.   SCIENCE

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

(2022) et al.   SCIENCE

Measuring biological age using omics data

(2022) Jarod Rutledge et al.   NATURE REVIEWS GENETICS

Construction of a cross-species cell landscape at single-cell level

(2022) Renying Wang et al.   NUCLEIC ACIDS RESEARCH

Deep learning of cross-species single-cell landscapes identifies conserved regulatory programs underlying cell types

(2022) Jiaqi Li et al.   NATURE GENETICS

Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation

(2022) Anna S. Nam et al.   NATURE GENETICS

The landscape of aging

(2022) Yusheng Cai et al.   Science China-Life Sciences

Molecular and spatial signatures of mouse brain aging at single-cell resolution

(2022) William E. Allen et al.   CELL

A single-nucleus transcriptomic atlas of primate testicular aging reveals exhaustion of the spermatogonial stem cell reservoir and loss of Sertoli cell homeostasis

(2022) Daoyuan Huang et al.   Protein & Cell

Single-nucleus profiling unveils a geroprotective role of the FOXO3 in primate skeletal muscle aging

(2022) Ying Jing et al.   Protein & Cell

Haematopoietic ageing through the lens of single-cell technologies

(2021) Paulina M. Strzelecka et al.   Disease Models & Mechanisms

Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes

(2021) Ruli Gao et al.   NATURE BIOTECHNOLOGY

Distinct amyloid-β and tau-associated microglia profiles in Alzheimer’s disease

(2021) Emma Gerrits et al.   ACTA NEUROPATHOLOGICA

ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

(2021) Jeffrey M. Granja et al.   NATURE GENETICS

Inference and analysis of cell-cell communication using CellChat

(2021) Suoqin Jin et al.   Nature Communications

Single human oocyte transcriptome analysis reveals distinct maturation stage‐dependent pathways impacted by age

(2021) Sílvia Llonch et al.   AGING CELL

Applications of Single-Cell DNA Sequencing

(2021) Gilad D. Evrony et al.   Annual Review of Genomics and Human Genetics

A cellular and spatial map of the choroid plexus across brain ventricles and ages

(2021) Neil Dani et al.   CELL

Mutant ASXL1 induces age-related expansion of phenotypic hematopoietic stem cells through activation of Akt/mTOR pathway

(2021) Takeshi Fujino et al.   Nature Communications

Age-related changes in polycomb gene regulation disrupt lineage fidelity in intestinal stem cells

(2021) Helen M Tauc et al.   eLife

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

The single-cell epigenomic and transcriptional landscape of immunity to influenza vaccination

(2021) Florian Wimmers et al.   CELL

Metabolic modeling of single Th17 cells reveals regulators of autoimmunity

(2021) Allon Wagner et al.   CELL

A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data

(2021) Norah Alghamdi et al.   GENOME RESEARCH

Single‐cell transcriptome analysis of human oocyte ageing

(2021) Lihua Yuan et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

A body map of somatic mutagenesis in morphologically normal human tissues

(2021) Ruoyan Li et al.   NATURE

Nanopore sequencing of single-cell transcriptomes with scCOLOR-seq

(2021) Martin Philpott et al.   NATURE BIOTECHNOLOGY

Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics

(2021) Sophia K. Longo et al.   NATURE REVIEWS GENETICS

Resolving cellular and molecular diversity along the hippocampal anterior-to-posterior axis in humans

(2021) Fatma Ayhan et al.   NEURON

Effects of sex and aging on the immune cell landscape as assessed by single-cell transcriptomic analysis

(2021) Zhaohao Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatiotemporal Immune Landscape of Colorectal Cancer Liver Metastasis at Single-Cell Level

(2021) Yingcheng Wu et al.   Cancer Discovery

Single-nucleus transcriptomic landscape of primate hippocampal aging

(2021) Hui Zhang et al.   Protein & Cell

Identification of distinct and age‐dependent p16 High microglia subtypes

(2021) Nynke Talma et al.   AGING CELL

Single-cell chromatin state analysis with Signac

(2021) Tim Stuart et al.   NATURE METHODS

Transcriptomic taxonomy and neurogenic trajectories of adult human, macaque, and pig hippocampal and entorhinal cells

(2021) Daniel Franjic et al.   NEURON

Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels

(2021) Yuansheng Zhang et al.   NUCLEIC ACIDS RESEARCH

scMethBank: a database for single-cell whole genome DNA methylation maps

(2021) Wenting Zong et al.   NUCLEIC ACIDS RESEARCH

MEF2 is a key regulator of cognitive potential and confers resilience to neurodegeneration

(2021) Scarlett J. Barker et al.   Science Translational Medicine

Aging weakens Th17 cell pathogenicity and ameliorates experimental autoimmune uveitis in mice

(2021) He Li et al.   Protein & Cell

Single-Cell Analysis Identify Transcription Factor BACH1 as a Master Regulator Gene in Vascular Cells During Aging

(2021) Fei Ge et al.   Frontiers in Cell and Developmental Biology

Advanced maternal age alters expression of maternal effect genes that are essential for human oocyte quality

(2020) Jing-Jing Zhang et al.   Aging-US

Caloric Restriction Reprograms the Single-Cell Transcriptional Landscape of Rattus Norvegicus Aging

(2020) Shuai Ma et al.   CELL

Single-Cell Transcriptomic Atlas of Primate Ovarian Aging

(2020) Si Wang et al.   CELL

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

(2020) Mirjana Efremova et al.   Nature Protocols

The ageing epigenome and its rejuvenation

(2020) Weiqi Zhang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Single-cell analysis reveals different age-related somatic mutation profiles between stem and differentiated cells in human liver

(2020) K. Brazhnik et al.   Science Advances

Deep learning for biological age estimation

(2020) Syed Ashiqur Rahman et al.   BRIEFINGS IN BIOINFORMATICS

When function follows form: Nuclear compartment structure and the epigenetic landscape of the aging neuron

(2020) Johannes C.M. Schlachetzki et al.   EXPERIMENTAL GERONTOLOGY

Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis

(2020) Chiaowen Joyce Hsiao et al.   GENOME RESEARCH

SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics

(2020) Simon Cabello-Aguilar et al.   NUCLEIC ACIDS RESEARCH

A single-cell transcriptomic landscape of primate arterial aging

(2020) Weiqi Zhang et al.   Nature Communications

Brain Endothelial Cells Are Exquisite Sensors of Age-Related Circulatory Cues

(2020) Michelle B. Chen et al.   Cell Reports

Aortic heterogeneity across segments and under high fat/salt/glucose conditions at the single-cell level

(2020) Dongxu He et al.   National Science Review

Single-cell RNA sequencing identifies senescent cerebromicrovascular endothelial cells in the aged mouse brain

(2020) Tamas Kiss et al.   GeroScience

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

(2020)   NATURE

Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling

(2020) Caleb A. Lareau et al.   NATURE BIOTECHNOLOGY

Maternal ageing causes changes in DNA methylation and gene expression profiles in mouse oocytes

(2020) Guanmei Hou et al.   ZYGOTE

A human circulating immune cell landscape in aging and COVID-19

(2020) Yingfeng Zheng et al.   Protein & Cell

A Single-cell Transcriptomic Atlas of Primate Pancreatic Islet Aging

(2020) Jingyi Li et al.   National Science Review

Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming

(2020) Llorenç Solé-Boldo et al.   Communications Biology

The Human and Mouse Enteric Nervous System at Single-Cell Resolution

(2020) Eugene Drokhlyansky et al.   CELL

Deciphering primate retinal aging at single-cell resolution

(2020) Si Wang et al.   Protein & Cell

Comprehensive Profiling of an Aging Immune System Reveals Clonal GZMK+ CD8+ T Cells as Conserved Hallmark of Inflammaging

(2020) Denis A. Mogilenko et al.   IMMUNITY

Neuroblast senescence in the aged brain augments natural killer cell cytotoxicity leading to impaired neurogenesis and cognition

(2020) Wei-Na Jin et al.   NATURE NEUROSCIENCE

Machine Learning of Hematopoietic Stem Cell Divisions from Paired Daughter Cell Expression Profiles Reveals Effects of Aging on Self-Renewal

(2020) Fumio Arai et al.   Cell Systems

A Single-Cell Transcriptomic Atlas of Human Skin Aging

(2020) Zhiran Zou et al.   DEVELOPMENTAL CELL

Integration of single-cell RNA-seq data into population models to characterize cancer metabolism

(2019) Chiara Damiani et al.   PLoS Computational Biology

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

(2019) Ilias Angelidis et al.   Nature Communications

Integrative single-cell analysis

(2019) Tim Stuart et al.   NATURE REVIEWS GENETICS

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Quiescence Modulates Stem Cell Maintenance and Regenerative Capacity in the Aging Brain

(2019) Georgios Kalamakis et al.   CELL

Single-cell whole-genome sequencing reveals the functional landscape of somatic mutations in B lymphocytes across the human lifespan

(2019) Lei Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Losing Sense of Self and Surroundings: Hematopoietic Stem Cell Aging and Leukemic Transformation

(2019) Evgenia V. Verovskaya et al.   TRENDS IN MOLECULAR MEDICINE

Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia

(2019) Emmalee R Adelman et al.   Cancer Discovery

Single-cell analysis reveals T cell infiltration in old neurogenic niches

(2019) Ben W. Dulken et al.   NATURE

Mitochondrial dysfunction and endoplasmic reticulum stress involved in oocyte aging: an analysis using single-cell RNA-sequencing of mouse oocytes

(2019) Tao Zhang et al.   Journal of Ovarian Research

Expansion of Luminal Progenitor Cells in the Aging Mouse and Human Prostate

(2019) Preston D. Crowell et al.   Cell Reports

Intestinal Stem Cell Aging: Origins and Interventions

(2019) Heinrich Jasper   Annual Review of Physiology

Haematopoietic stem cells in perisinusoidal niches are protected from ageing

(2019) Mehmet Saçma et al.   NATURE CELL BIOLOGY

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Clonal hematopoiesis in human aging and disease

(2019) Siddhartha Jaiswal et al.   SCIENCE

NicheNet: modeling intercellular communication by linking ligands to target genes

(2019) Robin Browaeys et al.   NATURE METHODS

Mutant p53 drives clonal hematopoiesis through modulating epigenetic pathway

(2019) Sisi Chen et al.   Nature Communications

B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle

(2018) Simone Rizzetto et al.   BIOINFORMATICS

Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations with Aging

(2018) Peggie Cheung et al.   CELL

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline

(2018) Marco L. Hennrich et al.   Nature Communications

Aging alters the epigenetic asymmetry of HSC division

(2018) M. Carolina Florian et al.   PLOS BIOLOGY

Artificial intelligence for aging and longevity research: Recent advances and perspectives

(2018) Alex Zhavoronkov et al.   AGEING RESEARCH REVIEWS

Single sample scoring of molecular phenotypes

(2018) Momeneh Foroutan et al.   BMC BIOINFORMATICS

PPM1D Mutations Drive Clonal Hematopoiesis in Response to Cytotoxic Chemotherapy

(2018) Joanne I. Hsu et al.   Cell Stem Cell

Testis development

(2018) Juho-Antti Mäkelä et al.   ENDOCRINE REVIEWS

Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes

(2018) Timothy R. Hammond et al.   IMMUNITY

Machine learning based classification of cells into chronological stages using single-cell transcriptomics

(2018) Sumeet Pal Singh et al.   Scientific Reports

Heterogeneous Responses of Hematopoietic Stem Cells to Inflammatory Stimuli Are Altered with Age

(2018) Mati Mann et al.   Cell Reports

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

Human Ageing Genomic Resources: new and updated databases

(2017) Robi Tacutu et al.   NUCLEIC ACIDS RESEARCH

Aging and neurodegeneration are associated with increased mutations in single human neurons

(2017) Michael A. Lodato 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

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

scRNASeqDB: A Database for RNA-Seq Based Gene Expression Profiles in Human Single Cells

(2017) Yuan Cao et al.   Genes

Single-Cell (Multi)omics Technologies

(2016) Lia Chappell et al.   Annual Review of Genomics and Human Genetics

BASIC: BCR assembly from single cells

(2016) Stefan Canzar et al.   BIOINFORMATICS

Systematic Analysis of Cell-to-Cell Expression Variation of T Lymphocytes in a Human Cohort Identifies Aging and Genetic Associations

(2016) Yong Lu et al.   IMMUNITY

Tissue-specific mutation accumulation in human adult stem cells during life

(2016) Francis Blokzijl et al.   NATURE

T cell fate and clonality inference from single-cell transcriptomes

(2016) Michael J T Stubbington et al.   NATURE METHODS

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

Single-cell RNA sequencing reveals molecular and functional platelet bias of aged haematopoietic stem cells

(2016) Amit Grover et al.   Nature Communications

Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq

(2016) David Redmond et al.   Genome Medicine

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

Interactive analysis and assessment of single-cell copy-number variations

(2015) Tyler Garvin et al.   NATURE METHODS

Paracrine signaling mediated at cell-cell contacts

(2014) Sougata Roy et al.   BIOESSAYS

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

(2014) Johanna Flach et al.   NATURE

The Digital Ageing Atlas: integrating the diversity of age-related changes into a unified resource

(2014) Thomas Craig et al.   NUCLEIC ACIDS RESEARCH

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

Perivascular cells in blood vessel regeneration

(2013) Maureen Wanjare et al.   Biotechnology Journal

The Hallmarks of Aging

(2013) Carlos López-Otín et al.   CELL

AgeFactDB—the JenAge Ageing Factor Database—towards data integration in ageing research

(2013) Rolf Hühne et al.   NUCLEIC ACIDS RESEARCH

DNA methylation age of human tissues and cell types

(2013) Steve Horvath   GENOME BIOLOGY

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS