Senescence atlas reveals an aged-like inflamed niche that blunts muscle regeneration

Novel insights from a multiomics dissection of the Hayflick limit

(2022) Michelle Chan et al.   eLife

Context‐dependent roles of cellular senescence in normal, aged, and disease states

(2022) Victoria Moiseeva et al.   FEBS Journal

Ageing and rejuvenation of tissue stem cells and their niches

(2022) Anne Brunet et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Mitochondrial dynamics maintain muscle stem cell regenerative competence throughout adult life by regulating metabolism and mitophagy

(2022) Xiaotong Hong et al.   Cell Stem Cell

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

An aged immune system drives senescence and ageing of solid organs

(2021) Matthew J. Yousefzadeh et al.   NATURE

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Untangling senescent and damage‐associated microglia in the aging and diseased brain

(2021) Pei Y. Ng et al.   FEBS Journal

Control of satellite cell function in muscle regeneration and its disruption in ageing

(2021) Pedro Sousa-Victor et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Mitochondria-to-nucleus retrograde signaling drives formation of cytoplasmic chromatin and inflammation in senescence

(2020) Maria Grazia Vizioli et al.   GENES & DEVELOPMENT

The nf-core framework for community-curated bioinformatics pipelines

(2020) Philip A. Ewels et al.   NATURE BIOTECHNOLOGY

Sestrin prevents atrophy of disused and aging muscles by integrating anabolic and catabolic signals

(2020) Jessica Segalés et al.   Nature Communications

Exercise enhances skeletal muscle regeneration by promoting senescence in fibro-adipogenic progenitors

(2020) Yuki Saito et al.   Nature Communications

A proteomic atlas of senescence-associated secretomes for aging biomarker development

(2020) Nathan Basisty et al.   PLOS BIOLOGY

Insights from In Vivo Studies of Cellular Senescence

(2020) Luis I. Prieto et al.   Cells

Interaction between high-density lipoproteins and inflammation: Function matters more than concentration!

(2020) Sumra Nazir et al.   ADVANCED DRUG DELIVERY REVIEWS

Tissue Stem Cells: Architects of Their Niches

(2020) Elaine Fuchs et al.   Cell Stem Cell

FoxO maintains a genuine muscle stem-cell quiescent state until geriatric age

(2020) Laura García-Prat et al.   NATURE CELL BIOLOGY

WikiPathways: connecting communities

(2020) Marvin Martens et al.   NUCLEIC ACIDS RESEARCH

L1 drives IFN in senescent cells and promotes age-associated inflammation

(2019) Marco De Cecco et al.   NATURE

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

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

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

(2019) Uku Raudvere et al.   NUCLEIC ACIDS RESEARCH

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

Benchmark and integration of resources for the estimation of human transcription factor activities

(2019) Luz Garcia-Alonso et al.   GENOME RESEARCH

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Age-Related Gene Expression Signature in Rats Demonstrate Early, Late, and Linear Transcriptional Changes from Multiple Tissues

(2019) Tea Shavlakadze et al.   Cell Reports

OUP accepted manuscript

(2018)   BIOINFORMATICS

CD36 initiates the secretory phenotype during the establishment of cellular senescence

(2018) Mengyang Chong et al.   EMBO REPORTS

Senolytics improve physical function and increase lifespan in old age

(2018) Ming Xu et al.   NATURE MEDICINE

Clearance of senescent glial cells prevents tau-dependent pathology and cognitive decline

(2018) Tyler J. Bussian et al.   NATURE

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Transcriptional Signatures of Aging

(2017) R. Stegeman et al.   JOURNAL OF MOLECULAR BIOLOGY

Autophagy maintains the metabolism and function of young and old stem cells

(2017) Theodore T. Ho et al.   NATURE

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

(2017) M Ryan Corces et al.   NATURE METHODS

TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions

(2017) Heonjong Han et al.   NUCLEIC ACIDS RESEARCH

A subcellular map of the human proteome

(2017) Peter J. Thul et al.   SCIENCE

Fibrosis development in early-onset muscular dystrophies: Mechanisms and translational implications

(2017) Antonio L. Serrano et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

VerSeDa: vertebrate secretome database

(2017) Ana R. Cortazar et al.   Database-The Journal of Biological Databases and Curation

In Vivo Amelioration of Age-Associated Hallmarks by Partial Reprogramming

(2016) Alejandro Ocampo et al.   CELL

Autophagy maintains stemness by preventing senescence

(2016) Laura García-Prat et al.   NATURE

Naturally occurring p16Ink4a-positive cells shorten healthy lifespan

(2016) Darren J. Baker et al.   NATURE

TGF-β: the master regulator of fibrosis

(2016) Xiao-ming Meng et al.   Nature Reviews Nephrology

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

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

Senescent intimal foam cells are deleterious at all stages of atherosclerosis

(2016) B. G. Childs et al.   SCIENCE

Tissue damage and senescence provide critical signals for cellular reprogramming in vivo

(2016) Lluc Mosteiro et al.   SCIENCE

The Achilles’ heel of senescent cells: from transcriptome to senolytic drugs

(2015) Yi Zhu et al.   AGING CELL

Mitochondrial DNA stress primes the antiviral innate immune response

(2015) A. Phillip West et al.   NATURE

Clearance of senescent cells by ABT263 rejuvenates aged hematopoietic stem cells in mice

(2015) Jianhui Chang et al.   NATURE MEDICINE

The DNA damage response induces inflammation and senescence by inhibiting autophagy of GATA4

(2015) C. Kang et al.   SCIENCE

Scavenger Receptor Structure and Function in Health and Disease

(2015) Izma Zani et al.   Cells

An Essential Role for Senescent Cells in Optimal Wound Healing through Secretion of PDGF-AA

(2014) Marco Demaria et al.   DEVELOPMENTAL CELL

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

(2014) Simone Picelli et al.   GENOME RESEARCH

NLRP3 inflammasome activation is required for fibrosis development in NAFLD

(2014) Alexander Wree et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

Chronic Inflammation (Inflammaging) and Its Potential Contribution to Age-Associated Diseases

(2014) C. Franceschi et al.   JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES

Geriatric muscle stem cells switch reversible quiescence into senescence

(2014) Pedro Sousa-Victor et al.   NATURE

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Y. Liao et al.   BIOINFORMATICS

Causal analysis approaches in Ingenuity Pathway Analysis

(2013) Andreas Krämer et al.   BIOINFORMATICS

Programmed Cell Senescence during Mammalian Embryonic Development

(2013) Daniel Muñoz-Espín et al.   CELL

Senescence Is a Developmental Mechanism that Contributes to Embryonic Growth and Patterning

(2013) Mekayla Storer et al.   CELL

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

NF-κB inhibition delays DNA damage–induced senescence and aging in mice

(2012) Jeremy S. Tilstra et al.   JOURNAL OF CLINICAL INVESTIGATION

Telomeric DNA damage is irreparable and causes persistent DNA-damage-response activation

(2012) Marzia Fumagalli et al.   NATURE CELL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Short Telomeres and Stem Cell Exhaustion Model Duchenne Muscular Dystrophy in mdx/mTR Mice

(2010) Alessandra Sacco et al.   CELL

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

Inflammatory networks during cellular senescence: causes and consequences

(2010) Adam Freund et al.   TRENDS IN MOLECULAR MEDICINE

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Protocols to detect senescence-associated beta-galactosidase (SA-βgal) activity, a biomarker of senescent cells in culture and in vivo

(2009) Florence Debacq-Chainiaux et al.   Nature Protocols

A novel signaling pathway impact analysis

(2008) Adi Laurentiu Tarca et al.   BIOINFORMATICS

Oncogene-Induced Senescence Relayed by an Interleukin-Dependent Inflammatory Network

(2008) Thomas Kuilman et al.   CELL

Senescence of Activated Stellate Cells Limits Liver Fibrosis

(2008) Valery Krizhanovsky et al.   CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY