Misexpression of genes lacking CpG islands drives degenerative changes during aging

Conserved dual-mode gene regulation programs in higher eukaryotes

(2021) Jun-Yeong Lee et al.   NUCLEIC ACIDS RESEARCH

Proteomic and transcriptomic profiling reveal different aspects of aging in the kidney

(2021) Yuka Takemon et al.   eLife

Personal aging markers and ageotypes revealed by deep longitudinal profiling

(2020) Sara Ahadi et al.   NATURE MEDICINE

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

(2020) Nathan Basisty et al.   PLOS BIOLOGY

Role of the Nuclear Lamina in Age-Associated Nuclear Reorganization and Inflammation

(2020) Lidya Kristiani et al.   Cells

HRT Atlas v1.0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets

(2020) Bidossessi Wilfried Hounkpe et al.   NUCLEIC ACIDS RESEARCH

Single-dose CRISPR–Cas9 therapy extends lifespan of mice with Hutchinson–Gilford progeria syndrome

(2019) Ergin Beyret et al.   NATURE MEDICINE

Risperidone effects on heterochromatin: the role of kinase signaling

(2019) B. Feiner et al.   CLINICAL AND EXPERIMENTAL IMMUNOLOGY

Lamin B1 loss promotes lung cancer development and metastasis by epigenetic derepression of RET

(2019) Yanhan Jia et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Acceleration of β Cell Aging Determines Diabetes and Senolysis Improves Disease Outcomes

(2019) Cristina Aguayo-Mazzucato et al.   Cell Metabolism

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

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

Undulating changes in human plasma proteome profiles across the lifespan

(2019) Benoit Lehallier et al.   NATURE MEDICINE

Plasma proteomic signature of age in healthy humans

(2018) Toshiko Tanaka et al.   AGING CELL

Hierarchical analysis of RNA-seq reads improves the accuracy of allele-specific expression

(2018) Narayanan Raghupathy et al.   BIOINFORMATICS

Cellular Senescence and Inflammaging in Age-Related Diseases

(2018) Fabiola Olivieri et al.   MEDIATORS OF INFLAMMATION

Implications of CpG islands on chromosomal architectures and modes of global gene regulation

(2018) Samuel Beck et al.   NUCLEIC ACIDS RESEARCH

Chromatin Architectural Changes during Cellular Senescence and Aging

(2018) Luyang Sun et al.   Genes

Inflammaging: a new immune–metabolic viewpoint for age-related diseases

(2018) Claudio Franceschi et al.   Nature Reviews Endocrinology

Kinetics of adult hematopoietic stem cell differentiation in vivo

(2018) Samik Upadhaya et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells

(2018) Jiangping He et al.   Nature Communications

Senescent cells: an emerging target for diseases of ageing

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

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

Major Shifts in Glial Regional Identity Are a Transcriptional Hallmark of Human Brain Aging

(2017) Lilach Soreq et al.   Cell Reports

Hematopoietic Stem Cells Are the Major Source of Multilineage Hematopoiesis in Adult Animals

(2016) Catherine M. Sawai et al.   IMMUNITY

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

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

Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins

(2015) Jennifer C. Harr et al.   JOURNAL OF CELL BIOLOGY

Characterization of Skin Aging–Associated Secreted Proteins (SAASP) Produced by Dermal Fibroblasts Isolated from Intrinsically Aged Human Skin

(2015) Daniel M. Waldera Lupa et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

A Werner syndrome stem cell model unveils heterochromatin alterations as a driver of human aging

(2015) W. Zhang et al.   SCIENCE

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Global Reorganization of the Nuclear Landscape in Senescent Cells

(2015) Tamir Chandra et al.   Cell Reports

Nucleolus and nuclear periphery: Velcro for heterochromatin

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Objective assessment of changes in nuclear morphology and cell distribution following induction of apoptosis

(2014) Jon R Eidet et al.   Diagnostic Pathology

CpG island-mediated global gene regulatory modes in mouse embryonic stem cells

(2014) Samuel Beck et al.   Nature Communications

The Hallmarks of Aging

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LBR and Lamin A/C Sequentially Tether Peripheral Heterochromatin and Inversely Regulate Differentiation

(2013) Irina Solovei et al.   CELL

Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape

(2013) P. P. Shah et al.   GENES & DEVELOPMENT

STAR: ultrafast universal RNA-seq aligner

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Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes

(2012) B. J. Beliveau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genetic pleiotropy of musculoskeletal aging

(2012) David Karasik et al.   Frontiers in Physiology

Restricted Heterochromatin Formation Links NFATc2 Repressor Activity With Growth Promotion in Pancreatic Cancer

(2011) Sandra Baumgart et al.   GASTROENTEROLOGY

CpG islands and the regulation of transcription

(2011) A. M. Deaton et al.   GENES & DEVELOPMENT

NEMO: a tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments

(2010) E. Iannuccelli et al.   BIOINFORMATICS

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

(2010) Robert C McLeay et al.   BMC BIOINFORMATICS

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

Skin regeneration and repair

(2010) Cédric Blanpain   NATURE

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome

(2010) Robert S. Illingworth et al.   PLoS Genetics

Role of the polycomb protein EED in the propagation of repressive histone marks

(2009) Raphael Margueron et al.   NATURE

Rapamycin fed late in life extends lifespan in genetically heterogeneous mice

(2009) David E. Harrison et al.   NATURE

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Senescence-Associated Secretory Phenotypes Reveal Cell-Nonautonomous Functions of Oncogenic RAS and the p53 Tumor Suppressor

(2008) Jean-Philippe Coppé et al.   PLOS BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY