Cell-free DNA as a biomarker of aging

Disease prediction by cell-free DNA methylation

(2018) Hao Feng et al.   BRIEFINGS IN BIOINFORMATICS

Allostatic load and subsequent all-cause mortality: which biological markers drive the relationship? Findings from a UK birth cohort

(2018) Raphaële Castagné et al.   EUROPEAN JOURNAL OF EPIDEMIOLOGY

Heterogeneity of Thyroid Function and Impact of Peripheral Thyroxine Deiodination in Centenarians and Semi-Supercentenarians: Association With Functional Status and Mortality

(2018) Rita Ostan et al.   JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES

Transposable Elements in Human Cancer: Causes and Consequences of Deregulation

(2017) Sumadi Anwar et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Cognitive status in the oldest old and centenarians: a condition crucial for quality of life methodologically difficult to assess

(2017) Beatrice Arosio et al.   MECHANISMS OF AGEING AND DEVELOPMENT

Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tumor tissue-of-origin mapping from plasma DNA

(2017) Shicheng Guo et al.   NATURE GENETICS

Inflammaging and ‘Garb-aging’

(2017) Claudio Franceschi et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Immunobiography and the Heterogeneity of Immune Responses in the Elderly: A Focus on Inflammaging and Trained Immunity

(2017) Claudio Franceschi et al.   Frontiers in Immunology

DNA methylation-based measures of biological age: meta-analysis predicting time to death

(2016) Brian H. Chen et al.   Aging-US

Glycomics and glycoproteomics focused on aging and age-related diseases — Glycans as a potential biomarker for physiological alterations

(2016) Yuri Miura et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin

(2016) Matthew W. Snyder et al.   CELL

Identification of tissue-specific cell death using methylation patterns of circulating DNA

(2016) Roni Lehmann-Werman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Chromatin Landscape of Cellular Senescence

(2016) Steven W. Criscione et al.   TRENDS IN GENETICS

MNase titration reveals differences between nucleosome occupancy and chromatin accessibility

(2016) Jakub Mieczkowski et al.   Nature Communications

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Obesity-induced DNA released from adipocytes stimulates chronic adipose tissue inflammation and insulin resistance

(2016) S. Nishimoto et al.   Science Advances

Transposable elements become active and mobile in the genomes of aging mammalian somatic tissues

(2016) Marco De Cecco et al.   Aging-US

Very Short Mitochondrial DNA Fragments and Heteroplasmy in Human Plasma

(2016) Ruoyu Zhang et al.   Scientific Reports

Programmed cell death in aging

(2015) John Tower   AGEING RESEARCH REVIEWS

Accelerated epigenetic aging in Down syndrome

(2015) Steve Horvath et al.   AGING CELL

Decreased epigenetic age of PBMCs from Italian semi-supercentenarians and their offspring

(2015) Steve Horvath et al.   Aging-US

Non-random fragmentation patterns in circulating cell-free DNA reflect epigenetic regulation

(2015) Maxim Ivanov et al.   BMC GENOMICS

MARK-AGE population: From the human model to new insights

(2015) Miriam Capri et al.   MECHANISMS OF AGEING AND DEVELOPMENT

Noninvasive monitoring of infection and rejection after lung transplantation

(2015) Iwijn De Vlaminck et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments

(2015) Kun Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MCMC Methods for Multi-Response Generalized Linear Mixed Models: TheMCMCglmmRPackage

(2015) Jarrod D. Hadfield   Journal of Statistical Software

Transcriptional landscape of repetitive elements in normal and cancer human cells

(2014) Steven W Criscione et al.   BMC GENOMICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Circulating mitochondrial DNA increases with age and is a familiar trait: Implications for “inflamm-aging”

(2014) Marcello Pinti et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging

(2014) Z. Hu et al.   GENES & DEVELOPMENT

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

3D genome reconstruction from chromosomal contacts

(2014) Annick Lesne et al.   NATURE METHODS

CTCF: an architectural protein bridging genome topology and function

(2014) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Chronic kidney disease and premature ageing

(2014) Jeroen P. Kooman et al.   Nature Reviews Nephrology

Characterization of the role of distinct plasma cell-free DNA species in age-associated inflammation and frailty

(2013) Juulia Jylhävä et al.   AGING CELL

Genomes of replicatively senescent cells undergo global epigenetic changes leading to gene silencing and activation of transposable elements

(2013) Marco De Cecco et al.   AGING CELL

Genome-Wide Identification of Chromatin Transitional Regions Reveals Diverse Mechanisms Defining the Boundary of Facultative Heterochromatin

(2013) Guangyao Li et al.   PLoS One

DNA methylation age of human tissues and cell types

(2013) Steve Horvath   GENOME BIOLOGY

DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing

(2012) K. Chen et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Comprehensive Identification and Annotation of Cell Type-Specific and Ubiquitous CTCF-Binding Sites in the Human Genome

(2012) Hebing Chen et al.   PLoS One

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

Cell-free DNA in the blood as a solid tumor biomarker—A critical appraisal of the literature

(2010) Klaus Jung et al.   CLINICA CHIMICA ACTA

Aging is associated with quantitative and qualitative changes in circulating cell-free DNA: The Vitality 90+ study

(2010) Juulia Jylhävä et al.   MECHANISMS OF AGEING AND DEVELOPMENT

Maternal Plasma DNA Sequencing Reveals the Genome-Wide Genetic and Mutational Profile of the Fetus

(2010) Y. M. D. Lo et al.   Science Translational Medicine

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome

(2008) Yutao Fu et al.   PLoS Genetics

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY