The chromatin accessibility signature of human immune aging stems from CD8+T cells

Chromatin states define tumour-specific T cell dysfunction and reprogramming

(2017) Mary Philip et al.   NATURE

Host and Environmental Factors Influencing Individual Human Cytokine Responses

(2016) Rob ter Horst et al.   CELL

Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients

(2016) Romain Banchereau et al.   CELL

Differential Effects of Environmental and Genetic Factors on T and B Cell Immune Traits

(2016) Raul Aguirre-Gamboa et al.   Cell Reports

Epigenetics and aging

(2016) S. Pal et al.   Science Advances

Blood Epigenetic Age may Predict Cancer Incidence and Mortality

(2016) Yinan Zheng et al.   EBioMedicine

Reduced naïve CD8+T-cell priming efficacy in elderly adults

(2015) Olivia Briceño et al.   AGING CELL

Transcriptomic profiles of aging in purified human immune cells

(2015) Lindsay M Reynolds et al.   BMC GENOMICS

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

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Epigenetic regulation of ageing: linking environmental inputs to genomic stability

(2015) Bérénice A. Benayoun et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Widespread seasonal gene expression reveals annual differences in human immunity and physiology

(2015) Xaquin Castro Dopico et al.   Nature Communications

Age-related profiling of DNA methylation in CD8+ T cells reveals changes in immune response and transcriptional regulator genes

(2015) Liina Tserel et al.   Scientific Reports

PathVisio 3: An Extendable Pathway Analysis Toolbox

(2015) Martina Kutmon et al.   PLoS Computational Biology

An Integrative Multi-scale Analysis of the Dynamic DNA Methylation Landscape in Aging

(2015) Tian Yuan et al.   PLoS Genetics

Individuality and Variation of Personal Regulomes in Primary Human T Cells

(2015) Kun Qu et al.   Cell Systems

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Geroscience: Linking Aging to Chronic Disease

(2014) Brian K. Kennedy et al.   CELL

Inflammation, ageing and chronic disease

(2014) Graham Pawelec et al.   CURRENT OPINION IN IMMUNOLOGY

New advances in CMV and immunosenescence

(2014) Paolo Sansoni et al.   EXPERIMENTAL GERONTOLOGY

HIF Transcription Factors, Inflammation, and Immunity

(2014) Asis Palazon et al.   IMMUNITY

Formation of IL-7R high and IL-7R low CD8 T Cells during Infection Is Regulated by the Opposing Functions of GABP  and Gfi-1

(2014) A. Chandele et al.   JOURNAL OF IMMUNOLOGY

Aging and Cytomegalovirus Infection Differentially and Jointly Affect Distinct Circulating T Cell Subsets in Humans

(2014) A. M. Wertheimer et al.   JOURNAL OF IMMUNOLOGY

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

(2014) Richard I Sherwood et al.   NATURE BIOTECHNOLOGY

Basal NF- B controls IL-7 responsiveness of quiescent naive T cells

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

Cytomegalovirus infection is associated with increased mortality in the older population

(2013) George M. Savva et al.   AGING CELL

The Hallmarks of Aging

(2013) Carlos López-Otín et al.   CELL

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Human plasma cells express granzyme B

(2013) Wei Xu et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Cellular senescence and the senescent secretory phenotype: therapeutic opportunities

(2013) Tamara Tchkonia et al.   JOURNAL OF CLINICAL INVESTIGATION

Understanding immunosenescence to improve responses to vaccines

(2013) Jörg J Goronzy et al.   NATURE IMMUNOLOGY

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

The Janus Head of T Cell Aging – Autoimmunity and Immunodeficiency

(2013) Jörg J. Goronzy et al.   Frontiers in Immunology

Human T Cell Aging and the Impact of Persistent Viral Infections

(2013) T. Fülöp et al.   Frontiers in Immunology

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

Aging, Rejuvenation, and Epigenetic Reprogramming: Resetting the Aging Clock

(2012) Thomas A. Rando et al.   CELL

Aging effects on DNA methylation modules in human brain and blood tissue

(2012) Steve Horvath et al.   GENOME BIOLOGY

Human aging is characterized by focused changes in gene expression and deregulation of alternative splicing

(2011) Lorna W. Harries et al.   AGING CELL

MotifMap: integrative genome-wide maps of regulatory motif sites for model species

(2011) Kenneth Daily et al.   BMC BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Evidence for age-related and individual-specific changes in DNA methylation profile of mononuclear cells during early immune development in humans

(2011) David J. Martino et al.   Epigenetics

T cell exhaustion

(2011) E John Wherry   NATURE IMMUNOLOGY

WikiPathways: building research communities on biological pathways

(2011) T. Kelder et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Phase I Study of Recombinant Human Interleukin-7 Administration in Subjects with Refractory Malignancy

(2010) C. Sportes et al.   CLINICAL CANCER RESEARCH

Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains

(2010) V. K. Rakyan et al.   GENOME RESEARCH

Variation of human natural killer cell phenotypes with age: Identification of a unique KLRG1-negative subset

(2010) Richard P.G. Hayhoe et al.   HUMAN IMMUNOLOGY

Ability to Walk 1/4 Mile Predicts Subsequent Disability, Mortality, and Health Care Costs

(2010) Susan E. Hardy et al.   JOURNAL OF GENERAL INTERNAL MEDICINE

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

TLR recognition of self nucleic acids hampers glucocorticoid activity in lupus

(2010) Cristiana Guiducci et al.   NATURE

An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis

(2010) Matthew P. R. Berry et al.   NATURE

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Age-related alterations of gene expression patterns in human CD8+T cells

(2009) Jia-Ning Cao et al.   AGING CELL

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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

CD2 Distinguishes Two Subsets of Human Plasmacytoid Dendritic Cells with Distinct Phenotype and Functions

(2009) T. Matsui et al.   JOURNAL OF IMMUNOLOGY

Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories

(2008) Michael J Boedigheimer et al.   BMC GENOMICS

A Modular Analysis Framework for Blood Genomics Studies: Application to Systemic Lupus Erythematosus

(2008) Damien Chaussabel et al.   IMMUNITY

Administration of rhIL-7 in humans increases in vivo TCR repertoire diversity by preferential expansion of naive T cell subsets

(2008) Claude Sportès et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY