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

Precursors for Nonlymphoid-Tissue Treg Cells Reside in Secondary Lymphoid Organs and Are Programmed by the Transcription Factor BATF

(2020) Michael Delacher et al.   IMMUNITY

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

(2020) Mirjana Efremova et al.   Nature Protocols

Developmental Relationships of Four Exhausted CD8+ T Cell Subsets Reveals Underlying Transcriptional and Epigenetic Landscape Control Mechanisms

(2020) Jean-Christophe Beltra et al.   IMMUNITY

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

(2020)   NATURE

Ageing hallmarks exhibit organ-specific temporal signatures

(2020) Nicholas Schaum et al.   NATURE

Single-cell atlas of colonic CD8+ T cells in ulcerative colitis

(2020) Daniele Corridoni et al.   NATURE MEDICINE

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

(2019) Ilias Angelidis et al.   Nature Communications

A clinically meaningful metric of immune age derived from high-dimensional longitudinal monitoring

(2019) Ayelet Alpert et al.   NATURE MEDICINE

Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry

(2019) Fan Zhang et al.   NATURE IMMUNOLOGY

TOX reinforces the phenotype and longevity of exhausted T cells in chronic viral infection

(2019) Francesca Alfei et al.   NATURE

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

(2019) Ben W. Dulken et al.   NATURE

TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion

(2019) Omar Khan et al.   NATURE

Senescent cells evade immune clearance via HLA-E-mediated NK and CD8+ T cell inhibition

(2019) Branca I. Pereira et al.   Nature Communications

Single-cell transcriptomic profiling of the aging mouse brain

(2019) Methodios Ximerakis et al.   NATURE NEUROSCIENCE

Aging promotes reorganization of the CD4 T cell landscape toward extreme regulatory and effector phenotypes

(2019) Yehezqel Elyahu et al.   Science Advances

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

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

TCF-1-Centered Transcriptional Network Drives an Effector versus Exhausted CD8 T Cell-Fate Decision

(2019) Zeyu Chen et al.   IMMUNITY

Heterogeneity in old fibroblasts is linked to variability in reprogramming and wound healing

(2019) Salah Mahmoudi et al.   NATURE

Single-cell transcriptomics reveals expansion of cytotoxic CD4 T cells in supercentenarians

(2019) Kosuke Hashimoto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Minimizing Batch Effects in Mass Cytometry Data

(2019) Ronald P. Schuyler et al.   Frontiers in Immunology

Epigenomic-Guided Mass Cytometry Profiling Reveals Disease-Specific Features of Exhausted CD8 T Cells

(2018) Bertram Bengsch et al.   IMMUNITY

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Age-Related Decline in Primary CD8 + T Cell Responses Is Associated with the Development of Senescence in Virtual Memory CD8 + T Cells

(2018) Kylie M. Quinn et al.   Cell Reports

Successful and Maladaptive T Cell Aging

(2017) Jörg J. Goronzy et al.   IMMUNITY

Granzyme K-deficient mice show no evidence of impaired antiviral immunity

(2017) Lars T Joeckel et al.   IMMUNOLOGY AND CELL BIOLOGY

A Hard(y) Look at B-1 Cell Development and Function

(2017) Nicole Baumgarth   JOURNAL OF IMMUNOLOGY

Antigen receptor repertoire profiling from RNA-seq data

(2017) Dmitriy A Bolotin et al.   NATURE BIOTECHNOLOGY

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

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

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

Cell lines generated from a chronic lymphocytic leukemia mouse model exhibit constitutive Btk and Akt signaling

(2017) Simar Pal Singh et al.   Oncotarget

Epigenetic stability of exhausted T cells limits durability of reinvigoration by PD-1 blockade

(2016) K. E. Pauken et al.   SCIENCE

Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data: Table 1.

(2015) Namita T. Gupta et al.   BIOINFORMATICS

The BioMart community portal: an innovative alternative to large, centralized data repositories

(2015) Damian Smedley et al.   NUCLEIC ACIDS RESEARCH

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

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

The Hallmarks of Aging

(2013) Carlos López-Otín et al.   CELL

Causes, consequences, and reversal of immune system aging

(2013) Encarnacion Montecino-Rodriguez et al.   JOURNAL OF CLINICAL INVESTIGATION

Cutting Edge: Central Memory CD8 T Cells in Aged Mice Are Virtual Memory Cells

(2013) B.-C. Chiu et al.   JOURNAL OF IMMUNOLOGY

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

(2013) El-ad David Amir et al.   NATURE BIOTECHNOLOGY

Ageing as a Risk Factor for Disease

(2012) Teresa Niccoli et al.   CURRENT BIOLOGY

Network Analysis Reveals Centrally Connected Genes and Pathways Involved in CD8+ T Cell Exhaustion versus Memory

(2012) Travis A. Doering et al.   IMMUNITY

Defective CD8 T Cell Responses in Aged Mice Are Due to Quantitative and Qualitative Changes in Virus-Specific Precursors

(2012) V. Decman et al.   JOURNAL OF IMMUNOLOGY

A B-cell subset uniquely responsive to innate stimuli accumulates in aged mice

(2011) Y. Hao et al.   BLOOD

Mouse granzyme K has pro-inflammatory potential

(2011) L T Joeckel et al.   CELL DEATH AND DIFFERENTIATION

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

Granzyme K Displays Highly Restricted Substrate Specificity That Only Partially Overlaps with Granzyme A

(2008) Niels Bovenschen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identification of two major types of age-associated CD8 clonal expansions with highly divergent properties

(2008) E. T. Clambey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA