Memory-like HCV-specific CD8+ T cells retain a molecular scar after cure of chronic HCV infection

Targeting p53 and histone methyltransferases restores exhausted CD8+ T cells in HCV infection

(2020) Valeria Barili et al.   Nature Communications

Intratumoral Tcf1+PD-1+CD8+ T Cells with Stem-like Properties Promote Tumor Control in Response to Vaccination and Checkpoint Blockade Immunotherapy

(2019) Imran Siddiqui et al.   IMMUNITY

Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade

(2019) Brian C. Miller et al.   NATURE IMMUNOLOGY

CD8 T Cell Exhaustion During Chronic Viral Infection and Cancer

(2019) Laura M. McLane et al.   Annual Review of Immunology

Elimination of Hepatitis C Virus has limited impact on the functional and mitochondrial impairment of HCV-specific CD8+ T cell responses

(2019) Amare Aregay et al.   JOURNAL OF HEPATOLOGY

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

(2019) Francesca Alfei et al.   NATURE

TOX is a critical regulator of tumour-specific T cell differentiation

(2019) Andrew C. Scott et al.   NATURE

TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion

(2019) Omar Khan et al.   NATURE

Single-cell RNA-seq reveals TOX as a key regulator of CD8+ T cell persistence in chronic infection

(2019) Chen Yao et al.   NATURE IMMUNOLOGY

Deep immune profiling by mass cytometry links human T and NK cell differentiation and cytotoxic molecule expression patterns

(2018) Bertram Bengsch et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data

(2018) Josip S Herman et al.   NATURE METHODS

Association Between Expression Level of PD1 by Tumor-Infiltrating CD8+ T Cells and Features of Hepatocellular Carcinoma

(2018) Hyung-Don Kim et al.   GASTROENTEROLOGY

Transcription Factor IRF4 Promotes CD8 + T Cell Exhaustion and Limits the Development of Memory-like T Cells during Chronic Infection

(2017) Kevin Man et al.   IMMUNITY

Early Transcriptional Divergence Marks Virus-Specific Primary Human CD8 + T Cells in Chronic versus Acute Infection

(2017) David Wolski et al.   IMMUNITY

Chromatin states define tumour-specific T cell dysfunction and reprogramming

(2017) Mary Philip et al.   NATURE

Targeting mitochondrial dysfunction can restore antiviral activity of exhausted HBV-specific CD8 T cells in chronic hepatitis B

(2017) Paola Fisicaro et al.   NATURE MEDICINE

TCF1+ hepatitis C virus-specific CD8+ T cells are maintained after cessation of chronic antigen stimulation

(2017) Dominik Wieland et al.   Nature Communications

De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

(2016) Dominic Grün et al.   Cell Stem Cell

T Cell Factor 1-Expressing Memory-like CD8 + T Cells Sustain the Immune Response to Chronic Viral Infections

(2016) Daniel T. Utzschneider et al.   IMMUNITY

Follicular CXCR5-expressing CD8+ T cells curtail chronic viral infection

(2016) Ran He et al.   NATURE

Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy

(2016) Se Jin Im et al.   NATURE

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

Memory re-differentiation and reduced lymphocyte activation in chronic HCV-infected patients receiving direct-acting antivirals

(2015) M. A. Burchill et al.   JOURNAL OF VIRAL HEPATITIS

MiXCR: software for comprehensive adaptive immunity profiling

(2015) Dmitriy A Bolotin et al.   NATURE METHODS

Dysfunctional CD8+T cells in hepatitis B and C are characterized by a lack of antigen-specific T-bet induction

(2014) Peter D. Kurktschiev et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Restoration of HCV-specific CD8+ T cell function by interferon-free therapy

(2014) Bianca Martin et al.   JOURNAL OF HEPATOLOGY

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

T cells maintain an exhausted phenotype after antigen withdrawal and population reexpansion

(2013) Daniel T Utzschneider et al.   NATURE IMMUNOLOGY

RNA-SeQC: RNA-seq metrics for quality control and process optimization

(2012) David S. DeLuca et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

(2012) Travis A. Doering et al.   IMMUNITY

Progressive Loss of Memory T Cell Potential and Commitment to Exhaustion during Chronic Viral Infection

(2012) J. M. Angelosanto et al.   JOURNAL OF VIROLOGY

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Progenitor and Terminal Subsets of CD8+ T Cells Cooperate to Contain Chronic Viral Infection

(2012) M. A. Paley et al.   SCIENCE

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Comparison of Immune Restoration in Early versus Late Alpha Interferon Therapy against Hepatitis C Virus

(2010) M. S. Abdel-Hakeem et al.   JOURNAL OF VIROLOGY

Coexpression of PD-1, 2B4, CD160 and KLRG1 on Exhausted HCV-Specific CD8+ T Cells Is Linked to Antigen Recognition and T Cell Differentiation

(2010) Bertram Bengsch et al.   PLoS Pathogens

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS