A unified atlas of CD8 T cell dysfunctional states in cancer and infection

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

(2020) Jean-Christophe Beltra et al.   IMMUNITY

Heterogenous Populations of Tissue-Resident CD8+ T Cells Are Generated in Response to Infection and Malignancy

(2020) J. Justin Milner et al.   IMMUNITY

Lineage tracing meets single-cell omics: opportunities and challenges

(2020) Daniel E. Wagner et al.   NATURE REVIEWS GENETICS

Early precursors and molecular determinants of tissue-resident memory CD8+ T lymphocytes revealed by single-cell RNA sequencing

(2020) Nadia S. Kurd et al.   Science Immunology

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Early precursor T cells establish and propagate T cell exhaustion in chronic infection

(2020) Daniel T. Utzschneider et al.   NATURE IMMUNOLOGY

Transcription factor Foxp1 regulates Foxp3 chromatin binding and coordinates regulatory T cell function

(2019) Catherine Konopacki et al.   NATURE IMMUNOLOGY

T cell stemness and dysfunction in tumors are triggered by a common mechanism

(2019) Suman Kumar Vodnala et al.   SCIENCE

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

(2019) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

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

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

NR4A transcription factors limit CAR T cell function in solid tumours

(2019) Joyce Chen et al.   NATURE

CD8 T Cell Exhaustion During Chronic Viral Infection and Cancer

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

Natural Genetic Variation Reveals Key Features of Epigenetic and Transcriptional Memory in Virus-Specific CD8 T Cells

(2019) Joris van der Veeken et al.   IMMUNITY

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

(2019) Uku Raudvere et al.   NUCLEIC ACIDS RESEARCH

Heterogeneity and fate choice: T cell exhaustion in cancer and chronic infections

(2019) Mary Philip et al.   CURRENT OPINION IN IMMUNOLOGY

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

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

(2019) Ansuman T. Satpathy et al.   NATURE BIOTECHNOLOGY

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

(2019) Zeyu Chen et al.   IMMUNITY

CXCR5+PD-1+ follicular helper CD8 T cells control B cell tolerance

(2019) Yuhong Chen et al.   Nature Communications

CD8 T Cell Exhaustion in Chronic Infection and Cancer: Opportunities for Interventions

(2018) Masao Hashimoto et al.   Annual Review of Medicine

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

(2018) Elham Azizi et al.   CELL

Human T Cell Development, Localization, and Function throughout Life

(2018) Brahma V. Kumar et al.   IMMUNITY

Understanding Subset Diversity in T Cell Memory

(2018) Stephen C. Jameson et al.   IMMUNITY

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

(2018) Bertram Bengsch et al.   IMMUNITY

Cancer immunotherapy using checkpoint blockade

(2018) Antoni Ribas et al.   SCIENCE

High-dimensional single cell analysis identifies stem-like cytotoxic CD8+T cells infiltrating human tumors

(2018) Jolanda Brummelman et al.   JOURNAL OF EXPERIMENTAL MEDICINE

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma

(2018) Moshe Sade-Feldman et al.   CELL

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

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

Cutting Edge: Chromatin Accessibility Programs CD8 T Cell Memory

(2017) Christopher D. Scharer et al.   JOURNAL OF IMMUNOLOGY

Runx3 programs CD8+ T cell residency in non-lymphoid tissues and tumours

(2017) J. Justin Milner et al.   NATURE

Chromatin states define tumour-specific T cell dysfunction and reprogramming

(2017) Mary Philip et al.   NATURE

Exhaustion-associated regulatory regions in CD8+tumor-infiltrating T cells

(2017) Giuliana P. Mognol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An integrated model for detecting significant chromatin interactions from high-resolution Hi-C data

(2017) Mark Carty et al.   Nature Communications

An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

(2017) Peter J Skene et al.   eLife

Hallmarks of Tissue-Resident Lymphocytes

(2016) Xiying Fan et al.   CELL

Tumor-Specific T Cell Dysfunction Is a Dynamic Antigen-Driven Differentiation Program Initiated Early during Tumorigenesis

(2016) Andrea Schietinger et al.   IMMUNITY

CD8 + T Cells Utilize Highly Dynamic Enhancer Repertoires and Regulatory Circuitry in Response to Infections

(2016) Bing He et al.   IMMUNITY

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

Dynamic Changes in Chromatin Accessibility Occur in CD8 + T Cells Responding to Viral Infection

(2016) James P. Scott-Browne et al.   IMMUNITY

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

(2016) Se Jin Im et al.   NATURE

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

The epigenetic landscape of T cell exhaustion

(2016) D. R. Sen et al.   SCIENCE

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

(2016) K. E. Pauken et al.   SCIENCE

Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance

(2015) James J Crowley et al.   NATURE GENETICS

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

EM for regularized zero-inflated regression models with applications to postoperative morbidity after cardiac surgery in children

(2014) Zhu Wang et al.   STATISTICS IN MEDICINE

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC 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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY