The epigenetic landscape of T cell exhaustion

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

Molecular profiling of CD8 T cells in autochthonous melanoma identifies Maf as driver of exhaustion

(2015) M. Giordano et al.   EMBO JOURNAL

The Transcription Factor NFAT Promotes Exhaustion of Activated CD8 + T Cells

(2015) Gustavo J. Martinez et al.   IMMUNITY

Genetic absence of PD-1 promotes accumulation of terminally differentiated exhausted CD8+T cells

(2015) Pamela M. Odorizzi et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease

(2015) Elizabeta Gjoneska et al.   NATURE

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

(2015) Matthew C. Canver et al.   NATURE

Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells

(2015) Ayal Hendel et al.   NATURE BIOTECHNOLOGY

4-1BB costimulation ameliorates T cell exhaustion induced by tonic signaling of chimeric antigen receptors

(2015) Adrienne H Long et al.   NATURE MEDICINE

Functional footprinting of regulatory DNA

(2015) Jeff Vierstra et al.   NATURE METHODS

Generation of knock-in primary human T cells using Cas9 ribonucleoproteins

(2015) Kathrin Schumann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STAT3, STAT4, NFATc1, and CTCF Regulate PD-1 through Multiple Novel Regulatory Regions in Murine T Cells

(2014) J. W. Austin et al.   JOURNAL OF IMMUNOLOGY

The transcription factor BATF operates as an essential differentiation checkpoint in early effector CD8+ T cells

(2014) Makoto Kurachi et al.   NATURE IMMUNOLOGY

UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions

(2014) Maxwell A. Hume et al.   NUCLEIC ACIDS RESEARCH

Chromatin state dynamics during blood formation

(2014) D. Lara-Astiaso et al.   SCIENCE

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

(2014) J. Vierstra et al.   SCIENCE

Increased Sequence Coverage through Combined Targeting of Variant and Conserved Epitopes Correlates with Control of HIV Replication

(2013) J. Sunshine et al.   JOURNAL OF VIROLOGY

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

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

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

(2012) Travis A. Doering et al.   IMMUNITY

Safety, Activity, and Immune Correlates of Anti–PD-1 Antibody in Cancer

(2012) Suzanne L. Topalian et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2012) M. A. Paley et al.   SCIENCE

Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection

(2012) Matthew R. Henn et al.   PLoS Pathogens

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Transcription factor Foxp1 exerts essential cell-intrinsic regulation of the quiescence of naive T cells

(2011) Xiaoming Feng et al.   NATURE IMMUNOLOGY

Chimeric Antigen Receptor–Modified T Cells in Chronic Lymphoid Leukemia

(2011) David L. Porter et al.   NEW ENGLAND JOURNAL OF MEDICINE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

Transcriptional analysis of HIV-specific CD8+ T cells shows that PD-1 inhibits T cell function by upregulating BATF

(2010) Michael Quigley et al.   NATURE MEDICINE

Ensembl 2011

(2010) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

A Role for the Transcriptional Repressor Blimp-1 in CD8+ T Cell Exhaustion during Chronic Viral Infection

(2009) Haina Shin et al.   IMMUNITY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL