Transcript-indexed ATAC-seq for precision immune profiling

Identifying specificity groups in the T cell receptor repertoire

(2017) Jacob Glanville et al.   NATURE

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements

(2017) Maxwell R Mumbach et al.   NATURE GENETICS

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state

(2017) Shaked Afik et al.   NUCLEIC ACIDS RESEARCH

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

(2016) M Ryan Corces et al.   NATURE GENETICS

T cell fate and clonality inference from single-cell transcriptomes

(2016) Michael J T Stubbington et al.   NATURE METHODS

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity

(2015) Jellert T. Gaublomme et al.   CELL

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

(2015) Franziska Paul et al.   CELL

T-cell clonality assessment by next-generation sequencing improves detection sensitivity in mycosis fungoides

(2015) Kari E. Sufficool et al.   JOURNAL OF THE AMERICAN ACADEMY OF DERMATOLOGY

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Genomic landscape of cutaneous T cell lymphoma

(2015) Jaehyuk Choi et al.   NATURE GENETICS

Genomic analysis of mycosis fungoides and Sézary syndrome identifies recurrent alterations in TNFR2

(2015) Alexander Ungewickell et al.   NATURE GENETICS

TH17 cells promote microbial killing and innate immune sensing of DNA via interleukin 26

(2015) Stephan Meller et al.   NATURE IMMUNOLOGY

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Dengue virus infection elicits highly polarized CX3CR1+cytotoxic CD4+T cells associated with protective immunity

(2015) Daniela Weiskopf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

TCR sequencing facilitates diagnosis and identifies mature T cells as the cell of origin in CTCL

(2015) Ilan R. Kirsch et al.   Science Translational Medicine

Deconstructing the Peptide-MHC Specificity of T Cell Recognition

(2014) Michael E. Birnbaum et al.   CELL

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

(2014) Alex K. Shalek et al.   NATURE

Linking T-cell receptor sequence to functional phenotype at the single-cell level

(2014) Arnold Han et al.   NATURE BIOTECHNOLOGY

Beyond model antigens: high-dimensional methods for the analysis of antigen-specific T cells

(2014) Evan W Newell et al.   NATURE BIOTECHNOLOGY

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

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

Minimal Residual Disease Monitoring with High-Throughput Sequencing of T Cell Receptors in Cutaneous T Cell Lymphoma

(2013) W.-K. Weng et al.   Science Translational Medicine

A Validated Regulatory Network for Th17 Cell Specification

(2012) Maria Ciofani et al.   CELL

Human Blood CXCR5+CD4+ T Cells Are Counterparts of T Follicular Cells and Contain Specific Subsets that Differentially Support Antibody Secretion

(2011) Rimpei Morita et al.   IMMUNITY

Regulatory T cells and immunodeficiency in mycosis fungoides and Sézary syndrome

(2011) T Krejsgaard et al.   LEUKEMIA

A critical role for TCF-1 in T-lineage specification and differentiation

(2011) Brittany Nicole Weber et al.   NATURE

Transcription factor c-Maf mediates the TGF-β-dependent suppression of IL-22 production in TH17 cells

(2011) Sascha Rutz et al.   NATURE IMMUNOLOGY

A human memory T cell subset with stem cell–like properties

(2011) Luca Gattinoni et al.   NATURE MEDICINE

A peripheral CD4+T cell precursor for naive, memory, and regulatory T cells

(2010) Chunfang Zhao et al.   JOURNAL OF EXPERIMENTAL MEDICINE

The AP-1 transcription factor Batf controls TH17 differentiation

(2009) Barbara U. Schraml et al.   NATURE

The Biological Functions of T Helper 17 Cell Effector Cytokines in Inflammation

(2008) Wenjun Ouyang et al.   IMMUNITY

T Helper 17 Lineage Differentiation Is Programmed by Orphan Nuclear Receptors RORα and RORγ

(2008) Xuexian O. Yang et al.   IMMUNITY

The costimulatory molecule ICOS regulates the expression of c-Maf and IL-21 in the development of follicular T helper cells and TH-17 cells

(2008) Aurelie T Bauquet et al.   NATURE IMMUNOLOGY

The Usefulness of CD26 in Flow Cytometric Analysis of Peripheral Blood in Sézary Syndrome

(2007) Katalin Kelemen et al.   AMERICAN JOURNAL OF CLINICAL PATHOLOGY