Mapping the evolution of T cell states during response and resistance to adoptive cellular therapy

Defining the Role of Donor Lymphocyte Infusion in High-Risk Hematologic Malignancies

(2021) Christoph Schmid et al.   JOURNAL OF CLINICAL ONCOLOGY

Single-cell genomic approaches for developing the next generation of immunotherapies

(2020) Ido Yofe et al.   NATURE MEDICINE

ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation

(2020) Jake J. Reske et al.   Epigenetics & Chromatin

Activation of CAR and non-CAR T cells within the tumor microenvironment following CAR T cell therapy

(2020) Pei-Hsuan Chen et al.   JCI Insight

Distinct evolutionary paths in chronic lymphocytic leukemia during resistance to the graft-versus-leukemia effect

(2020) Pavan Bachireddy et al.   Science Translational Medicine

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

(2019) Moshe Sade-Feldman et al.   CELL

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

CD73 expression on effector T cells sustained by TGF-β facilitates tumor resistance to anti-4-1BB/CD137 therapy

(2019) Siqi Chen et al.   Nature Communications

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

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

Long-Term Temperature Stress in the Coral Model Aiptasia Supports the “Anna Karenina Principle” for Bacterial Microbiomes

(2019) Hanin Ibrahim Ahmed et al.   Frontiers in Microbiology

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

Clonal replacement of tumor-specific T cells following PD-1 blockade

(2019) Kathryn E. Yost et al.   NATURE MEDICINE

RNase H–dependent PCR-enabled T-cell receptor sequencing for highly specific and efficient targeted sequencing of T-cell receptor mRNA for single-cell and repertoire analysis

(2019) Shuqiang Li et al.   Nature Protocols

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

(2019) Zeyu Chen et al.   IMMUNITY

VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium

(2019) Dmitry V Bagaev et al.   NUCLEIC ACIDS RESEARCH

CD4+ T Cell Help Is Required for the Formation of a Cytolytic CD8+ T Cell Subset that Protects against Chronic Infection and Cancer

(2019) Ryan Zander et al.   IMMUNITY

Reversal of T Cell Exhaustion by the First Donor Lymphocyte Infusion Is Associated with the Persistently Effective Antileukemic Responses in Patients with Relapsed AML after Allo-HSCT

(2018) Long Liu et al.   BIOLOGY OF BLOOD AND MARROW TRANSPLANTATION

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

(2018) Elham Azizi et al.   CELL

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

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

Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma

(2018) Hanjie Li et al.   CELL

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

Variational Inference: A Review for Statisticians

(2017) David M. Blei et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Origin and differentiation of human memory CD8 T cells after vaccination

(2017) Rama S. Akondy et al.   NATURE

Effector CD8 T cells dedifferentiate into long-lived memory cells

(2017) Ben Youngblood et al.   NATURE

T memory stem cells in health and disease

(2017) Luca Gattinoni et al.   NATURE MEDICINE

Dynamic versus static biomarkers in cancer immune checkpoint blockade: unravelling complexity

(2017) W. Joost Lesterhuis et al.   NATURE REVIEWS DRUG DISCOVERY

TRACERx Renal: tracking renal cancer evolution through therapy

(2017) Samra Turajlic et al.   Nature Reviews Urology

Rescue of exhausted CD8 T cells by PD-1–targeted therapies is CD28-dependent

(2017) Alice O. Kamphorst et al.   SCIENCE

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

(2016) Diego Adhemar Jaitin et al.   CELL

A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells

(2016) Meromit Singer et al.   CELL

Abundant cytomegalovirus (CMV) reactive clonotypes in the CD8+T cell receptor alpha repertoire following allogeneic transplantation

(2016) C. S. Link et al.   CLINICAL AND EXPERIMENTAL IMMUNOLOGY

Impact of the X Chromosome and sex on regulatory variation

(2016) Kimberly R. Kukurba et al.   GENOME RESEARCH

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

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

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

(2016) M Ryan Corces et al.   NATURE GENETICS

CXCR5+ follicular cytotoxic T cells control viral infection in B cell follicles

(2016) Yew Ann Leong et al.   NATURE IMMUNOLOGY

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

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

(2015) Jacob H. Levine et al.   CELL

Functional coordination and HuR-mediated regulation of mRNA stability during T cell activation

(2015) Jeff G. Blackinton et al.   NUCLEIC ACIDS RESEARCH

Understanding anti-leukemia responses to donor lymphocyte infusion

(2014) Pavan Bachireddy et al.   OncoImmunology

Reversal of in situ T-cell exhaustion during effective human antileukemia responses to donor lymphocyte infusion

(2013) P. Bachireddy et al.   BLOOD

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

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

GATA-3 Regulates the Homeostasis and Activation of CD8+ T Cells

(2012) T.-S. Tai et al.   JOURNAL OF IMMUNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) M. A. Paley et al.   SCIENCE

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The ethical use of mandatory research biopsies

(2011) Erin M. Olson et al.   Nature Reviews Clinical Oncology

Antigen-specific CD4 T-cell help rescues exhausted CD8 T cells during chronic viral infection

(2011) R. D. Aubert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Graft-versus-Leukemia Antigen CML66 Elicits Coordinated B-Cell and T-Cell Immunity after Donor Lymphocyte Infusion

(2010) W. Zhang et al.   CLINICAL CANCER RESEARCH

Regulation of CD45 Alternative Splicing by Heterogeneous Ribonucleoprotein, hnRNPLL

(2008) S. Oberdoerffer et al.   SCIENCE

Exploratory and Confirmatory Factor Analysis: Understanding Concepts and Applications

(2008) Linda Reichwein Zientek   STRUCTURAL EQUATION MODELING-A MULTIDISCIPLINARY JOURNAL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY