T-cell dysfunction in the glioblastoma microenvironment is mediated by myeloid cells releasing interleukin-10

CellRank for directed single-cell fate mapping

(2022) Marius Lange et al.   NATURE METHODS

Inhibitory CD161 receptor identified in glioma-infiltrating T cells by single-cell analysis

(2021) Nathan D. Mathewson et al.   CELL

SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes

(2021) Marc Elosua-Bayes et al.   NUCLEIC ACIDS RESEARCH

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Glioblastomas acquire myeloid-affiliated transcriptional programs via epigenetic immunoediting to elicit immune evasion

(2021) Ester Gangoso et al.   CELL

Interactions between cancer cells and immune cells drive transitions to mesenchymal-like states in glioblastoma

(2021) Toshiro Hara et al.   CANCER CELL

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

CD4 T-Cell Exhaustion: Does It Exist and What Are Its Roles in Cancer?

(2021) Alexandra M. Miggelbrink et al.   CLINICAL CANCER RESEARCH

Inhibition of metabotropic glutamate receptor III facilitates sensitization to alkylating chemotherapeutics in glioblastoma

(2021) Julian P. Maier et al.   Cell Death & Disease

Understanding the glioblastoma immune microenvironment as basis for the development of new immunotherapeutic strategies

(2020) Ana Rita Pombo Antunes et al.   eLife

Use of Mass Cytometry to Profile Human T Cell Exhaustion

(2020) Frances Winkler et al.   Frontiers in Immunology

Dissecting cellular crosstalk by sequencing physically interacting cells

(2020) Amir Giladi et al.   NATURE BIOTECHNOLOGY

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

Single-cell RNA-seq denoising using a deep count autoencoder

(2019) Gökcen Eraslan et al.   Nature Communications

Single-Cell Transcriptomics of Regulatory T Cells Reveals Trajectories of Tissue Adaptation

(2019) Ricardo J. Miragaia et al.   IMMUNITY

Adaptive plasticity of IL-10+ and IL-35+ Treg cells cooperatively promotes tumor T cell exhaustion

(2019) Deepali V. Sawant et al.   NATURE IMMUNOLOGY

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma

(2019) Cyril Neftel et al.   CELL

Tumor-associated reactive astrocytes aid the evolution of immunosuppressive environment in glioblastoma

(2019) Dieter Henrik Heiland et al.   Nature Communications

SCINA: Semi-Supervised Analysis of Single Cells in Silico

(2019) Zhang et al.   Genes

Astrogliosis Releases Pro-Oncogenic Chitinase 3-Like 1 Causing MAPK Signaling in Glioblastoma

(2019) Julian Wurm et al.   Cancers

Mapping microglia states in the human brain through the integration of high-dimensional techniques

(2019) Roman Sankowski et al.   NATURE NEUROSCIENCE

Neuroprotection after Hemorrhagic Stroke Depends on Cerebral Heme Oxygenase-1

(2019) Sandra Kaiser et al.   Antioxidants

NicheNet: modeling intercellular communication by linking ligands to target genes

(2019) Robin Browaeys et al.   NATURE METHODS

CONICS integrates scRNA-seq with DNA sequencing to map gene expression to tumor sub-clones

(2018) Sören Müller et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

T-cell Dysfunction in Glioblastoma: Applying a New Framework

(2018) Karolina I. Woroniecka et al.   CLINICAL CANCER RESEARCH

T-Cell Exhaustion Signatures Vary with Tumor Type and Are Severe in Glioblastoma

(2018) Karolina Woroniecka et al.   CLINICAL CANCER RESEARCH

STAT3 labels a subpopulation of reactive astrocytes required for brain metastasis

(2018) Neibla Priego et al.   NATURE MEDICINE

Immune Microenvironment in Glioblastoma Subtypes

(2018) Zhihong Chen et al.   Frontiers in Immunology

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Heme Oxygenase-1 as a Modulator of Intestinal Inflammation Development and Progression

(2018) Valentina P. Sebastián et al.   Frontiers in Immunology

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

(2018) Hanjie Li et al.   CELL

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer

(2018) Lei Zhang et al.   NATURE

Rindopepimut with temozolomide for patients with newly diagnosed, EGFRvIII-expressing glioblastoma (ACT IV): a randomised, double-blind, international phase 3 trial

(2017) Michael Weller et al.   LANCET ONCOLOGY

Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq

(2017) Andrew S. Venteicher et al.   SCIENCE

Recurrent glioma clinical trial, CheckMate-143: the game is not over yet

(2017) Anna C. Filley et al.   Oncotarget

Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma

(2017) Spyros Darmanis et al.   Cell Reports

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

(2016) Meromit Singer et al.   CELL

Lag-3, Tim-3, and TIGIT: Co-inhibitory Receptors with Specialized Functions in Immune Regulation

(2016) Ana C. Anderson et al.   IMMUNITY

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

(2016) Se Jin Im et al.   NATURE

Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma

(2016) Itay Tirosh et al.   NATURE

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

(2016) I. Tirosh et al.   SCIENCE

Integrative Modeling Reveals Annexin A2-mediated Epigenetic Control of Mesenchymal Glioblastoma

(2016) Teresia Kling et al.   EBioMedicine

IL-10/HMOX1 Signaling Modulates Cochlear Inflammation via Negative Regulation of MCP-1/CCL2 Expression in Cochlear Fibrocytes

(2015) Jeong-Im Woo et al.   JOURNAL OF IMMUNOLOGY

Blimp1/Prdm1 Functions in Opposition to Irf1 to Maintain Neonatal Tolerance during Postnatal Intestinal Maturation

(2015) Arne W. Mould et al.   PLoS Genetics

Heme oxygenase-1 and anti-inflammatory M2 macrophages

(2014) Yuji Naito et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Microenvironmental Clues for Glioma Immunotherapy

(2014) Michael Platten et al.   Current Neurology and Neuroscience Reports

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

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

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Unique Features of Naive CD8+ T Cell Activation by IL-2

(2013) J.-H. Cho et al.   JOURNAL OF IMMUNOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

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

IL-2 family cytokines: new insights into the complex roles of IL-2 as a broad regulator of T helper cell differentiation

(2011) Wei Liao et al.   CURRENT OPINION IN IMMUNOLOGY

Exhaustion of tumor-specific CD8+ T cells in metastases from melanoma patients

(2011) Lukas Baitsch et al.   JOURNAL OF CLINICAL INVESTIGATION

T cell exhaustion

(2011) E John Wherry   NATURE IMMUNOLOGY

Mild oxidative stress activates Nrf2 in astrocytes, which contributes to neuroprotective ischemic preconditioning

(2010) K. F. Bell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA