Glioma progression is shaped by genetic evolution and microenvironment interactions

Single-cell RNA sequencing reveals functional heterogeneity of glioma-associated brain macrophages

(2021) Natalia Ochocka et al.   Nature Communications

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

(2021) Ester Gangoso et al.   CELL

Single-cell profiling of myeloid cells in glioblastoma across species and disease stage reveals macrophage competition and specialization

(2021) Ana Rita Pombo Antunes et al.   NATURE NEUROSCIENCE

Single-cell characterization of macrophages in glioblastoma reveals MARCO as a mesenchymal pro-tumor marker

(2021) Andrew X. Chen et al.   Genome Medicine

Perspective of mesenchymal transformation in glioblastoma

(2021) Yona Kim et al.   Acta Neuropathologica Communications

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

(2021) Toshiro Hara et al.   CANCER CELL

Radiotherapy is associated with a deletion signature that contributes to poor outcomes in patients with cancer

(2021) Emre Kocakavuk et al.   NATURE GENETICS

Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response

(2021) Kevin C. Johnson et al.   NATURE GENETICS

Outer Radial Glia-like Cancer Stem Cells Contribute to Heterogeneity of Glioblastoma

(2020) Aparna Bhaduri et al.   Cell Stem Cell

Interrogation of the Microenvironmental Landscape in Brain Tumors Reveals Disease-Specific Alterations of Immune Cells

(2020) Florian Klemm et al.   CELL

CD8+ T-cell-mediated immunoediting influences genomic evolution and immune evasion in murine gliomas

(2020) Joshua Robert Kane et al.   CLINICAL CANCER RESEARCH

Visualizing and interpreting cancer genomics data via the Xena platform

(2020) Mary J. Goldman et al.   NATURE BIOTECHNOLOGY

Glioblastoma in Adults: A Society for Neuro-Oncology (SNO) and European Society of Neuro-Oncology (EANO) Consensus Review on Current Management and Future Directions

(2020) Patrick Y Wen et al.   NEURO-ONCOLOGY

Surveying brain tumor heterogeneity by single-cell RNA sequencing of multi-sector biopsies

(2020) Kai Yu et al.   National Science Review

iGLASS: Imaging integration into the Glioma Longitudinal AnalySiS Consortium

(2020) S Bakas et al.   NEURO-ONCOLOGY

Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy

(2020) Charles P. Couturier et al.   Nature Communications

Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma

(2019) Junfei Zhao et al.   NATURE MEDICINE

Neoadjuvant anti-PD-1 immunotherapy promotes a survival benefit with intratumoral and systemic immune responses in recurrent glioblastoma

(2019) Timothy F. Cloughesy et al.   NATURE MEDICINE

Neoantigen-directed immune escape in lung cancer evolution

(2019) Rachel Rosenthal et al.   NATURE

Evolutionary Trajectories of IDHWT Glioblastomas Reveal a Common Path of Early Tumorigenesis Instigated Years ahead of Initial Diagnosis

(2019) Verena Körber et al.   CANCER CELL

Molecular Pathology of Tumors of the Central Nervous System

(2019) B W Kristensen et al.   ANNALS OF ONCOLOGY

Determining cell type abundance and expression from bulk tissues with digital cytometry

(2019) Aaron M. Newman et al.   NATURE BIOTECHNOLOGY

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

Electrical and synaptic integration of glioma into neural circuits

(2019) Humsa S. Venkatesh et al.   NATURE

Glutamatergic synaptic input to glioma cells drives brain tumour progression

(2019) Varun Venkataramani et al.   NATURE

The phenotypes of proliferating glioblastoma cells reside on a single axis of variation

(2019) Lin Wang et al.   Cancer Discovery

Longitudinal molecular trajectories of diffuse glioma in adults

(2019) Floris P. Barthel et al.   NATURE

OUP accepted manuscript

(2018)   BIOINFORMATICS

IL-1 receptor antagonist controls transcriptional signature of inflammation in patients with metastatic breast cancer

(2018) Te-Chia Wu et al.   CANCER RESEARCH

Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer

(2018) Allen W. Zhang et al.   CELL

Humanized mice in studying efficacy and mechanisms of PD-1-targeted cancer immunotherapy

(2018) Minan Wang et al.   FASEB JOURNAL

Cancer-Cell-Intrinsic Mechanisms Shaping the Tumor Immune Landscape

(2018) Max D. Wellenstein et al.   IMMUNITY

Glioma through the looking GLASS: molecular evolution of diffuse gliomas and the Glioma Longitudinal Analysis Consortium

(2018) et al.   NEURO-ONCOLOGY

An anatomic transcriptional atlas of human glioblastoma

(2018) Ralph B. Puchalski et al.   SCIENCE

Genetic Mechanisms of Immune Evasion in Colorectal Cancer

(2018) Catherine S. Grasso et al.   Cancer Discovery

Single-cell transcriptome analysis of lineage diversity in high-grade glioma

(2018) Jinzhou Yuan et al.   Genome Medicine

How to analyse the spatiotemporal tumour samples needed to investigate cancer evolution: A case study using paired primary and recurrent glioblastoma

(2017) Alastair Droop et al.   INTERNATIONAL JOURNAL OF CANCER

Targeting neuronal activity-regulated neuroligin-3 dependency in high-grade glioma

(2017) Humsa S. Venkatesh et al.   NATURE

Oncostatin M promotes cancer cell plasticity through cooperative STAT3-SMAD3 signaling

(2017) D J Junk et al.   ONCOGENE

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

(2017) Andrew S. Venteicher et al.   SCIENCE

The 2016 World Health Organization Classification of Tumors of the Central Nervous System: a summary

(2016) David N. Louis et al.   ACTA NEUROPATHOLOGICA

Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma

(2016) Michele Ceccarelli et al.   CELL

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

(2016) Itay Tirosh et al.   NATURE

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Clonal evolution of glioblastoma under therapy

(2016) Jiguang Wang et al.   NATURE GENETICS

pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens

(2016) Jasreet Hundal et al.   Genome Medicine

Spatiotemporal Evolution of the Primary Glioblastoma Genome

(2015) Jinkuk Kim et al.   CANCER CELL

DNA Methylation and Somatic Mutations Converge on the Cell Cycle and Define Similar Evolutionary Histories in Brain Tumors

(2015) Tali Mazor et al.   CANCER CELL

Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity

(2015) Michael S. Rooney et al.   CELL

Neuronal Activity Promotes Glioma Growth through Neuroligin-3 Secretion

(2015) Humsa S. Venkatesh et al.   CELL

Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution

(2015) Hoon Kim et al.   GENOME RESEARCH

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas

(2015)   NEW ENGLAND JOURNAL OF MEDICINE

A draft network of ligand–receptor-mediated multicellular signalling in human

(2015) Jordan A. Ramilowski et al.   Nature Communications

OptiType: precision HLA typing from next-generation sequencing data

(2014) András Szolek et al.   BIOINFORMATICS

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data

(2014) Gavin Ha et al.   GENOME RESEARCH

Transcriptome-Based Network Analysis Reveals a Spectrum Model of Human Macrophage Activation

(2014) Jia Xue et al.   IMMUNITY

MRI-localized biopsies reveal subtype-specific differences in molecular and cellular composition at the margins of glioblastoma

(2014) B. J. Gill et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mesenchymal Differentiation Mediated by NF-κB Promotes Radiation Resistance in Glioblastoma

(2013) Krishna P.L. Bhat et al.   CANCER CELL

The Somatic Genomic Landscape of Glioblastoma

(2013) Cameron W. Brennan et al.   CELL

The Tumor Microenvironment Strongly Impacts Master Transcriptional Regulators and Gene Expression Class of Glioblastoma

(2012) Lee A.D. Cooper et al.   AMERICAN JOURNAL OF PATHOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Histo-Cytometry: A Method for Highly Multiplex Quantitative Tissue Imaging Analysis Applied to Dendritic Cell Subset Microanatomy in Lymph Nodes

(2012) Michael Y. Gerner et al.   IMMUNITY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1

(2010) Roel G.W. Verhaak et al.   CANCER CELL

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS