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

Tumor-Specific T Cell Activation in Malignant Brain Tumors

(2020) Malte Mohme et al.   Frontiers in Immunology

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

(2020) Florian Klemm et al.   CELL

The Emerging Role of Myeloid-Derived Suppressor Cells in the Glioma Immune Suppressive Microenvironment

(2020) Yajing Mi et al.   Frontiers in Immunology

Challenges to curing primary brain tumours

(2019) Kenneth Aldape et al.   Nature Reviews Clinical Oncology

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

(2019) Cyril Neftel et al.   CELL

Experimental models and tools to tackle glioblastoma

(2019) Faye L. Robertson et al.   Disease Models & Mechanisms

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

(2019) Lin Wang et al.   Cancer Discovery

Immune profiling of human tumors identifies CD73 as a combinatorial target in glioblastoma

(2019) Sangeeta Goswami et al.   NATURE MEDICINE

DNA methylation-based classification of central nervous system tumours

(2018) David Capper et al.   NATURE

Strelka2: fast and accurate calling of germline and somatic variants

(2018) Sangtae Kim et al.   NATURE METHODS

Current state of immunotherapy for glioblastoma

(2018) Michael Lim et al.   Nature Reviews Clinical Oncology

Human glioblastoma arises from subventricular zone cells with low-level driver mutations

(2018) Joo Ho Lee et al.   NATURE

E-cadherin loss induces targetable autocrine activation of growth factor signalling in lobular breast cancer

(2018) Katy Teo et al.   Scientific Reports

Mouse Genome Database (MGD) 2019

(2018) Carol J Bult et al.   NUCLEIC ACIDS RESEARCH

The chromatin accessibility landscape of primary human cancers

(2018) M. Ryan Corces et al.   SCIENCE

The Dark Side of IFN-γ: Its Role in Promoting Cancer Immunoevasion

(2017) Marija Mojic et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Emerging targets in cancer immunotherapy

(2017) Samantha Burugu et al.   SEMINARS IN CANCER BIOLOGY

Atropos: specific, sensitive, and speedy trimming of sequencing reads

(2017) John P. Didion et al.   PeerJ

Differential methylation analysis for BS-seq data under general experimental design

(2016) Yongseok Park et al.   BIOINFORMATICS

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Tumor Interferon Signaling Regulates a Multigenic Resistance Program to Immune Checkpoint Blockade

(2016) Joseph L. Benci et al.   CELL

The macrophage IRF8/IRF1 regulome is required for protection against infections and is associated with chronic inflammation

(2016) David Langlais et al.   JOURNAL OF EXPERIMENTAL MEDICINE

ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization

(2016) Guangchuang Yu et al.   Molecular BioSystems

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research

(2016) Zhongwu Lai et al.   NUCLEIC ACIDS RESEARCH

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing

(2016) Eric Talevich et al.   PLoS Computational Biology

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications

(2015) Xiaoyu Chen et al.   BIOINFORMATICS

Cancer stem cells in glioblastoma

(2015) Justin D. Lathia et al.   GENES & DEVELOPMENT

Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells

(2015) Van Trung Chu et al.   NATURE BIOTECHNOLOGY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants

(2014) V. Obenchain et al.   BIOINFORMATICS

SAMBLASTER: fast duplicate marking and structural variant read extraction

(2014) G. G. Faust et al.   BIOINFORMATICS

Gene disruption by cell-penetrating peptide-mediated delivery of Cas9 protein and guide RNA

(2014) S. Ramakrishna et al.   GENOME RESEARCH

Ward’s Hierarchical Agglomerative Clustering Method: Which Algorithms Implement Ward’s Criterion?

(2014) Fionn Murtagh et al.   JOURNAL OF CLASSIFICATION

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

(2014) A. P. Patel et al.   SCIENCE

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

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

CSF-1R inhibition alters macrophage polarization and blocks glioma progression

(2013) Stephanie M Pyonteck et al.   NATURE MEDICINE

Low-level processing of Illumina Infinium DNA Methylation BeadArrays

(2013) Timothy J. Triche et al.   NUCLEIC ACIDS RESEARCH

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

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

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

CCL2 recruits inflammatory monocytes to facilitate breast-tumour metastasis

(2011) Bin-Zhi Qian et al.   NATURE

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Cancer Immunoediting: Integrating Immunity's Roles in Cancer Suppression and Promotion

(2011) R. D. Schreiber et al.   SCIENCE

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC 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

Glioma Stem Cell Lines Expanded in Adherent Culture Have Tumor-Specific Phenotypes and Are Suitable for Chemical and Genetic Screens

(2009) Steven M. Pollard et al.   Cell Stem Cell

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE

The transcriptional network for mesenchymal transformation of brain tumours

(2009) Maria Stella Carro et al.   NATURE

Long-term tripotent differentiation capacity of human neural stem (NS) cells in adherent culture

(2008) Yirui Sun et al.   MOLECULAR AND CELLULAR NEUROSCIENCE