Sequential fate-switches in stem-like cells drive the tumorigenic trajectory from human neural stem cells to malignant glioma

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

(2020) Aparna Bhaduri et al.   Cell Stem Cell

Decoding the development of the human hippocampus

(2020) Suijuan Zhong et al.   NATURE

Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells

(2020) Tomoyuki Koga et al.   Nature Communications

Bulk tissue cell type deconvolution with multi-subject single-cell expression reference

(2019) Xuran Wang et al.   Nature Communications

Cell-of-origin susceptibility to glioblastoma formation declines with neural lineage restriction

(2019) Sheila Alcantara Llaguno et al.   NATURE NEUROSCIENCE

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

NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis

(2019) Guangyan Zhou et al.   NUCLEIC ACIDS RESEARCH

GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis

(2019) Zefang Tang et al.   NUCLEIC ACIDS RESEARCH

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

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex

(2018) Suijuan Zhong et al.   NATURE

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

A glial blueprint for gliomagenesis

(2018) Dylan Laug et al.   NATURE REVIEWS NEUROSCIENCE

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

(2018) Jeffrey A. Farrell et al.   SCIENCE

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

(2018) Joo Ho Lee et al.   NATURE

An Experimenter’s Guide to Glioblastoma Invasion Pathways

(2018) Mark C. de Gooijer et al.   TRENDS IN MOLECULAR MEDICINE

Maftools: efficient and comprehensive analysis of somatic variants in cancer

(2018) Anand Mayakonda et al.   GENOME RESEARCH

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

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

(2017) Andrew S. Venteicher et al.   SCIENCE

Single-Cell Transcriptomic Analysis Defines Heterogeneity and Transcriptional Dynamics in the Adult Neural Stem Cell Lineage

(2017) Ben W. Dulken et al.   Cell Reports

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

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

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Induced Pluripotent Stem Cells Meet Genome Editing

(2016) Dirk Hockemeyer et al.   Cell Stem Cell

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

(2016) Itay Tirosh et al.   NATURE

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

(2016) Eric Talevich et al.   PLoS Computational Biology

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

Diffusion maps for high-dimensional single-cell analysis of differentiation data

(2015) Laleh Haghverdi et al.   BIOINFORMATICS

PTEN deficiency reprogrammes human neural stem cells towards a glioblastoma stem cell-like phenotype

(2015) Shunlei Duan et al.   Nature Communications

The Secreted Protein C1QL1 and Its Receptor BAI3 Control the Synaptic Connectivity of Excitatory Inputs Converging on Cerebellar Purkinje Cells

(2015) Séverine M. Sigoillot et al.   Cell Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Reconstructing and Reprogramming the Tumor-Propagating Potential of Glioblastoma Stem-like Cells

(2014) Mario L. Suvà et al.   CELL

Targeting Self-Renewal in High-Grade Brain Tumors Leads to Loss of Brain Tumor Stem Cells and Prolonged Survival

(2014) Zhe Zhu et al.   Cell Stem Cell

An iCRISPR Platform for Rapid, Multiplexable, and Inducible Genome Editing in Human Pluripotent Stem Cells

(2014) Federico González et al.   Cell Stem Cell

Glioblastoma Recurrence Patterns After Radiation Therapy With Regard to the Subventricular Zone

(2014) Sebastian Adeberg et al.   INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS

Small Molecule Inhibitors Targeting Activator Protein 1 (AP-1)

(2014) Na Ye et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

(2014) A. P. Patel et al.   SCIENCE

Glioblastoma Stem Cells Generate Vascular Pericytes to Support Vessel Function and Tumor Growth

(2013) Lin Cheng et al.   CELL

The Somatic Genomic Landscape of Glioblastoma

(2013) Cameron W. Brennan et al.   CELL

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Derivation and Expansion Using Only Small Molecules of Human Neural Progenitors for Neurodegenerative Disease Modeling

(2013) Peter Reinhardt et al.   PLoS One

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster 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

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Mosaic Analysis with Double Markers Reveals Tumor Cell of Origin in Glioma

(2011) Chong Liu et al.   CELL

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

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

Essential Roles of Notch Signaling in Maintenance of Neural Stem Cells in Developing and Adult Brains

(2010) I. Imayoshi et al.   JOURNAL OF NEUROSCIENCE

Tumour vascularization via endothelial differentiation of glioblastoma stem-like cells

(2010) Lucia Ricci-Vitiani et al.   NATURE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Expression of Mutant p53 Proteins Implicates a Lineage Relationship between Neural Stem Cells and Malignant Astrocytic Glioma in a Murine Model

(2009) Yuan Wang et al.   CANCER CELL

Malignant Astrocytomas Originate from Neural Stem/Progenitor Cells in a Somatic Tumor Suppressor Mouse Model

(2009) Sheila Alcantara Llaguno 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

A Transcriptome Database for Astrocytes, Neurons, and Oligodendrocytes: A New Resource for Understanding Brain Development and Function

(2008) J. D. Cahoy et al.   JOURNAL OF NEUROSCIENCE

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE