Human fetal cerebellar cell atlas informs medulloblastoma origin and oncogenesis

Medulloblastoma group 3 and 4 tumors comprise a clinically and biologically significant expression continuum reflecting human cerebellar development

(2022) Daniel Williamson et al.   Cell Reports

Failure of human rhombic lip differentiation underlies medulloblastoma formation

(2022) Liam D. Hendrikse et al.   NATURE

Unified rhombic lip origins of group 3 and group 4 medulloblastoma

(2022) Kyle S. Smith et al.   NATURE

ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

(2021) Jeffrey M. Granja et al.   NATURE GENETICS

Metastasis-Initiating Cells and Ecosystems

(2021) Joan Massagué et al.   Cancer Discovery

Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes

(2021) Xiaotao Wang et al.   NATURE METHODS

Spatial and cell type transcriptional landscape of human cerebellar development

(2021) Kimberly A. Aldinger et al.   NATURE NEUROSCIENCE

Neoplastic and immune single-cell transcriptomics define subgroup-specific intra-tumoral heterogeneity of childhood medulloblastoma

(2021) Kent A Riemondy et al.   NEURO-ONCOLOGY

Interpretation of T cell states from single-cell transcriptomics data using reference atlases

(2021) Massimo Andreatta et al.   Nature Communications

Epigenomic landscape and 3D genome structure in pediatric high-grade glioma

(2021) Juan Wang et al.   Science Advances

HNRNPH1 Is a Novel Regulator Of Cellular Proliferation and Disease Progression in Chronic Myeloid Leukemia

(2021) Menghan Liu et al.   Frontiers in Oncology

Single nucleus RNA-sequencing: how it's done, applications and limitations

(2021) Juliane Fischer et al.   Emerging Topics in Life Sciences

A CIBERSORTx-based immune cell scoring system could independently predict the prognosis of patients with myelodysplastic syndromes

(2021) Yu-Hung Wang et al.   Blood Advances

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

(2020) Michal Slyper et al.   NATURE MEDICINE

DDX3X Suppresses the Susceptibility of Hindbrain Lineages to Medulloblastoma

(2020) Deanna M. Patmore et al.   DEVELOPMENTAL CELL

Unsupervised Inference of Developmental Directions for Single Cells Using VECTOR

(2020) Feng Zhang et al.   Cell Reports

SOX11 promotes epithelial/mesenchymal hybrid state and alters tropism of invasive breast cancer cells

(2020) Erik Oliemuller et al.   eLife

Childhood cerebellar tumours mirror conserved fetal transcriptional programs

(2019) Maria C. Vladoiu et al.   NATURE

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

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

Cellular Plasticity in Cancer

(2019) Salina Yuan et al.   Cancer Discovery

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

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

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

(2019) Joshua D. Welch et al.   CELL

Resolving medulloblastoma cellular architecture by single-cell genomics

(2019) Volker Hovestadt et al.   NATURE

Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM

(2019) Huidong Chen et al.   Nature Communications

Improved CUT&RUN chromatin profiling tools

(2019) Michael P Meers et al.   eLife

Single-Cell Transcriptomics in Medulloblastoma Reveals Tumor-Initiating Progenitors and Oncogenic Cascades during Tumorigenesis and Relapse

(2019) Liguo Zhang et al.   CANCER CELL

Spatiotemporal expansion of primary progenitor zones in the developing human cerebellum

(2019) Parthiv Haldipur et al.   SCIENCE

Medulloblastoma: From Molecular Subgroups to Molecular Targeted Therapies

(2018) Jun Wang et al.   Annual Review of Neuroscience

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

Programming of Schwann Cells by Lats1/2-TAZ/YAP Signaling Drives Malignant Peripheral Nerve Sheath Tumorigenesis

(2018) Lai Man Natalie Wu et al.   CANCER CELL

Differential patterns of metastatic dissemination across medulloblastoma subgroups

(2018) Michal Zapotocky et al.   Journal of Neurosurgery-Pediatrics

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

The chromatin accessibility landscape of primary human cancers

(2018) M. Ryan Corces et al.   SCIENCE

The whole-genome landscape of medulloblastoma subtypes

(2017) Paul A. Northcott et al.   NATURE

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

A Novel and Multivalent Role of Pax6 in Cerebellar Development

(2016) J. Yeung et al.   JOURNAL OF NEUROSCIENCE

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

(2016) Itay Tirosh et al.   NATURE

CPI-17 drives oncogenic Ras signaling in human melanomas via Ezrin-Radixin-Moesin family proteins

(2016) Lars Björn Riecken et al.   Oncotarget

Convergence of Developmental and Oncogenic Signaling Pathways at Transcriptional Super-Enhancers

(2015) Denes Hnisz et al.   MOLECULAR CELL

A splicing variant of Merlin promotes metastasis in hepatocellular carcinoma

(2015) Zai-Li Luo et al.   Nature Communications

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

BET Bromodomain Inhibition of MYC-Amplified Medulloblastoma

(2013) P. Bandopadhayay et al.   CLINICAL CANCER RESEARCH

Molecular subgroups of medulloblastoma: an international meta-analysis of transcriptome, genetic aberrations, and clinical data of WNT, SHH, Group 3, and Group 4 medulloblastomas

(2012) Marcel Kool et al.   ACTA NEUROPATHOLOGICA

Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations

(2012) Trevor J. Pugh et al.   NATURE

The Hippo pathway target, YAP, promotes metastasis through its TEAD-interaction domain

(2012) J. M. Lamar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development and Evolution of the Human Neocortex

(2011) Jan H. Lui et al.   CELL

Subtypes of medulloblastoma have distinct developmental origins

(2010) Paul Gibson et al.   NATURE

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cerebellum of the Premature Infant: Rapidly Developing, Vulnerable, Clinically Important

(2009) Joseph J. Volpe   JOURNAL OF CHILD NEUROLOGY