Spatial transcriptomics reveals niche-specific enrichment and vulnerabilities of radial glial stem-like cells in malignant gliomas

SpotClean adjusts for spot swapping in spatial transcriptomics data

(2022) Zijian Ni et al.   Nature Communications

Spatially resolved multi-omics deciphers bidirectional tumor-host interdependence in glioblastoma

(2022) Vidhya M. Ravi et al.   CANCER CELL

Spatially aware dimension reduction for spatial transcriptomics

(2022) Lulu Shang et al.   Nature Communications

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

(2021) Xiaofei Wang et al.   CELL RESEARCH

A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain

(2021) Anoushka Joglekar et al.   Nature Communications

H3.3-K27M drives neural stem cell-specific gliomagenesis in a human iPSC-derived model

(2021) Daniel Haag et al.   CANCER CELL

Robust decomposition of cell type mixtures in spatial transcriptomics

(2021) Dylan M. Cable et al.   NATURE BIOTECHNOLOGY

Inference and analysis of cell-cell communication using CellChat

(2021) Suoqin Jin et al.   Nature Communications

Potentiating CD8+ T cell antitumor activity by inhibiting PCSK9 to promote LDLR-mediated TCR recycling and signaling

(2021) Juanjuan Yuan et al.   Protein & Cell

Single cell transcriptome sequencing on the Nanopore platform with ScNapBar

(2021) Qi Wang et al.   RNA

Spatial transcriptomics at subspot resolution with BayesSpace

(2021) Edward Zhao et al.   NATURE BIOTECHNOLOGY

A single-cell and spatially resolved atlas of human breast cancers

(2021) Sunny Z. Wu et al.   NATURE GENETICS

Spatial and cell type transcriptional landscape of human cerebellar development

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

Nanopore sequencing technology, bioinformatics and applications

(2021) Yunhao Wang et al.   NATURE BIOTECHNOLOGY

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

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

APPRIS: selecting functionally important isoforms

(2021) Jose Manuel Rodriguez et al.   NUCLEIC ACIDS RESEARCH

Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions

(2021) Alma Andersson et al.   Nature Communications

Comprehensive analysis of spatial architecture in primary liver cancer

(2021) Rui Wu et al.   Science Advances

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

(2020) Aparna Bhaduri et al.   Cell Stem Cell

Mechanisms and therapeutic implications of hypermutation in gliomas

(2020) Mehdi Touat et al.   NATURE

Modeling glioblastoma invasion using human brain organoids and single-cell transcriptomics

(2020) Teresa G Krieger et al.   NEURO-ONCOLOGY

Management of glioblastoma: State of the art and future directions

(2020) Aaron C. Tan et al.   CA-A CANCER JOURNAL FOR CLINICIANS

Long-read human genome sequencing and its applications

(2020) Glennis A. Logsdon et al.   NATURE REVIEWS GENETICS

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

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

Identification of diverse tumor endothelial cell populations in malignant glioma

(2020) Jeff C Carlson et al.   NEURO-ONCOLOGY

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

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

(2019) Sangeeta Goswami et al.   NATURE MEDICINE

NicheNet: modeling intercellular communication by linking ligands to target genes

(2019) Robin Browaeys et al.   NATURE METHODS

TranscriptClean: Variant-aware correction of indels, mismatches, and splice junctions in long-read transcripts

(2018) Dana Wyman et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

A Glial Signature and Wnt7 Signaling Regulate Glioma-Vascular Interactions and Tumor Microenvironment

(2018) Amelie Griveau et al.   CANCER CELL

Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq

(2018) Mariella G. Filbin et al.   SCIENCE

An anatomic transcriptional atlas of human glioblastoma

(2018) Ralph B. Puchalski et al.   SCIENCE

Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types

(2018) Michael Seiler et al.   Cell Reports

Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex

(2017) Tomasz J. Nowakowski 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

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Therapeutic targeting of splicing in cancer

(2016) Stanley Chun-Wei Lee et al.   NATURE MEDICINE

The long non-coding RNA, SNHG6-003, functions as a competing endogenous RNA to promote the progression of hepatocellular carcinoma

(2016) C Cao et al.   ONCOGENE

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

A Single Kinase Generates the Majority of the Secreted Phosphoproteome

(2015) Vincent S. Tagliabracci et al.   CELL

GWmodel: AnRPackage for Exploring Spatial Heterogeneity Using Geographically Weighted Models

(2015) Isabella Gollini et al.   Journal of Statistical Software

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

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

(2014) Federico González et al.   Cell Stem Cell

Decoding long nanopore sequencing reads of natural DNA

(2014) Andrew H Laszlo et al.   NATURE BIOTECHNOLOGY

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

(2014) A. P. Patel et al.   SCIENCE

Use of human embryonic stem cells to model pediatric gliomas with H3.3K27M histone mutation

(2014) Kosuke Funato et al.   SCIENCE

REDItools: high-throughput RNA editing detection made easy

(2013) Ernesto Picardi et al.   BIOINFORMATICS

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

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

The Somatic Genomic Landscape of Glioblastoma

(2013) Cameron W. Brennan et al.   CELL

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas

(2012) Gang Wu et al.   NATURE GENETICS

Culturing pyramidal neurons from the early postnatal mouse hippocampus and cortex

(2012) Gerard M J Beaudoin et al.   Nature Protocols

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

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

ggbio: an R package for extending the grammar of graphics for genomic data

(2012) Tengfei Yin et al.   GENOME BIOLOGY

A YKL-40-Neutralizing Antibody Blocks Tumor Angiogenesis and Progression: A Potential Therapeutic Agent in Cancers

(2011) M. Faibish et al.   MOLECULAR CANCER THERAPEUTICS

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 Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS