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

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Spatial concordance of DNA methylation classification in diffuse glioma

(2021) Niels Verburg et al.   NEURO-ONCOLOGY

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

(2020) Aparna Bhaduri et al.   Cell Stem Cell

The repertoire of mutational signatures in human cancer

(2020) Ludmil B. Alexandrov et al.   NATURE

Single-cell transcriptional diversity is a hallmark of developmental potential

(2020) Gunsagar S. Gulati et al.   SCIENCE

A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase

(2020) Janne Purhonen et al.   NUCLEIC ACIDS RESEARCH

Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers

(2020) Hoon Kim et al.   NATURE GENETICS

Exploring the landscape of focal amplifications in cancer using AmpliconArchitect

(2019) Viraj Deshpande et al.   Nature Communications

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

Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia

(2019) Federico Gaiti et al.   NATURE

Genome-Wide CRISPR-Cas9 Screens Expose Genetic Vulnerabilities and Mechanisms of Temozolomide Sensitivity in Glioblastoma Stem Cells

(2019) Graham MacLeod et al.   Cell Reports

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

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

(2019) Lin Wang et al.   Cancer Discovery

Functional Enhancers Shape Extrachromosomal Oncogene Amplifications

(2019) Andrew R. Morton et al.   CELL

Longitudinal molecular trajectories of diffuse glioma in adults

(2019) Floris P. Barthel et al.   NATURE

Circular ecDNA promotes accessible chromatin and high oncogene expression

(2019) Sihan Wu et al.   NATURE

Ageing affects DNA methylation drift and transcriptional cell-to-cell variability in mouse muscle stem cells

(2019) Irene Hernando-Herraez et al.   Nature Communications

Multi-omics profiling of mouse gastrulation at single-cell resolution

(2019) Ricard Argelaguet et al.   NATURE

Snakemake—a scalable bioinformatics workflow engine

(2018) Johannes Köster et al.   BIOINFORMATICS

Cellular Stress Associated with Aneuploidy

(2018) Jin Zhu et al.   DEVELOPMENTAL CELL

DNA methylation-based classification of central nervous system tumours

(2018) David Capper et al.   NATURE

Discordant inheritance of chromosomal and extrachromosomal DNA elements contributes to dynamic disease evolution in glioblastoma

(2018) Ana C. deCarvalho et al.   NATURE GENETICS

A Distinct DNA Methylation Shift in a Subset of Glioma CpG Island Methylator Phenotypes during Tumor Recurrence

(2018) Camila Ferreira de Souza et al.   Cell Reports

MutationalPatterns: comprehensive genome-wide analysis of mutational processes

(2018) Francis Blokzijl et al.   Genome Medicine

The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space

(2018) Johanna Klughammer et al.   NATURE MEDICINE

Pan-cancer deconvolution of tumour composition using DNA methylation

(2018) Ankur Chakravarthy et al.   Nature Communications

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

(2018) Jinzhou Yuan et al.   Genome Medicine

High-Resolution Single-Cell DNA Methylation Measurements Reveal Epigenetically Distinct Hematopoietic Stem Cell Subpopulations

(2018) Tony Hui et al.   Stem Cell Reports

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Single-cell multiomics sequencing and analyses of human colorectal cancer

(2018) Shuhui Bian et al.   SCIENCE

Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance

(2017) Sydney M. Shaffer et al.   NATURE

Targeting glioma stem cells through combined BMI1 and EZH2 inhibition

(2017) Xun Jin et al.   NATURE MEDICINE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Epigenetic plasticity and the hallmarks of cancer

(2017) William A. Flavahan et al.   SCIENCE

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

(2017) Andrew S. Venteicher et al.   SCIENCE

Single-cell epigenomics: Recording the past and predicting the future

(2017) Gavin Kelsey et al.   SCIENCE

Impact of cytosine methylation on DNA binding specificities of human transcription factors

(2017) Yimeng Yin 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

DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation

(2016) Matthias Farlik et al.   Cell Stem Cell

Tumour hypoxia causes DNA hypermethylation by reducing TET activity

(2016) Bernard Thienpont et al.   NATURE

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

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

(2016) Christof Angermueller et al.   NATURE METHODS

5-Hydroxymethylcytosine localizes to enhancer elements and is associated with survival in glioblastoma patients

(2016) Kevin C. Johnson et al.   Nature Communications

LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor

(2015) Nathan C. Sheffield et al.   BIOINFORMATICS

dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering

(2015) Tal Galili   BIOINFORMATICS

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

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Interactive analysis and assessment of single-cell copy-number variations

(2015) Tyler Garvin et al.   NATURE METHODS

Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing

(2015) Hongshan Guo et al.   Nature Protocols

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas

(2015)   NEW ENGLAND JOURNAL OF MEDICINE

Cyclin-dependent kinase 2 (CDK2) is a key mediator for EGF-induced cell transformation mediated through the ELK4/c-Fos signaling pathway

(2015) C Peng et al.   ONCOGENE

PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors

(2015) Amit G Deshwar et al.   GENOME BIOLOGY

Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data

(2014) F. Favero et al.   ANNALS OF ONCOLOGY

Locally Disordered Methylation Forms the Basis of Intratumor Methylome Variation in Chronic Lymphocytic Leukemia

(2014) Dan A. Landau et al.   CANCER CELL

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

(2014) Gavin Ha et al.   GENOME RESEARCH

Cancer Epigenetics: Tumor Heterogeneity, Plasticity of Stem-like States, and Drug Resistance

(2014) Hariharan Easwaran et al.   MOLECULAR CELL

A promoter-level mammalian expression atlas

(2014)   NATURE

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

(2013) B. J. Raney et al.   BIOINFORMATICS

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

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

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

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

The CpG Island Methylator Phenotype: What's in a Name?

(2013) L. A. E. Hughes et al.   CANCER RESEARCH

What a difference a hydroxyl makes: mutant IDH, (R)-2-hydroxyglutarate, and cancer

(2013) J.-A. Losman et al.   GENES & DEVELOPMENT

Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing

(2013) H. Guo et al.   GENOME RESEARCH

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Differential Relationship of DNA Replication Timing to Different Forms of Human Mutation and Variation

(2012) Amnon Koren et al.   AMERICAN JOURNAL OF HUMAN GENETICS

IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype

(2012) Sevin Turcan et al.   NATURE

Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues

(2012) Gilad Landan et al.   NATURE GENETICS

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

(2011) Felix Krueger et al.   BIOINFORMATICS

Identification of functional TFAP2A and SP1 binding sites in new TFAP2A-modulated genes

(2010) Francesca Orso et al.   BMC GENOMICS

Hypoxia inducible factors in cancer stem cells

(2010) J M Heddleston et al.   BRITISH JOURNAL OF CANCER

Identification of a CpG Island Methylator Phenotype that Defines a Distinct Subgroup of Glioma

(2010) Houtan Noushmehr et al.   CANCER CELL

A Chromatin-Mediated Reversible Drug-Tolerant State in Cancer Cell Subpopulations

(2010) Sreenath V. Sharma et al.   CELL

Hypoxia-Inducible Factors Regulate Tumorigenic Capacity of Glioma Stem Cells

(2009) Zhizhong Li et al.   CANCER CELL

Cancer-associated IDH1 mutations produce 2-hydroxyglutarate

(2009) Lenny Dang et al.   NATURE