Oncogene expression from extrachromosomal DNA is driven by copy number amplification and does not require spatial clustering in glioblastoma stem cells

The evolutionary dynamics of extrachromosomal DNA in human cancers

(2022) Joshua T. Lange et al.   NATURE GENETICS

Proteogenomic and metabolomic characterization of human glioblastoma

(2021) Liang-Bo Wang et al.   CANCER CELL

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription

(2021) Yanfen Zhu et al.   CANCER CELL

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

(2021) Ester Gangoso et al.   CELL

ecDNA party bus: Bringing the enhancer to you

(2021) Karen Adelman et al.   MOLECULAR CELL

ecDNA hubs drive cooperative intermolecular oncogene expression

(2021) King L. Hung et al.   NATURE

Chromothripsis followed by circular recombination drives oncogene amplification in human cancer

(2021) Carolina Rosswog et al.   NATURE GENETICS

The solid and liquid states of chromatin

(2021) Jeffrey C. Hansen et al.   Epigenetics & Chromatin

Live-Cell Imaging Shows Uneven Segregation of Extrachromosomal DNA Elements and Transcriptionally Active Extrachromosomal DNA Hubs in Cancer

(2021) Eunhee Yi et al.   Cancer Discovery

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

(2020) Hoon Kim et al.   NATURE GENETICS

Chromothripsis drives the evolution of gene amplification in cancer

(2020) Ofer Shoshani et al.   NATURE

Exploring the landscape of focal amplifications in cancer using AmpliconArchitect

(2019) Viraj Deshpande et al.   Nature Communications

Developmentally regulated Shh expression is robust to TAD perturbations

(2019) Iain Williamson et al.   DEVELOPMENT

Functional Enhancers Shape Extrachromosomal Oncogene Amplifications

(2019) Andrew R. Morton et al.   CELL

The liquid nucleome – phase transitions in the nucleus at a glance

(2019) Amy R. Strom et al.   JOURNAL OF CELL SCIENCE

Circular ecDNA promotes accessible chromatin and high oncogene expression

(2019) Sihan Wu et al.   NATURE

Strelka2: fast and accurate calling of germline and somatic variants

(2018) Sangtae Kim et al.   NATURE METHODS

Mapping of genomic EGFRvIII deletions in glioblastoma: insight into rearrangement mechanisms and biomarker development

(2018) Tomoyuki Koga et al.   NEURO-ONCOLOGY

Imaging dynamic and selective low-complexity domain interactions that control gene transcription

(2018) Shasha Chong et al.   SCIENCE

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

(2018) Won-Ki Cho et al.   SCIENCE

An efficient and scalable pipeline for epitope tagging in mammalian stem cells using Cas9 ribonucleoprotein

(2018) Pooran Singh Dewari et al.   eLife

Kinase-controlled phase transition of membraneless organelles in mitosis

(2018) Arpan Kumar Rai et al.   NATURE

Elevated FOXG1 and SOX2 in glioblastoma enforces neural stem cell identity through transcriptional control of cell cycle and epigenetic regulators

(2017) Harry Bulstrode et al.   GENES & DEVELOPMENT

Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity

(2017) Kristen M. Turner et al.   NATURE

Shhand ZRS enhancer colocalisation is specific to the zone of polarising activity

(2016) Iain Williamson et al.   DEVELOPMENT

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Patterns of HER2 Gene Amplification and Response to Anti-HER2 Therapies

(2015) Rocio Vicario et al.   PLoS One

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

(2014) Mario L. Suvà et al.   CELL

The Somatic Genomic Landscape of Glioblastoma

(2014) Cameron W. Brennan et al.   CELL

Targeted Therapy Resistance Mediated by Dynamic Regulation of Extrachromosomal Mutant EGFR DNA

(2013) David A. Nathanson et al.   SCIENCE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Correlation Functions Quantify Super-Resolution Images and Estimate Apparent Clustering Due to Over-Counting

(2012) Sarah L. Veatch et al.   PLoS One

Intratumoral heterogeneity of receptor tyrosine kinases EGFR and PDGFRA amplification in glioblastoma defines subpopulations with distinct growth factor response

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

Mosaic Amplification of Multiple Receptor Tyrosine Kinase Genes in Glioblastoma

(2011) Matija Snuderl et al.   CANCER CELL

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

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

Tumor heterogeneity is an active process maintained by a mutant EGFR-induced cytokine circuit in glioblastoma

(2010) M.-d.-M. Inda et al.   GENES & DEVELOPMENT

Extrachromosomal amplification mechanisms in a glioma with amplified sequences from multiple chromosome loci

(2010) Anne Gibaud et al.   HUMAN MOLECULAR GENETICS

Frequency of double minute chromosomes and combined cytogenetic abnormalities and their characteristics

(2010) Yihui Fan et al.   JOURNAL OF APPLIED GENETICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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