Clonal evolution of glioblastoma under therapy

Spatiotemporal Evolution of the Primary Glioblastoma Genome

(2015) Jinkuk Kim et al.   CANCER CELL

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

Detection, Characterization, and Inhibition of FGFR-TACC Fusions in IDH Wild-type Glioma

(2015) A. L. Di Stefano et al.   CLINICAL CANCER RESEARCH

Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution

(2015) Hoon Kim et al.   GENOME RESEARCH

Mutational landscape and clonal architecture in grade II and III gliomas

(2015) Hiromichi Suzuki et al.   NATURE GENETICS

The genomic landscape of juvenile myelomonocytic leukemia

(2015) Elliot Stieglitz et al.   NATURE GENETICS

An information theoretic method to identify combinations of genomic alterations that promote glioblastoma

(2015) Rachel D. Melamed et al.   Journal of Molecular Cell Biology

PRADA: pipeline for RNA sequencing data analysis

(2014) Wandaliz Torres-García et al.   BIOINFORMATICS

Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer

(2014) Francesco Abate et al.   BMC Systems Biology

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

MRI-localized biopsies reveal subtype-specific differences in molecular and cellular composition at the margins of glioblastoma

(2014) B. J. Gill et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) A. P. Patel et al.   SCIENCE

MutComFocal: an integrative approach to identifying recurrent and focal genomic alterations in tumor samples

(2013) Vladimir Trifonov et al.   BMC Systems Biology

SAVI: a statistical algorithm for variant frequency identification

(2013) Vladimir Trifonov et al.   BMC Systems Biology

The Somatic Genomic Landscape of Glioblastoma

(2013) Cameron W. Brennan et al.   CELL

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

The integrated landscape of driver genomic alterations in glioblastoma

(2013) Veronique Frattini et al.   NATURE GENETICS

Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics

(2013) A. Sottoriva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutational Analysis Reveals the Origin and Therapy-Driven Evolution of Recurrent Glioma

(2013) B. E. Johnson et al.   SCIENCE

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

EXCAVATOR: detecting copy number variants from whole-exome sequencing data

(2013) Alberto Magi et al.   GENOME BIOLOGY

TGF-β as a therapeutic target in high grade gliomas – Promises and challenges

(2012) Justin V. Joseph et al.   BIOCHEMICAL PHARMACOLOGY

Mesenchymal high-grade glioma is maintained by the ID-RAP1 axis

(2012) Francesco Niola et al.   JOURNAL OF CLINICAL INVESTIGATION

Primary brain tumours in adults

(2012) Damien Ricard et al.   LANCET

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

Evolution of the cancer genome

(2012) Lucy R. Yates et al.   NATURE REVIEWS GENETICS

Transforming Fusions of FGFR and TACC Genes in Human Glioblastoma

(2012) D. Singh et al.   SCIENCE

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

In silico prediction of tumor antigens derived from functional missense mutations of the cancer gene census

(2012) Jahan S. Khalili et al.   OncoImmunology

ChimeraScan: a tool for identifying chimeric transcription in sequencing data

(2011) Matthew K. Iyer et al.   BIOINFORMATICS

Mutual exclusivity analysis identifies oncogenic network modules

(2011) G. Ciriello et al.   GENOME RESEARCH

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

TGF-β Receptor Inhibitors Target the CD44high/Id1high Glioma-Initiating Cell Population in Human Glioblastoma

(2010) Judit Anido et al.   CANCER CELL

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

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

MSH6 Mutations Arise in Glioblastomas during Temozolomide Therapy and Mediate Temozolomide Resistance

(2009) S. Yip et al.   CLINICAL CANCER RESEARCH

The transcriptional network for mesenchymal transformation of brain tumours

(2009) Maria Stella Carro et al.   NATURE

TGFβ in Cancer

(2008) Joan Massagué   CELL

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

The HECT-domain ubiquitin ligase Huwe1 controls neural differentiation and proliferation by destabilizing the N-Myc oncoprotein

(2008) Xudong Zhao et al.   NATURE CELL BIOLOGY