Cooperation of cancer drivers with regulatory germline variants shapes clinical outcomes

The lncRNA TP73-AS1 is linked to aggressiveness in glioblastoma and promotes temozolomide resistance in glioblastoma cancer stem cells

(2019) Gal Mazor et al.   Cell Death & Disease

The landscape of genomic alterations across childhood cancers

(2018) Susanne N. Gröbner et al.   NATURE

Systematic identification of cancer-specific MHC-binding peptides with RAVEN

(2018) Michaela C. Baldauf et al.   OncoImmunology

Ewing sarcoma

(2018) Thomas G. P. Grünewald et al.   Nature Reviews Disease Primers

Epigenome editing of microsatellite repeats defines tumor-specific enhancer functions and dependencies

(2018) Gaylor Boulay et al.   GENES & DEVELOPMENT

Rearrangement bursts generate canonical gene fusions in bone and soft tissue tumors

(2018) Nathaniel D. Anderson et al.   SCIENCE

Genome-wide association study identifies multiple new loci associated with Ewing sarcoma susceptibility

(2018) Mitchell J. Machiela et al.   Nature Communications

Genome-wide profiling of heritable and de novo STR variations

(2017) Thomas Willems et al.   NATURE METHODS

Identification of two types of GGAA-microsatellites and their roles in EWS/FLI binding and gene regulation in Ewing sarcoma

(2017) Kirsten M. Johnson et al.   PLoS One

MYBL2 (B-Myb): a central regulator of cell proliferation, cell survival and differentiation involved in tumorigenesis

(2017) Julian Musa et al.   Cell Death & Disease

Robust diagnosis of Ewing sarcoma by immunohistochemical detection of super-enhancer-driven EWSR1-ETS targets

(2017) Michaela C. Baldauf et al.   Oncotarget

Preclinical Justification of pbi-shRNA EWS/FLI1 Lipoplex (LPX) Treatment for Ewing's Sarcoma

(2016) Donald D. Rao et al.   MOLECULAR THERAPY

Integration of TP53, DREAM, MMB-FOXM1 and RB-E2F target gene analyses identifies cell cycle gene regulatory networks

(2016) Martin Fischer et al.   NUCLEIC ACIDS RESEARCH

Homozygous G/G variant of SNP309 in the human MDM2 gene is associated with earlier tumor onset in Caucasian female renal cell carcinoma patients

(2016) C G Stoehr et al.   Oncogenesis

Removing batch effects from purified plasma cell gene expression microarrays with modified ComBat

(2015) Caleb K Stein et al.   BMC BIOINFORMATICS

Genetic Variation Determines PPARγ Function and Anti-diabetic Drug Response In Vivo

(2015) Raymond E. Soccio et al.   CELL

Natural Variation in Gene Expression Modulates the Severity of Mutant Phenotypes

(2015) Victoria Vu et al.   CELL

Identification of Genetic Factors that Modify Clinical Onset of Huntington’s Disease

(2015) Jong-Min Lee et al.   CELL

Chimeric EWSR1-FLI1 regulates the Ewing sarcoma susceptibility gene EGR2 via a GGAA microsatellite

(2015) Thomas G P Grünewald et al.   NATURE GENETICS

Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements

(2015) Pratiksha I Thakore et al.   NATURE METHODS

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

EWS-FLI1 Utilizes Divergent Chromatin Remodeling Mechanisms to Directly Activate or Repress Enhancer Elements in Ewing Sarcoma

(2014) Nicolò Riggi et al.   CANCER CELL

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

(2014) Luke A. Gilbert et al.   CELL

MDM2 promotor polymorphism and disease characteristics in chronic lymphocytic leukemia: results of an individual patient data-based meta-analysis

(2014) A. Benner et al.   HAEMATOLOGICA

The Genomic Landscape of Pediatric Ewing Sarcoma

(2014) B. D. Crompton et al.   Cancer Discovery

Genomic Landscape of Ewing Sarcoma Defines an Aggressive Subtype with Co-Association of STAG2 and TP53 Mutations

(2014) F. Tirode et al.   Cancer Discovery

The Genomic Landscape of the Ewing Sarcoma Family of Tumors Reveals Recurrent STAG2 Mutation

(2014) Andrew S. Brohl et al.   PLoS Genetics

PAVIS: a tool for Peak Annotation and Visualization

(2013) Weichun Huang et al.   BIOINFORMATICS

A Polymorphic p53 Response Element in KIT Ligand Influences Cancer Risk and Has Undergone Natural Selection

(2013) Jorge Zeron-Medina et al.   CELL

Oncogenic ETS fusions deregulate E2F3 target genes in Ewing sarcoma and prostate cancer

(2013) Sven Bilke et al.   GENOME RESEARCH

Precision Oncology: An Overview

(2013) Levi A. Garraway et al.   JOURNAL OF CLINICAL ONCOLOGY

Inferring tumour purity and stromal and immune cell admixture from expression data

(2013) Kosuke Yoshihara et al.   Nature Communications

The MuvB complex sequentially recruits B-Myb and FoxM1 to promote mitotic gene expression

(2012) S. Sadasivam et al.   GENES & DEVELOPMENT

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Common variants near TARDBP and EGR2 are associated with susceptibility to Ewing sarcoma

(2012) Sophie Postel-Vinay et al.   NATURE GENETICS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Single-vector inducible lentiviral RNAi system for oncology target validation

(2011) Dmitri Wiederschain et al.   CELL CYCLE

Tumor-specific retargeting of an oncogenic transcription factor chimera results in dysregulation of chromatin and transcription

(2011) M. Patel et al.   GENOME RESEARCH

A High-Frequency Regulatory Polymorphism in the p53 Pathway Accelerates Tumor Development

(2010) Sean M. Post et al.   CANCER CELL

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Overcoming Resistance to Conventional Drugs in Ewing Sarcoma and Identification of Molecular Predictors of Outcome

(2009) Katia Scotlandi et al.   JOURNAL OF CLINICAL ONCOLOGY

The Oncogenic EWS-FLI1 Protein Binds In Vivo GGAA Microsatellite Sequences with Potential Transcriptional Activation Function

(2009) Noëlle Guillon et al.   PLoS One

An embryonic stem cell–like gene expression signature in poorly differentiated aggressive human tumors

(2008) Ittai Ben-Porath et al.   NATURE GENETICS

Microsatellites as EWS/FLI response elements in Ewing's sarcoma

(2008) K. Gangwal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY