Related references
Note: Only part of the references are listed.Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer
Tamara Ouspenskaia et al.
NATURE BIOTECHNOLOGY (2022)
Opposing immune and genetic mechanisms shape oncogenic programs in synovial sarcoma
Livnat Jerby-Arnon et al.
NATURE MEDICINE (2021)
Gene regulation by long non-coding RNAs and its biological functions
Luisa Statello et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2021)
Ewing's Sarcoma
Nicolo Riggi et al.
NEW ENGLAND JOURNAL OF MEDICINE (2021)
Cross-HLA targeting of intracellular oncoproteins with peptide-centric CARs
Mark Yarmarkovich et al.
NATURE (2021)
Most non-canonical proteins uniquely populate the proteome or immunopeptidome
Maria Virginia Ruiz Cuevas et al.
CELL REPORTS (2021)
STAG2 mutations alter CTCF-anchored loop extrusion, reduce cis-regulatory interactions and EWSR1-FLI1 activity in Ewing sarcoma
Didier Surdez et al.
CANCER CELL (2021)
Unraveling Ewing Sarcoma Tumorigenesis Originating from Patient-Derived Mesenchymal Stem Cells
Anna Sole et al.
CANCER RESEARCH (2021)
Pervasive functional translation of noncanonical human open reading frames
Jin Chen et al.
SCIENCE (2020)
Transcriptional Programs Define Intratumoral Heterogeneity of Ewing Sarcoma at Single-Cell Resolution
Marie-Ming Aynaud et al.
CELL REPORTS (2020)
Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes
Chloe Chong et al.
NATURE COMMUNICATIONS (2020)
Desmoplastic small round cell tumor is dependent on the EWS-WT1 transcription factor
Jenna M. Gedminas et al.
ONCOGENESIS (2020)
Germline Elongator mutations in Sonic Hedgehog medulloblastoma
Sebastian M. Waszak et al.
NATURE (2020)
Functional Long Non-coding RNAs Evolve from Junk Transcripts
Alexander F. Palazzo et al.
CELL (2020)
Quantification of translation uncovers the functions of the alternative transcriptome
Lorenzo Calviello et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2020)
Transcriptome analysis of desmoplastic small round cell tumors identifies actionable therapeutic targets: a report from the Children's Oncology Group
Pooja Hingorani et al.
SCIENTIFIC REPORTS (2020)
The PRIDE database and related tools and resources in 2019: improving support for quantification data
Yasset Perez-Riverol et al.
NUCLEIC ACIDS RESEARCH (2019)
Targeting transcription factors in cancer - from undruggable to reality
John H. Bushweller
NATURE REVIEWS CANCER (2019)
Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression
Christoph Hafemeister et al.
GENOME BIOLOGY (2019)
Transcriptomic definition of molecular subgroups of small round cell sarcomas
Sarah Watson et al.
JOURNAL OF PATHOLOGY (2018)
Ewing sarcoma
Thomas G. P. Gruenewald et al.
NATURE REVIEWS DISEASE PRIMERS (2018)
Epigenome editing of microsatellite repeats defines tumor-specific enhancer functions and dependencies
Gaylor Boulay et al.
GENES & DEVELOPMENT (2018)
Noncoding regions are the main source of targetable tumor-specific antigens
Celine M. Laumont et al.
SCIENCE TRANSLATIONAL MEDICINE (2018)
Accurate assembly of transcripts through phase-preserving graph decomposition
Mingfu Shao et al.
NATURE BIOTECHNOLOGY (2017)
DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma
Nathan C. Sheffield et al.
NATURE MEDICINE (2017)
Mechanisms regulating T-cell infiltration and activity in solid tumors
E. Lanitis et al.
ANNALS OF ONCOLOGY (2017)
Cancer-Specific Retargeting of BAF Complexes by a Prion-like Domain
Gaylor Boulay et al.
CELL (2017)
Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0
Matthew The et al.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2016)
Three-year Follow up of GMCSF/bi-shRNAfurin DNA-transfected Autologous Tumor Immunotherapy (Vigil) in Metastatic Advanced Ewing's Sarcoma
Maurizio Ghisoli et al.
MOLECULAR THERAPY (2016)
HiChIP: efficient and sensitive analysis of protein-directed genome architecture
Maxwell R. Mumbach et al.
NATURE METHODS (2016)
Global proteogenomic analysis of human MHC class I-associated peptides derived from non-canonical reading frames
Celine M. Laumont et al.
NATURE COMMUNICATIONS (2016)
The landscape of long noncoding RNAs in the human transcriptome
Matthew K. Iyer et al.
NATURE GENETICS (2015)
Tissue-based map of the human proteome
Mathias Uhlen et al.
SCIENCE (2015)
Epigenome Mapping Reveals Distinct Modes of Gene Regulation and Widespread Enhancer Reprogramming by the Oncogenic Fusion Protein EWS-FLI1
Eleni M. Tomazou et al.
CELL REPORTS (2015)
Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species
Hadas Hezroni et al.
CELL REPORTS (2015)
HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
Nicolas Servant et al.
GENOME BIOLOGY (2015)
EWS-FLI1 Utilizes Divergent Chromatin Remodeling Mechanisms to Directly Activate or Repress Enhancer Elements in Ewing Sarcoma
Nicolo Riggi et al.
CANCER CELL (2014)
Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ
Juergen Cox et al.
MOLECULAR & CELLULAR PROTEOMICS (2014)
Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers
Leighton J. Core et al.
NATURE GENETICS (2014)
Kinetic competition during the transcription cycle results in stochastic RNA processing
Antoine Coulon et al.
ELIFE (2014)
STAR: ultrafast universal RNA-seq aligner
Alexander Dobin et al.
BIOINFORMATICS (2013)
Transcriptional Regulation and Its Misregulation in Disease
Tong Ihn Lee et al.
CELL (2013)
Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
NATURE METHODS (2012)
MassChroQ: A versatile tool for mass spectrometry quantification
Benoit Valot et al.
PROTEOMICS (2011)
The Sequence Alignment/Map format and SAMtools
Heng Li et al.
BIOINFORMATICS (2009)
The Oncogenic EWS-FLI1 Protein Binds In Vivo GGAA Microsatellite Sequences with Potential Transcriptional Activation Function (Publication with Expression of Concern. See vol. 17, 2022)
Noelle Guillon et al.
PLOS ONE (2009)
Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
Nicholas T. Ingolia et al.
SCIENCE (2009)
Microsatellites as EWIS/FLI response elements in Ewing's sarcoma
Kunal Gangwal et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang et al.
GENOME BIOLOGY (2008)
MyProMs, a web server for management and validation of mass spectrometry-based proteomic data
Patrick Poullet et al.
PROTEOMICS (2007)
Cholecystokinin down-regulation by RNA interference impairs Ewing tumor growth
Jaime Carrillo et al.
CLINICAL CANCER RESEARCH (2007)
Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes
K Kimura et al.
GENOME RESEARCH (2006)
An improved model for prediction of retention times of tryptic peptides in ion pair reversed-phase HPLC - Its application to protein peptide mapping by off-line HPLC-MALDI MS
OV Krokhin et al.
MOLECULAR & CELLULAR PROTEOMICS (2004)
WebLogo: A sequence logo generator
GE Crooks et al.
GENOME RESEARCH (2004)
Precise nanometer localization analysis for individual fluorescent probes
RE Thompson et al.
BIOPHYSICAL JOURNAL (2002)