Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data

Bivalent Chromatin Domains in Glioblastoma Reveal a Subtype-Specific Signature of Glioma Stem Cells

(2018) Amelia Weber Hall et al.   CANCER RESEARCH

Global, Regional, and National Cancer Incidence, Mortality, Years of Life Lost, Years Lived With Disability, and Disability-Adjusted Life-years for 32 Cancer Groups, 1990 to 2015

(2017) et al.   JAMA Oncology

Allelic imbalance of somatic mutations in cancer genomes and transcriptomes

(2017) Je-Keun Rhee et al.   Scientific Reports

Problems of glioblastoma multiforme drug resistance

(2016) A. A. Stavrovskaya et al.   BIOCHEMISTRY-MOSCOW

SNooPer: a machine learning-based method for somatic variant identification from low-pass next-generation sequencing

(2016) Jean-François Spinella et al.   BMC GENOMICS

High-throughput Phenotyping of Lung Cancer Somatic Mutations

(2016) Alice H. Berger et al.   CANCER CELL

Abstract 1514: Significance assessment of mutations in 944 MDS patients using publicly available variant databases and mutation impact prediction software

(2016) Niroshan Nadarajah et al.   CANCER RESEARCH

Quantitative proteomics revealed novel proteins associated with molecular subtypes of breast cancer

(2016) Shankar Suman et al.   Journal of Proteomics

Neomorphic mutations create therapeutic challenges in cancer

(2016) V Takiar et al.   ONCOGENE

Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exome and Targeted Deep Sequencing Data

(2016) Anne Bruun Krøigård et al.   PLoS One

An integrative approach to predicting the functional effects of non-coding and coding sequence variation

(2015) Hashem A. Shihab et al.   BIOINFORMATICS

Inconsistency and features of single nucleotide variants detected in whole exome sequencing versus transcriptome sequencing: A case study in lung cancer

(2015) Timothy D. O’Brien et al.   METHODS

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing

(2015) Tyler S. Alioto et al.   Nature Communications

Profiling RNA editing in human tissues: towards the inosinome Atlas

(2015) Ernesto Picardi et al.   Scientific Reports

Whole Transcriptome Sequencing Reveals Extensive Unspliced mRNA in Metastatic Castration-Resistant Prostate Cancer

(2014) Adam G. Sowalsky et al.   MOLECULAR CANCER RESEARCH

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine

(2014) Benjamin J Raphael et al.   Genome Medicine

Comparative multidimensional molecular analyses of pediatric diffuse intrinsic pontine glioma reveals distinct molecular subtypes

(2013) Amanda M. Saratsis et al.   ACTA NEUROPATHOLOGICA

Reliable Identification of Genomic Variants from RNA-Seq Data

(2013) Robert Piskol et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Predicting the functional consequences of cancer-associated amino acid substitutions

(2013) Hashem A. Shihab et al.   BIOINFORMATICS

Stromal expression of SPARC in pancreatic adenocarcinoma

(2013) Cindy Neuzillet et al.   CANCER AND METASTASIS REVIEWS

The Somatic Genomic Landscape of Glioblastoma

(2013) Cameron W. Brennan et al.   CELL

Edgotype: a fundamental link between genotype and phenotype

(2013) Nidhi Sahni et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Tumour heterogeneity and cancer cell plasticity

(2013) Corbin E. Meacham et al.   NATURE

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

RADAR: a rigorously annotated database of A-to-I RNA editing

(2013) Gokul Ramaswami et al.   NUCLEIC ACIDS RESEARCH

SIFT Indel: Predictions for the Functional Effects of Amino Acid Insertions/Deletions in Proteins

(2013) Jing Hu et al.   PLoS One

The roles of MAGE-D1 in the neuronal functions and pathology of the central nervous system

(2013) Akihiro Mouri et al.   REVIEWS IN THE NEUROSCIENCES

Properties and rates of germline mutations in humans

(2013) Catarina D. Campbell et al.   TRENDS IN GENETICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Targeting EGFR for Treatment of Glioblastoma: Molecular Basis to Overcome Resistance

(2012) T. E. Taylor et al.   CURRENT CANCER DRUG TARGETS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models

(2012) Hashem A. Shihab et al.   HUMAN MUTATION

Modelling and simulating generic RNA-Seq experiments with the flux simulator

(2012) Thasso Griebel et al.   NUCLEIC ACIDS RESEARCH

Darned in 2013: inclusion of model organisms and linking with Wikipedia

(2012) Anmol M. Kiran et al.   NUCLEIC ACIDS RESEARCH

Screening the human exome: a comparison of whole genome and whole transcriptome sequencing

(2012) Elizabeth T Cirulli et al.   GENOME BIOLOGY

High levels of RNA-editing site conservation amongst 15 laboratory mouse strains

(2012) Petr Daneck et al.   GENOME BIOLOGY

Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)

(2011) Gregory R. Grant et al.   BIOINFORMATICS

Feature-based classifiers for somatic mutation detection in tumour–normal paired sequencing data

(2011) Jiarui Ding et al.   BIOINFORMATICS

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia

(2011) Xose S. Puente et al.   NATURE

Filamin A regulates focal adhesion disassembly and suppresses breast cancer cell migration and invasion

(2010) Yingjie Xu et al.   JOURNAL OF EXPERIMENTAL MEDICINE

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Noisy Splicing Drives mRNA Isoform Diversity in Human Cells

(2010) Joseph K. Pickrell et al.   PLoS Genetics

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Effects of radiotherapy with concomitant and adjuvant temozolomide versus radiotherapy alone on survival in glioblastoma in a randomised phase III study: 5-year analysis of the EORTC-NCIC trial

(2009) Roger Stupp et al.   LANCET ONCOLOGY

High-Resolution Genomic Copy Number Profiling of Glioblastoma Multiforme by Single Nucleotide Polymorphism DNA Microarray

(2009) D. Yin et al.   MOLECULAR CANCER RESEARCH

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE