Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets
Abstract Molecular subtypes, such as defined by The Cancer Genome Atlas (TCGA), delineate a cancer’s underlying biology, bringing hope to…
Ilya Shmulevich
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
Abstract The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome…
Comprehensive molecular characterization of mitochondrial genomes in human cancers
Abstract Mitochondria are essential cellular organelles that play critical roles in cancer. Here, as part of the International Cancer Genome…
Divergent mutational processes distinguish hypoxic and normoxic tumours
Abstract Many primary tumours have low levels of molecular oxygen (hypoxia), and hypoxic tumours respond poorly to therapy. Pan-cancer molecular…
Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context
Abstract Long noncoding RNAs (lncRNAs) are commonly dysregulated in tumors, but only a handful are known to play pathophysiological roles…
Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas
Abstract DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide…
Driver Fusions and Their Implications in the Development and Treatment of Human Cancers
Abstract Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across…