Long-term cancer survival prediction using multimodal deep learning
Abstract The age of precision medicine demands powerful computational techniques to handle high-dimensional patient data. We present MultiSurv, a multimodal…
Cancer genomics
A pan-cancer survey of cell line tumor similarity by feature-weighted molecular profiles
Abstract Patient-derived cell lines are often used in pre-clinical cancer research, but some cell lines are too different from tumors…
Deep generative neural network for accurate drug response imputation
Abstract Drug response differs substantially in cancer patients due to inter- and intra-tumor heterogeneity. Particularly, transcriptome context, especially tumor microenvironment,…
Mutations of Intrinsically Disordered Protein Regions Can Drive Cancer but Lack Therapeutic Strategies
Abstract Many proteins contain intrinsically disordered regions (IDRs) which carry out important functions without relying on a single well-defined conformation.…
Uniform genomic data analysis in the NCI Genomic Data Commons
Abstract The goal of the National Cancer Institute’s (NCI’s) Genomic Data Commons (GDC) is to provide the cancer research community…
A Clinical Genomics-Guided Prioritizing Strategy Enables Selecting Proper Cancer Cell Lines for Biomedical Research
Abstract Selecting appropriate cell lines to represent a disease is crucial for the success of biomedical research, because the usage…
Systematic investigation of promoter substitutions resulting from somatic intrachromosomal structural alterations in diverse human cancers
Abstract One of the ways in which genes can become activated in tumors is by somatic structural genomic rearrangements leading…
Pan-cancer driver copy number alterations identified by joint expression/CNA data analysis
Abstract Analysis of large gene expression datasets from biopsies of cancer patients can identify co-expression signatures representing particular biomolecular events…
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…
Co-expression based cancer staging and application
Abstract A novel method is developed for predicting the stage of a cancer tissue based on the consistency level between…