Publications

Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges

Challenges are achieving broad acceptance for addressing many biomedical questions and enabling tool assessment. But ensuring that the …

Neoepiscope improves neoepitope prediction with multi-variant phasing

MOTIVATION: The vast majority of tools for neoepitope prediction from DNA sequencing of complementary tumor and normal patient samples …

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

The Cancer Genome Atlas (TCGA) cancer genomics dataset includes over 10,000 tumor-normal exome pairs across 33 different cancer types, …

The Cancer Genome Atlas Pan-Cancer analysis project.

The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular …

TOPSAN: a dynamic web database for structural genomics.

The Open Protein Structure Annotation Network (TOPSAN) is a web-based collaboration platform for exploring and annotating structures …