Institute for Systems Biology

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

The Cancer Genome Atlas Pan-Cancer analysis project

The Immune Landscape of Cancer

We performed an extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled by TCGA. Across cancer types, we identi...

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors ac...

RepeatModeler2 for automated genomic discovery of transposable element families

The accelerating pace of genome sequencing throughout the tree of life is driving the need for improved unsupervised annotation of genome components such as transposable element...

Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner

We define a “threaded blockset,” which is a novel generalization of the classic notion of a multiple alignment. A new computer program called TBA (for “threaded blockset aligner...

Probabilistic analysis of gene expression measurements from heterogeneous tissues

Abstract Motivation: Tissue heterogeneity, arising from multiple cell types, is a major confounding factor in experiments that focus on studying cell types, e.g. their expressio...