Institute for Systems Biology

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

The Cancer Genome Atlas Pan-Cancer analysis project

Circulating microRNAs as stable blood-based markers for cancer detection

Improved approaches for the detection of common epithelial malignancies are urgently needed to reduce the worldwide morbidity and mortality caused by cancer. MicroRNAs (miRNAs) ...

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...

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

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...

Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing

Runs in the Family The power to detect mutations involved in disease by genome sequencing is enhanced when combined with the ability to discover specific mutations that may have...

Pyogenic Bacterial Infections in Humans with IRAK-4 Deficiency

Members of the Toll-like receptor (TLR) and interleukin-1 receptor (IL-1R) superfamily share an intracytoplasmic Toll–IL-1 receptor (TIR) domain, which mediates recruitment of t...