Computational biology develops and applies tools to suggest answers to biological questions that can be answered through analysis of large complex datasets.
We use these tools to study humans in both health and disease, by exploiting natural variation across large cohorts of samples.
Much of our work is in cancer and neurodegenerative disease, but we have collaborations in various areas.
Here are a few current projects:
The role of lymph nodes in facilitating distant metastasis
As part of the Stanford Center for Cancer Systems Biology we are using computational approaches with genomic data to integrate gene expression and molecular imaging (CODEX) to understand how immune cells become brainwashed in lymph nodes to tolerate cancer cells that have migrated there, and to spread this tolerance to the rest of the body – allowing cancer to spread to other sites in the body. We are developing meta-analysis resources for head and neck cancer and melanoma, and developing new tools to identify key sub-populations of cells from single cell data.
Pan-cancer identification of prognostically relevant cell types
We are developing several tools for identifying cell states that represent potential new therapeutic targets. We use a combination of deconvolution based on CIBERSORTx in collaboration with the Newman lab, as well as exploiting single cell RNA-seq and genomic atlases. Key questions include how the spatial organization of cells influences tissue behaviour. We collaborate closely with several labs on the “wet” side including the Fantl lab for CODEX data and analysis.
Neurodegenerative disease
Intriguingly, there are many pathways and biological functions that recur as significant in both cancer and neurodegenerative studies that exploit genomic data to understand the mechanisms behind these diverse diseases. We are developing and using new computational approaches to understand the similarities and their implications. We collaborate with researchers in the Wu Tsai Neurosciences Institute on projects including Alzheimer Disease, and vascular-induced dementia.
We are in the Department of Pathology at Stanford University.