Welcome to Fiveprime

Nathan Siemers

I am a consultant for research in pharmaceutical translational medicine, with a heavy emphasis on genomics and bioinformatics. I'm cross-trained in immunology, oncology, bioinformatics, genomics, and chemistry. My training and experience have made able to integrate information and synthesize hypotheses and conclusions across diverse domains of science and medicine.

Below is a small collection of tools I've created to answer questions about cancer and immunology genomic studies, including the analysis of single-cell RNA information.

T2: a new browser for the 2018 release of TCGA (pan-cancer study group)
This tool captures and plots RNA, gene-level mutation events (.mut), position-specific mutations (.fmut), continuous and thresholded copy number estimates (.cnv and .cnc), signature projections, subtype classifications, purity estimates, and much more. It also contains advanced captilities for adjusting for biases and covariates in multi-model TCGA data.

"Faux Flow" viewer for single cell Melanoma RNA-seq data
There's only so much you can get out of a T-SNE or UMAP clustering. I built tools that are modeled on the behavior of flow cytometry tools. Here's one that interrogates the Tirosh et al. Melanoma paper (fantastic paper),

Faux Flow viewer for single cell liver cancer RNA-seq data
Hepatocellular carcinoma T cell data set from Zheng et al.

Faux Flow viewer for single cell, blood derived, monocytes and dendritic cells
Alexandra-ChloƩ Villani et al.

Results browser to support the 2017 Siemers et al. genome-wide association study of tumor genetics with immune cell estimates.
(Link to paper)

Unified TCGA (cancer), TARGET (childhood cancer), and GTEX (normal human tissue) RNA data browser.
Many thanks to the UCSC Xena team and the TOIL project to make unified data available!

Network relationships of genes across TCGA
The PLOS paper (referenced above) used signatures for immune cell types that were derived from a mutual-rank distance network across TCGA. In particular, we discovered the association of CCR8 with tumor Tregs using these networks. The AllNets application will let you interrogate these relationships across all of TCGA, or any specific tumor type.