About Me

Hello! I'm Natalie Davidson, a Post-Doctoral researcher in the Greene Lab at the University of Colorado School of Medicine. I received my Ph.D. from Tri-Institutional Program for Computational Biology and Medicine in New York, while conducting research at ETH Z├╝rich.

I am interested in building methods that can integrate both single-cell and bulk expression data to better understand disease. Single-cell experiments provide greater resolution within a single sample, however in comparison to the currently available bulk samples, they lack coverage across diseases, tissues, and perturbations. Using both data types can help us make the most use of the available datasets, which is especially beneficial for rare diseases. The methods I am most excited to explore in this space are structurally restricted neural networks. Through careful design of these networks, we can leverage our existing biological knowledge of cells, tissues, signaling pathways, and experimental design to obtain more generalizable and interpretable models.


Prior Work

During my Ph.D., I conducted single cancer and pan-cancer analyses using RNA-Seq and Ribosome Profiling data. I typically use generalized linear models and generalized linear mixed models. I was a part of the International Cancer Genome Consortium, where I integrated multiple transcriptional aberrations such as splicing, fusions, over/under expression, allele specific expression, and others in over 1,000 samples to identify cancer relevant genes and alteration patterns. I received my B.Sc. in computer science and minor in applied mathematics from University of California, Santa Barbara.  I received my M.Sc. in computer science from University of California, Los Angeles under the advisement of Dr. Jason Ernst.

Thesis Title: "Identification and Characterization of Aberrations in Cancer through the lens of RNA." (link)

Published in Nature and other Nature journals (Feb. 2020). Photo credit: Nik Spencer/Nature.

Code

Presentations

(full publications)

Integrating Diverse Transcriptomic Alterations to Identify Cancer-Relevant Genes

( link to paper )

Identification and Characterization of HIF-Dependent Altenative Splicing Events in Pancreatic Cancer

( link to paper )