[talks] Vicky Yao will present her FPO "Integrative network-based approaches to analyze genomics data" on Friday, 8/24/2018 at 1:00pm in 200 CIL.

[Nicki Gotsis]

Vicky Yao will present her FPO "Integrative network-based approaches to analyze genomics data" on Friday, 8/24/2018 at 1:00pm in 200 CIL. 

The members of her committee are as follows: Readers: Mona Singh and Barbara Engelhardt; Examiners: Ryan Adams, Coleen Murphy (MOL), and Olga Troyanskaya (adviser). 

A copy of her thesis is available upon request. 

Everyone is invited to attend her talk. The talk abstract follows below. 
The generation of diverse genome-scale data across organisms and experimental 
conditions is becoming increasingly commonplace, creating unprecedented opportunities 
for understanding the molecular underpinnings of human disease. However, these 
large data are often noisy, highly heterogeneous, and lack the resolution required to 
study key aspects of metazoan complexity, such as tissue and cell-type specificity. Furthermore, 
targeted data collection and experimental verification is often infeasible in 
humans, underscoring the need for methods that can integrate -omics data, computational 
predictions, and biological knowledge across organisms. 
In this dissertation, I describe several novel, integrative computational approaches 
to address these challenges. First, I will describe a statistical and machine learning 
approach that takes advantage of high-quality neuron-specific molecular profiles of 
cells that vary in vulnerability to Alzheimer’s disease obtained in mouse to generate 
neuron-specific functional networks in human. We then combine these network 
models with human quantitative genetics data to prioritize likely Alzheimer’s disease 
candidates. Next, I present an in-depth analysis of all major adult C. elegans tissues 
and genome-wide expression predictions across 76 tissues and cell types. The tissue 
expression prediction method is one of the building blocks of diseaseQUEST, an integrative 
computational-experimental framework that combines human quantitative 
genetics with in silico functional network representations of model organism biology 
to systematically identify disease gene candidates. This framework leverages a 
novel semi-supervised Bayesian network integration approach to predict tissue- and 
cell-type specific functional relationships between genes in model organisms. We use 
diseaseQUEST to construct 203 tissue- and cell-type specific functional networks and 
predict candidate genes for 25 different human diseases and traits using C. elegans as 
a model system, with a particular focus on Parkinson’s disease. Finally, I will present a 
network-based approach that systematically identifies differential isoforminteractions. 
We apply this approach to the study of tissue and environment dynamics in Alzheimer’s 
disease. Together, these approaches provide a framework for addressing the challenges 
of data heterogeneity, noise, and biological resolution in human molecular data to 
better understand the etiology of human disease. 

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