Physical Sciences and Mathematics Commons^™

Gemini: A Computationally-Efficient Search Engine For Large Gene Expression Datasets, Timothy Defreitas, Hachem Saddiki, Patrick Flaherty

Mathematics and Statistics Department Faculty Publication Series

Background

Low-cost DNA sequencing allows organizations to accumulate massive amounts of genomic data and use that data to answer a diverse range of research questions. Presently, users must search for relevant genomic data using a keyword, accession number of meta-data tag. However, in this search paradigm the form of the query – a text-based string – is mismatched with the form of the target – a genomic profile.

Results

To improve access to massive genomic data resources, we have developed a fast search engine, GEMINI, that uses a genomic profile as a query to search for similar genomic profiles. GEMINI …

Robust Optimization Of Biological Protocols, Patrick Flaherty, Ronald W. Davis

Mathematics and Statistics Department Faculty Publication Series

When conducting high-throughput biological experiments, it is often necessary to develop a protocol that is both inexpensive and robust. Standard approaches are either not cost-effective or arrive at an optimized protocol that is sensitive to experimental variations. Here, we describe a novel approach that directly minimizes the cost of the protocol while ensuring the protocol is robust to experimental variation. Our approach uses a risk-averse conditional value-at-risk criterion in a robust parameter design framework. We demonstrate this approach on a polymerase chain reaction protocol and show that our improved protocol is less expensive than the standard protocol and more robust …