Project Description:

RNA is critical to cell regulation but there remains about 25% of RNA that we have no idea of their function (long noncoding RNAs). The goal of the project is to discover topologically similar RNAs. Because they share a conserved a similar structure, it is very likely that they share a similar function. The students role is to implement and test software for comparing graphlet fingerprints of RNA structures to find the similar classes. The problem is at the stage of feature engineering - identifying an informative feature vectors as input for unsupervised learning approaches that will be able to find the similar structures. Requires experience in OO programming in Python. Background in graph theory might and machine learning might be useful but is not essential.

Requirements:

Python programming experience, Some exposure to Statistics, linear algebra, and machine learning would be helpful but not essential

Project Description:

Abiotic stress is an import aspect of plant biology. We have two current datasets: Phureja potatoes grown in the Andes in Colombia have been exposed to heat stress similar to what we expect to see due to global warming. We have gene expression data (RNASeq) from 1 susceptable and 3 heat-resistant varieties. Biochemichal data suggests the the three resistant variety use different resistant mechanisms. The goal is to identify genes/potato varieties that can be developed for agricultural use as the climate continues to warm.

A second dataset looks at a novel Cadmium resistant fungus , also from Colombia. High Cd in the soil in some regions of Colombia restrict the export of chocolate from Colombia because the European Union limits the Cd level in chocolate. Soil fungi that have the ability to take up and sequester or immobilize Cd may be useful in bio-remediation of high Cd soils. The samples in this dataset have been grown at normal and high (300ppm) Cd levels. RNASeq data will allow us to identify the genes that respond to high CD and identify the mechanism of Cd resistance in this fungus.

This is an entirely computational project; the student will analyze the differentially expressed genes using several different approaches. Experience with the the R statistics system will be useful but not essential. New project arrive all the time so we may other similarly interesting projects by summer 2025.

Requirements:

Basic background in molecular biology very useful, some experience with statistics and/or genomics useful but not essential

Project Description:

Learn how to program XR headsets like the Quest 3, develop XR applications, and advance the XR state of the art.

Requirements:

Any of these qualifications would be a plus:

Virtual Reality, Mixed Reality, Augmented Reality
Unity 3D
C#, C++
Computer Graphics
Computer Vision