In this project, we aim to develop cheap methods for evaluating ecology using shallow sequencing. Methods such as genome skimming have the potential to enhance the study of biodiversity, but new algorithms are needed to enable such studies. That's the goal of this effort. Most methods we develop are kmer-based. The work involves both working with real data and simulations. We work with partners from outside academia as well. The work is shared with Prof. Bafna.

In this broadly defined project, we develop new machine-learning methods to infer or use phylogenies. The goal is to see if machine learning methods can beat existing methods in specific tasks such as phylogenetic placement or outlier detection. The focus is on finding innovative ways to update machine learning methods or adopt them to phylogenetics. We also work on incorporating phylogenies as prior data into machine learning methods for answering other questions (e.g., metagenomic classification).

In this broadly defined project, we develop novel methods for inferring phylogenetic trees from genome-wide datasets. The project involves modeling evolutionary processes, developing scalable algorithms, analyzing their statistical properties in theory, applying them to large simulated and biological data to evaluate them, and providing software to the community.

Extrachromosomal DNA formation is an important pathological condition found in nearly a third of cancers and all cancer subtypes. Our lab is developing computational tools to characterize their structural and functional properties of ecDNA and related focal amplifications. 

The interested students should have an interest in learning about,  designing and implementing graph algorithms, and should commit to taking my winter class CSE280A.