Research Experiences for Undergrads in the Warnow Lab

Research Director: Tandy Warnow, Founder Professor of Computer Science

Research Overview: My research combines mathematics, computer science, probability, and statistics, in order to develop algorithms with improved accuracy for large-scale and complex estimation problems in phylogenomics (genome-scale phylogeny estimation), multiple sequence alignment, metagenomics, and historical linguistics. I am a big fan of Blue Waters, and have benefitted from two allocations. Click here for the 2017 annual report for my Blue Waters allocation on algorithms for big data phylogenomics, proteomics, and metagenomics. Click here or here for more about my research and the students I work with, and here for a brief biosketch.

Funding available from NSF: I have some REU funding available for qualified undergraduate students from one of my National Science Foundation grants (see this page). This REU funding can support any research relevant to constructing and using multiple sequence alignments, including for phylogenetic tree (i.e., evolutionary tree) estimation, protein structure and function prediction, metagenomic taxon identification, etc. The only important restriction is that the funding is limited to U.S. citizens, nationals, and permanent residents. If you are a foreign student and not eligible for the REU funding, you can still do research with me.

CS/ECE/Stats/Math students: You do not need to know any biology to do this research! To succeed in this research you should have very strong programming skills (especially in Python), be interested in challenging yourself, good at working with others and also independently, and have strong communication skills (both oral and written). You should already have completed CS 173 and be enrolled in (or have completed) CS 225. If you have completed 374 and 225, it would be great if you also took my graduate class CS 581, where I teach the basics of discrete algorithm design in computational biology, focusing on phylogenetics, multiple sequence alignment, and the applications of these tools in other problems in biological analysis (e.g., in metagenomics and protein structure prediction). If you are a student in CS 196 (honors section for 173) in Fall 2018, I can potentially give you homework problems that are related to computational biology research. However, the research itself would not begin until after you have completed 173.

Biology students: REU support for undergrads in biology is also possible. Let me know what you would like to do reseach on, and how it fits into the overall objectives of my NSF grant (see this page). We might be able to make this work!

Possible research projects: I am open to many different possible research projects, but the most likely ones to succeed would be ones where you would work with one of my current PhD students. However, if you have something specific in mind, please let me know what you would like to do. Here are some types of research projects that I would be glad to support:

As an example of an undergraduate research project, a former student (Kodi Collins) from CS 173 did research with me after completing 173, and published a paper: see PASTA for Proteins, Kodi Collins and Tandy Warnow. She is now a PhD student in Computer Science at UCLA!

Doing a research project with me involves a substantial commitment. Research students have individual meetings (at least weekly, but more often when you are implementing and testing methods, or writing up results for publication) with me and one or more of my graduate students. It will also involve attendance in weekly group meetings. I provide mentoring in learning how to present research results, analyze data, read scientific papers, and design methods. In other words, being a research student involves a substantial effort and time commitment on your part, but also from me and from graduate students in my group.

How to apply

I receive many applications for research positions in my lab, and can only accept students who are serious about the effort involved and where there is a good fit with my group. Please send me an email with your current transcript, and an answer to the following questions: