Research Experiences for Undergrads in the Warnow Lab

Research Overview

My research is in two areas: computational biology and (to a lesser extent) scientometrics. Students interested in working with me should have already completed the coursework required for each area (see below), and be able to provide the information requested in the "How to apply" section, listed below.

Scientometrics. I work with CS Professor George Chacko in method development for scientometrics. If you are interested in this work, self-funded, and have already taken CS 361 and 374, STAT 400 and 410, and at least one of CS 412, 446, 498 (Applied Machine Learning), then you are encouraged to contact me. Otherwise, please wait until you have completed the coursework listed above.

Computational biology research. 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. I welcome strong undergraduate students currently enrolled at UIUC from computational disciplines (CS, ECE, Statistics, and Mathematics) who are keenly interested in research, ambitious, and either planning to go to graduate school or considering this seriously. I can supervise projects that include testing and developing new computational methods in phylogenomics, analysis of biological datasets using different methods, etc. To join my lab, you should first take CS 581, my graduate class in Algorithmic Genomic Biology. This course introduces students to computational phylogenomics, and many students do research as a course project. These research projects often result in published journal and conference papers, and thus are a great way to learn about the research area. I am teaching this course in Spring 2020, and expect to teach it again in Fall 2021. Anyone who takes the course and does well will be able to work with me the semester following the course, to finish their research project and (hopefully) get a publication. (I will also consider you if you have taken CS 466 and received an A+ in the course. However, in this case, you will need to be a junior, and your first semester with me will involve reading my textbook and scientific papers and doing homework problems from the textbook.)

Summer 2019 REU students

During the summer 2019 semester, I worked with 10 undergraduate students (all from UIUC). These REU students learn the mathematical foundations of the material, which is covered in my textbook. In addition, they are looking at the lectures for CS 581, and doing modified homeworks (suitable for undergrads) at this page. Finally, they are doing initial projects, which are described in my notes on first projects.

My textbook: Computational Phylogenetics: An introduction to designing methods for phylogeny estimation, published by Cambridge University Press.

Interested in applying?

CS/ECE/Stats/Math students: Note that 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).

Biology students: I am also interested in working with biology undergraduate students, as long as you have practical experience in phylogeny estimation or multiple sequence alignment, and your research interests involve doing analyses of this type. Let me know what you would like to do reseach on, and how it fits into my research.

Papers to read: Before you apply to work with me, please first read a few of my recent papers. The following is a good representative of the kinds of work I am doing in my three active NSF projects (the parenthetical numbers refer to the number in my online publication list):

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:

Here are two examples of publications done by undergraduate students with me:

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. Also note that I will not consider your application unless you have taken the required courses (CS 581 for students interested in computational biology, and the other courses, listed above, for students interested in scientometrics). Please send me an email with your current transcript, and an answer to the following questions: