CSCI 494/594: Bioinformatics Seminar
Seminar goals
Our seminar has a number of goals. These may change as we go!
- To practice reading academic research papers.
- To practice presenting and discussing academic research.
- To learn about recent research in bioinformatics.
- To learn about foundational topics in bioinformatics.
- To start research conversations and find new research directions.
How it works
Every semester, we will choose a set of papers to read as a group. Each paper will have two leaders, who will lead two weeks of discussion of the paper.
If you are a discussion leader
- Get started early! Research papers are dense and you will need to gain a solid understanding of at least the basics of the paper in order to lead discussion. I suggest skimming the paper two weeks in advance at least. Also, sometimes we start reading a paper and realize that one of its sources or follow-on papers gives a better view into the subject, so starting early allows us to pivot if needed.
- Leading discussion can look different for different groups and different papers. However you choose to do it, be sure to explain the big picture of the paper (what problem is it solving? why was the problem previously unsolved? what allowed them to solve the problem? why do we care?) and give lots of opportunity for interaction and discussion.
- Meet with your partner at least once to plan how you will lead discussion.
- (At least) a few days before the meeting, send a message in Discord saying which parts of the paper you will be focusing on and sharing any other information you think will be helpful for the rest of the group to prepare to have a productive discussion.
If you are not a discussion leader
- Spend 1-2 hours prepping for each meeting, focusing on the sections of the paper that the discussion leaders posted about in Discord. This often looks like skimming the paper, trying to understand the big picture at least, and only looking at details if you have time. You may also find other resources to help you understand the paper, such as author talks on YouTube, explanation of topics you are unfamiliar with, or other related academic papers. If you find resources others might find helpful, feel free to post them in Discord!
- Before the meeting, post a short paragraph about your interaction with the paper so far, ideally specifically relating to the parts that the discussion leaders told you to focus on. This could range from: “I don’t understand a single thing about this paper and here are some specific questions I have that I think could help me at least start to understand it” to “this paper is blowing my mind and here are my favorite things that the authors have done” or even “I totally forgot to read the paper this week but will do my best to follow the discussion anyway.”
- During the meeting, stay engaged with the discussion leaders and the group. Ask questions, share your thoughts or critiques of the paper, etc.
- After the meeting, share (1) something you thought the discussion leaders did well and (2) something you are still confused about or would like to learn more about regarding the paper.
Fall 2025 schedule
| Week | paper |
|---|---|
| 1 (8/25–8/29) | No meeting; see Discord for organizational tasks such as choosing a weekly meeting time, signing up for discussion leadership, etc. |
| 2 (9/1–9/5) | Paper 1 |
| 3 (9/8–9/12) | Paper 1 |
| 4 (9/15–9/19) | Paper 2 |
| 5 (9/22–9/26) | Paper 2 |
| 6 (9/29–10/3) | Paper 3 |
| 7 (10/6–10/10) | Paper 3 |
| 8 (10/13–10/17) | Paper 4 |
| 9 (10/20–10/24) | Paper 4 |
| 10 (10/27–10/31) | Paper 5 |
| 11 (11/3–11/7) | Paper 5 |
| 12 (11/10–11/14) | Paper 6 |
| 13 (11/17–11/21) | Paper 6 |
| 14 (11/24–11/28) | Paper 7 |
| 14 (12/1–12/5) | Paper 7 |
Spring 2025 schedule
| Week | paper |
|---|---|
| 1 (1/13-1/17) | Intro–meeting but no paper |
| 2 (1/20-1/24) | Sign up for papers–no meeting |
| 3 (1/27-1/31) | Paper 1–BLAST (Tara and McKayl) |
| 4 (2/3-2/7) | Paper 1 |
| 5 (2/10-2/14) | Paper 2–HMMER (Afra and Jacob) |
| 6 (2/17-2/21) | Paper 2 |
| 7 (2/24-2/28) | INBRE Regional Meeting and SIGCSE–no meeting |
| 8 (3/3-3/7) | Paper 3–An information-based sequence distance and its application to whole mitochondrial genome phylogeny |
| 9 (3/10-3/14) | Paper 3 |
| Spring break (3/17-3/21) | No meeting! |
| 10 (3/24-3/28) | Paper 4–Gene Structure Prediction by Linguistic Methods |
| 11 (3/31-4/4) | Paper 4 |
| 12 (4/7-4/11) | Paper 5–Prediction of miRNA-disease associations based on PCA and cascade forest |
| 13 (4/14-4/18) | Paper 5 |
| 14 (4/21-4/25) | RECOMB–no meeting |
| 15 (4/28-5/2) | Paper 6–Logan: Planetary-Scale Genome Assembly Surveys Life’s Diversity |