COMPSCI 260: Introduction to Computational Genomics


A computational perspective on the exploration and analysis of genomic and genome-scale information. Provides an integrated introduction to genome biology, algorithm design and analysis, and probabilistic and statistical modeling. Topics include genome sequencing, genome sequence assembly, read mapping, local and global sequence alignment, sequence database search, gene finding, phylogenetic tree construction, and elementary gene expression analysis. Methods include dynamic programming, indexing, hidden Markov models, and elementary supervised machine learning. Focuses on foundational algorithmic principles. Development of practical experience with handling, analyzing, and visualizing genomic data using the computer language Python.

The course requires students to program often in Python. Students coming in to the course must already know how to program in some computer language, but it need not be Python. If it is not Python, students will be expected to come quickly up to speed in Python on their own. Additionally, students should be comfortable with mathematical thinking and formulas, and should have had some exposure to basic probability as well as molecular or cellular biology; however, the course has no formal course prerequisites, and quick refreshers of relevant background will be provided. Please speak to the instructor if you are unsure about your background. This course is a valid elective in both biology and computer science.


Professor Alex Hartemink

Email: amink at
Office Location: LSRC D239
Office Phone: (919) 660-6514

Kyle Pinheiro, TA Email: kyle.pinheiro at
Lara Breithaupt, TA Email: lara.breithaupt at
Nhat Duong, TA Email: nhat.duong at
Gene Yang, UTA Email: gene.yang at
Helen Xu, UTA Email: helen.z.xu at
Henry Gussis, UTA Email: henry.gussis at
Holly Zhuang, UTA Email: mingming.zhuang at
Joshua Tennyson, UTA Email: joshua.tennyson at
Kash Sreeram, UTA Email: kashyap.sreeram at
Lola Maglione Silva, UTA    Email: carola.maglione.silva at
Michelle Kwan, UTA Email: michelle.kwan at
Naomie Gao, UTA Email: naomie.gao at
Sierra Seifert, UTA Email: sierra.seifert at
Zach Pracher, UTA Email: zachary.pracher at

Office hours

Office hours with TAs and UTAs will be held at the following times, starting on Tuesday 16 January; all sessions are in-person. Most sessions will be held in Reuben-Cooke 133 (go through the front door, turn right at the hallway, and it's the room immediately on your right), but Monday sessions from 2:30–5:30pm will instead be held in LSRC D344 (D-wing entrance is at the far end, closest to Research Drive: climb the stairs to the third floor, and D344 will be straight ahead). Remember that if your question is pretty simple, you are likely to get help quickest by asking on Ed (in fact, your question may already be answered there).

Sunday 5–6pm Naomie Gao Reuben-Cooke 133
8–10pm Helen Xu Reuben-Cooke 133
Monday 10am–12pm Sierra Seifert Reuben-Cooke 133
12:30–2:30pm Lara Breithaupt Reuben-Cooke 133
Monday 2:30–3:30pm Naomie Gao LSRC D344
3:30–5:30pm Michelle Kwan LSRC D344
Tuesday 2–4pm Gene Yang Reuben-Cooke 133
4–6pm Holly Zhuang Reuben-Cooke 133
6–8pm Zach Pracher Reuben-Cooke 133
7–9pm Kash Sreeram Reuben-Cooke 133
Wednesday 1–3pm Kyle Pinheiro Reuben-Cooke 133
3–5pm Nhat Duong Reuben-Cooke 133
5–7pm Henry Gussis Reuben-Cooke 133
7–9pm Joshua Tennyson Reuben-Cooke 133
Thursday 3–5pm Lola Maglione Silva Reuben-Cooke 133

If you would like to speak with the instructor about anything, you are welcome to stick around after lecture to chat, or you can send an email to schedule a meeting at a time that is convenient for you.


The class meets 10:05–11:20am on Tuesdays and Thursdays in 111 BioSci.