CS 481/583: Bioinformatics Algorithms

Bilkent University, Spring 2025

Lecture Cancellation🥳: Thanks to the RECOMB 2025, the following lectures are going to be canceled.

  • April 25, 2025
  • April 29, 2025

RECOMB is one of our all-time favourite annual bioinformatics conferences and it’s the coolest one out there 😎. So, if you haven’t heard of it yet you might wanna check it out 👀.

This year, it’s happening in Seoul 🇰🇷 (honestly, should be renamed to K-RECOMB), and every year, it hops to a different continent like it’s on a world tour. In 2023, it was in İstanbul 🇹🇷 and obviously that made it the best one.

If you’re curious (or just wanna see some top-tier science talks), you can binge the presentations from past RECOMBs — including the iconic 2023 edition — right here.

more like: (bio)informatics ALGORITHMS

Instructor: Can Alkan

Class Hours: Tue 13:30-15:20 - Fri 09:30-10:20

Class room: B-Z08

Office hour: By appointment (Public calendar, changes frequently)

Staff contact: Staff

NOTE: Some biology, molecular biology, genetics background would help, but not required. Basics regarding the topic will be covered in class.

Prerequisites: Elementary discrete mathematics, basic algorithms and data structures, and programming proficiency with, e.g., C/C++/Java will be expected. Knowledge of elementary combinatorics and probability, fundamental algorithms for sorting, searching, hashing and dynamic programming, elementary graph algorithms would be very helpful.

Textbook: None mandatory, some recommended material

Grading: There will be one midterm exam (25%) and a final exam (35%). A further 30% of the final grade will be based on homework/programming assignments, and 10% will be based on quizzes.

Grading Policy: Note that we do not discuss with students about grades. Therefore, we will not answer any questions about the passing grades and/or students’ requests for passing the course. Any emails sent to this effect will be omitted.

Course Slides: CHECK HERE

Key Dates (tentative, subject to change):

  • Midterm: April 8, 2025 – during class hours
  • Quizzes:
    • Quiz 1: February 11, 2025
    • Quiz 2: March 4, 2025
    • Quiz 3: March 18, 2025
    • Quiz 4: April 15, 2025
    • Quiz 5: May 6, 2025
  • Homeworks:
    • HW0:
      • Assigned: February 7, 2025
      • Deadline: February 15, 2025
    • HW1:
      • Assigned: February 17, 2025
      • Deadline: February 28, 2025
    • HW2:
      • Assigned: March 6, 2025
      • Deadline: March 23, 2025
    • HW3:
      • Assigned: April 8, 2025
      • Deadline: April 18, 2025
    • HW4:
      • Assigned: April 21, 2025
      • Deadline: May 1, 2025
    • HW5:
      • Assigned: TBA
      • Deadline: TBA

Important information for exams:

  • You will be given the opportunity to bring cheat sheet to the midterm and final exams (not the quizzes). DO NOT try to memorize anything, instead grasp the logic behind each algorithm & data structure.
  • Write legibly, and make your answers clear.
  • Unintelligible answers may fail to receive credit.
  • In the case of a "design an algorithm" question, you are expected to give only pseudocode. Any "real" code may not be graded.

Frequently Asked Questions: Here