The Exelixis Lab

Enabling Research in Evolutionary Biology


Bioinformatics courses are taught by Alexis at the Karlsruhe Institute of Technology with the occasional help of his PostDocs and PhD students from the Heidelberg Institute for Theoretical Studies. See here for contact details.

As of winter 2023/24 the lectures on "Introduction to Bioinformatics for Computer Scientists" will be taught jointly and simultaneously at KIT and the Univesrity of Crete (see below for further information).

Winter Semester: Introduction to Bioinformatics for Computer Scientists

General Information

Reading List and on-line material

  • General books:
    • Carlos Setubal, Joao Meidanis: "Introduction to Computational Molecular Biology"
    • Fritz Wrba, Helmut Dolzing, Christine Mannhalter: "Genetik vesrtehen"
    • Volker Knoop, Kai Müller: "Gene und Stammbäume"
    • Andrzej Polanski, Marek Kimmel: "Bioinformatics"
    • Michael S. Waterman: "Introduction to Computational Biology"
  • Book on phylogenetics: Ziheng Yang: "Computational Molecular Evolution". This book is available as e-book at the KIT library. To access it via this link you will need to have an IP from the KIT network.
  • New: a very nice on-line course on genetics which my lab members (mostly CS people) have found very useful
  • Debunking the 100X GPU vs. CPU myth: an evaluation of throughput computing on CPU and GPU
  • a link to a tutorial and examples for gcc compiler intrinsics
  • a nice video lecture about 3rd generation (also called next-next generation sequencing)
  • A very nice and readable paper on assessing the quality/benchmarking of multiple sequence alignment methods
  • Two public outreach texts about evolution and what we need phylogenetic trees for
  • Link to the denormalized floating point number micro-benchmark


At KIT A 20 minute oral exam at the end of the semester, dates will be scheduled via doodle.

The exam modalities at UoC will be announced later on.

Course Mailing List

Write an email to Alexis such that he can add you to the course mailing list, very important!

Semester-specific information (winter 2024/25)

The Master level course on “Introduction to Bioinformatics for Computer Scientists” deviates substantially from the standard course schemes at KIT (Karlsruhe Institute of Technology) and UoC (University of Crete) as your lecturer (Prof. Alexandros (Alexis) Stamatakis) is currently setting up a second research lab in Crete while maintaining his lab and position in Germany.

The course will be taught simultaneously at both Universities. Live lectures will either take place at UoC or at KIT (exact schedule for live lectures to be determined) and be streamed via Zoom to the respective other university. Keep in mind the time difference between Greece and Germany - Greece is one hour ahead!

Further, because winter semester lecture periods between Greece and Germany deviate substantially, the course has been condensed into 8 lectures of three hours each to fit the time period during which the respective winter semesters do overlap.

The exams will take place during the standard exam periods of the respective universities (to be discussed with the KIT students).

Live Lectures at KIT will take place in Room: -120 in building 50.34

Live lectures at UoC will take place in Multimedia Room: K.206

KIT Students: Please register properly for the course via the KIT campus system.

KIT & UoC Students: send an Email to to make sure to be added to the course mailing list.

UoC Students: The UoC course web-site can be found here.

Course material from previous semesters including links to the video lectures on youtube is available on-line; updated slides will be provided shortly after the course.

Lecture day & time: Mondays at 09:45 German local time / 10:45 Greek local time

Lecture Block duration: 2 hours 30 minutes (1:15 of lecture, 15 mins break, 1 hour of lecture)

No Lecture on Monday October 28:this is a national holiday in Greece !!!!

Lecture Schedule - University Acronym after block number indicates where the lecture will be given live (subject to change) and in parentheses it is indicated who will be teaching this lecture.

Lecture SCHEDULE, subject to change

  • September 23
    • Block 0 UoC (Alexis)
    • Meeting with Greek students only to say hello as well as introduce the course and concept during the first week of the Greek semester, before the joint course starts on October 23.
  • October 21
    • Block 1 LIVE at KIT (Alexis)
    • Lecture 1: Introduction
    • Lecture 2: Basic Molecular Biology
  • November 4
    • Block 2 LIVE at KIT (Alexey & Lukas)
    • Lecture 3: Pair-wise Sequence Alignment
    • Lecture 4: BLAST & Genome Assembly
  • November 11
    • Block 3 LIVE at UoC (Alexis)
    • Lecture 5: Multiple Sequence Alignment
    • Lecture 6: Introduction to Phylogenetics
  • November 18
    • Block 4 LIVE at UoC (Alexis)
    • Lecture 6: Introduction to Phylogenetics (continued)
    • Lecture 7: Phylogenetic Search Algorithms
  • November 25
    • Block 5 LIVE at KIT (Alexis)
    • Lecture 9: A brief introduction to Markov Chains
    • Lecture 10: Maximum Likelihood Lecture
  • December 2
    • Block 6 LIVE at UoC (Alexis)
    • Lecture 10: Maximum Likelihood Lecture (continued)
    • Lecture 11: Advanced Maximum Likelihood Stuff
  • December 9
    • Block 7 LIVE at UoC (Alexis)
    • Lecture 12: Bayesian inference & MCMC
    • Lecture 13: Advanced Bayesian inference & MCMC
  • December 16
    • Block 8 LIVE at KIT (Alexis)
    • Lecture 13: Advanced Bayesian inference & MCMC (continued)
    • Lecture 14: Wrap up & exam preparation

Summer Semester: Seminar on Hot Topics in Bioinformatics

General Information

You will need to select papers to present, give a presentation and write a report.

This main seminar allows students to understand and present the contents of current papers in Bioinformatics such as published for instance in the journals Bioinformatics, BMC Bioinformatics, Journal of Computational Biology etc. or at conferences such as ISMB or RECOMB.

We will provide a list of interesting papers but students can also propose papers they are interested in. Students may also chose to cover broader topics of more general interest such as multiple sequence alignment, Bayesian phylogenetic inference, read assembly etc.

Each student will be assigned a lab member (a PhD student or PostDoc) for help with understanding the article and preparing the slides as well as the report.

Students should give a 35 minute presentation on their topic of choice and write a report (Seminararbeit) comprising 8 pages (including references)!

Below you will find some useful material on writing reports in English:

Latex template for reports: We are going to use the Springer LNCS (Lecture Notes in Computer Science) Latex template available here.

Please make sure to download file:!

Here are some examples from well-written reports of previous years. Note that in earlier years we had a higher report page limit!. The current page limited is reflected by the 2021 example.

Here are some examples of nice slides from previous years:

Semester-specific Information (summer 2024)

The seminar on "Hot topics on Bioinformatics" is only intended for students that attended the lecture taught in winter 2023/24 and passed the exam.

The kick off meeting will take place on April 25 from 09:45 - 11:15 in SR236.

The presentations will take place on July 23 in room SR 010 - exact time to be determined.

There is a limited number of 10 places available for this seminar: students must register via the KIT campus system and will receive places (or not) on a first come first served basis. Please also drop Alexis an email once you have registered to be included in the seminar mailing list! In case of difficulties with the registration please contact Alexis via Email.

Deadlines & Dates

  • April 25 Seminar Introduction by Alexis
  • May 3 Topics fixed, supervisors assigned, and presentation slots agreed. Meet with assigned supervisor at least three times for (i) paper discussion and (ii) presentation review and (iii) for written report review. You can find the contact data of your potential supervisors here.
  • Seminar presentations will take place in one single block toward the end of the semester on July 23 between 08:00 and 19:00 (exact times to be determined alter on) in room SR 010.
  • September 27 Report submission deadline - reports via email to Alexis, submission time: any time zone in the world where it will still be September 27.

Intro slides (April 25)


    To be determined.

Block Presentations July 23, 2024: 08:00 - 19:00

Room ATIS Seminar Room SR010, final presentation times to be determined.

Teaching Evaluation Results and Awards

Course Evaluation Results (Learning Quality Indices)

  • Winter 2012/13: 100 out of 100. PDF
  • Summer 2014: 97.9 out of 100. PDF
  • Winter 2014/15: 100 out of 100. PDF
  • Winter 2015/2016: 100 out of 100. PDF
  • Winter 2016/2017: 100 out of 100. PDF
  • Winter 2017/2018: 100 out of 100. PDF
  • Winter 2018/2019: 100 out of 100. PDF
  • Winter 2019/2020: 100 out of 100. PDF
  • Winter 2020/2021: 100 out of 100. PDF
  • Winter 2022/2023: 100 out of 100. PDF

Practical Evaluation results (Learning Quality Indices)

  • Summer 2015: 100 out of 100. PDF
  • Summer 2017: 100 out of 100. PDF

Seminar Evaluation results (Learning Quality Indices)

  • Summer 2018: 100 out of 100. PDF

Teaching Awards

  • Alexis and Michael Hamann (PhD student from the chair of Prof. Wagner at KIT) received a certificate for teaching excellence from the dean of the CS faculty at the Karlsruhe Institute of Technology for their programming practical "Hands-on Bioinformatics Practical" tought in summer 2017 based on the practical evaluation by the students. This practical also resulted in a peer-reviewed publication in the high quality journal Bioinformatics.
  • The three former students of the programming practical (Michael Hoff, Stefan Orf and Benedikt Riehm) will receive a prize from KIT on October 14, 2016, for research work conducted by students, since they published a peer-reviewed paper presenting the results of the practical.
  • Alexis and Tomas received a certificate for teaching excellence from the dean of the CS faculty at the Karlsruhe Institute of Technology for their programming practical "Hands-on Bioinformatics Practical" tought in summer 2015 based on the practical evaluation by the students.
  • Alexey, Alexis, Andre, Kassian, Mark Holder, and Tomas received a certificate for teaching excellence from the dean of the CS faculty at the Karlsruhe Institute of Technology for the course "Introduction to Bioinformatics for Computer Scientists" tought in winter 2014/15 based on the course evaluation by the students.