The Exelixis Lab


Enabling Research in Evolutionary Biology

Bioinformatics

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

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

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.

General Information

Course Slides

Please send Alexis an email to be added to the course mailing list and thereby obtain access to the course slides.

Lecture (Winter)

Knowledge Quiz Answers:

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

Exam

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

Course Mailing List

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

Course beers

We will try to go for course beers with the entire course, the pandemic permitting. All drinks will be on Alexis.

Seminar: Bioinformatics (Summer)

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 an Exelixis lab member 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!

Below you will find some general material for the Bioinformatics seminar:

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: llncs2e.zip!

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:

winter 2022/23 course

The lectures will take place live in the seminar room (SR) -120 before Christmas and on-line after Christmas. It will be explained during the first lecture why this is the case. The exact schedule (i.e., classroom versus type of on-line lecture setup) will be announced via email but is also available and will be updated on this page here further below.

All lectures are also available as pre-recorded videos on youtube from previous semesters.

Please register properly for the course via the KIT campus system, but also send an Email to Alexandros.Stamatakis@h-its.org to make sure to be added to the course mailing list.

For the on-line lectures you will most probably be expected to watch the respective lecture on youtube before Wednesday. During the lecture slot on Wednesday and starting at 10:15, we will then most likely hold a Question and Answer session via Zoom (instead of MS Teams) as Zoom has shown to be more stable. The Zoom meeting link will be made available shortly before Christmas.

The last lecture (course wrap up and exam preparation) will be LIVE either in the class room or via Zoom.

Updated slides will be provided shortly before the course (typically on Tuesdays).

The course material including links to the video lectures on youtube is available here.

Lecture plan, subject to change

  • Lecture 1 (Alexis CLASSROOM): Introduction
  • Lecture 2 (Alexis CLASSROOM): Basic Molecular Biology
  • Lecture 3 (Lukas CLASSROOM): Pair-wise Sequence Alignment
  • Lecture 4 (Alexey CLASSROOM): BLAST & Genome Assembly
  • Lecture 5 (Alexis CLASSROOM): Multiple Sequence Alignment
  • Lecture 6 (Alexis CLASSROOM): Introduction to Phylogenetics
  • Lecture 7 (Alexis CLASSROOM): Phylogenetic Search Algorithms
  • Lecture 8 (Alexis CLASSROOM): Markov Chains
  • Lecture 9 (Benoit CLASSROOM): Discrete Operations on Trees
  • Lecture 10 (Alexis ON-LINE): Statistical Models of Evolution I
  • Lecture 11 (Alexis ON-LINE): Statistical Models of Evolution II
  • Lecture 12 (Alexis ON-LINE): Bayesian Phylogenetic Inference
  • Lecture 13 (Alexis ON-LINE): Advanced Bayesian Inference
  • Lecture 14 (Alexis ON-LINE): Population Genetics
  • Lecture 15 (Alexis CLASSROOM or LIVE zoom conference): Course wrap-up and exam preparation

summer 2022 courses

Main Seminar: Hot Topics in Bioinformatics

The seminar on "Hot topics on Bioinformatics" is only intended for students that attended the lecture taught in winter 2021/22 and passed the exam. It will be taking place on Thursdays from 09:45 - 11:15 in room SR236.

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 21 Seminar Introduction by Alexis
  • May 5 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.
  • Presentation slots We might either conduct presentations on the reserved regular time slots (see below), or in a block toward the end of the semester, we will discuss the options together.
  • September 30 Report submission deadline - reports via email to Alexis.

Intro slides (April 21)


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