636-0017-00L  Computational Biology

SemesterAutumn Semester 2020
LecturersT. Stadler, T. Vaughan
Periodicityyearly recurring course
Language of instructionEnglish



Courses

NumberTitleHoursLecturers
636-0017-00 GComputational Biology
The lecture will be available as a recording, and questions can be asked Monday (14-15h) online. Tutorials will happen in Basel, Zurich, and online.
Tutorials in Zurich: Monday 16-17h (CHN C14)
Tutorials in Basel: Thursday 12-13h (BSA E46)
Tutorials online: Monday 15-16h
ATTENTION: Lecture starts on Monday, September 21, First Tutorial in Basel on Thursday September 24
The lecturers will communicate the exact lesson times of ONLINE courses.
3 hrs
Mon14:00-16:00ON LI NE »
16:15-17:00CHN C 14 »
Thu12:15-13:00BSA E 46 »
T. Stadler, T. Vaughan
636-0017-00 AComputational Biology
Project Work (compulsory continuous performance assessments), no fixed presence required.
2 hrsT. Stadler, T. Vaughan

Catalogue data

AbstractThe aim of the course is to provide up-to-date knowledge on how we can study biological processes using genetic sequencing data. Computational algorithms extracting biological information from genetic sequence data are discussed, and statistical tools to understand this information in detail are introduced.
ObjectiveAttendees will learn which information is contained in genetic sequencing data and how to extract information from this data using computational tools. The main concepts introduced are:
* stochastic models in molecular evolution
* phylogenetic & phylodynamic inference
* maximum likelihood and Bayesian statistics
Attendees will apply these concepts to a number of applications yielding biological insight into:
* epidemiology
* pathogen evolution
* macroevolution of species
ContentThe course consists of four parts. We first introduce modern genetic sequencing technology, and algorithms to obtain sequence alignments from the output of the sequencers. We then present methods for direct alignment analysis using approaches such as BLAST and GWAS. Second, we introduce mechanisms and concepts of molecular evolution, i.e. we discuss how genetic sequences change over time. Third, we employ evolutionary concepts to infer ancestral relationships between organisms based on their genetic sequences, i.e. we discuss methods to infer genealogies and phylogenies. Lastly, we introduce the field of phylodynamics, the aim of which is to understand and quantify population dynamic processes (such as transmission in epidemiology or speciation & extinction in macroevolution) based on a phylogeny. Throughout the class, the models and methods are illustrated on different datasets giving insight into the epidemiology and evolution of a range of infectious diseases (e.g. HIV, HCV, influenza, Ebola). Applications of the methods to the field of macroevolution provide insight into the evolution and ecology of different species clades. Students will be trained in the algorithms and their application both on paper and in silico as part of the exercises.
Lecture notesLecture slides will be available on moodle.
LiteratureThe course is not based on any of the textbooks below, but they are excellent choices as accompanying material:
* Yang, Z. 2006. Computational Molecular Evolution.
* Felsenstein, J. 2004. Inferring Phylogenies.
* Semple, C. & Steel, M. 2003. Phylogenetics.
* Drummond, A. & Bouckaert, R. 2015. Bayesian evolutionary analysis with BEAST.
Prerequisites / NoticeBasic knowledge in linear algebra, analysis, and statistics will be helpful. Programming in R will be required for the project work (compulsory continuous performance assessments). We provide an R tutorial and help sessions during the first two weeks of class to learn the required skills. However, in case you do not have any previous experience with R, we strongly recommend to get familiar with R prior to the semester start. For the D-BSSE students, we highly recommend the voluntary course „Introduction to Programming“, which takes place at D-BSSE from Wednesday, September 12 to Friday, September 14, i.e. BEFORE the official semester starting date http://www.cbb.ethz.ch/news-events.html
For the Zurich-based students without R experience, we recommend the R course Link, or working through the script provided as part of this R course.

Performance assessment

Performance assessment information (valid until the course unit is held again)
Performance assessment as a semester course
ECTS credits6 credits
ExaminersT. Vaughan, T. Stadler
Typesession examination
Language of examinationEnglish
RepetitionThe performance assessment is offered every session. Repetition possible without re-enrolling for the course unit.
Mode of examinationwritten 90 minutes
Additional information on mode of examinationCompulsory continuous performance assessment in form of homework project assignments amounts to 25% of the final grade. The project work has to be re-done in case of repetition.
Written aidsNone
This information can be updated until the beginning of the semester; information on the examination timetable is binding.

Learning materials

No public learning materials available.
Only public learning materials are listed.

Groups

No information on groups available.

Restrictions

There are no additional restrictions for the registration.

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