636-0017-00L  Computational Biology

SemesterAutumn Semester 2017
LecturersC. Magnus, T. Stadler, T. Vaughan
Periodicityyearly course
Language of instructionEnglish



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 phylodynamics is to understand and quantify the 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 "Central Element". We provide an R tutorial and help sessions during the first two weeks of class to learn the required skills.

Performance assessment

Performance assessment information (valid until the course unit is held again)
Performance assessment as a semester course
ECTS credits6 credits
ExaminersC. Magnus, T. Stadler, T. Vaughan
Typesession examination
Language of examinationEnglish
Course attendance confirmation requiredNo
RepetitionThe performance assessment is only offered in the session after the course unit. Repetition only possible after re-enrolling.
Mode of examinationwritten 90 minutes
Additional information on mode of examinationCentral element amounts to 25% of the final grade
The central element 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

 
Main linkCB Materials
Only public learning materials are listed.

Courses

NumberTitleHoursLecturers
636-0017-00 GComputational Biology
The lecture will be held each Monday either in Zurich or Basel and will be transmitted via videoconference to the second location. Tutorials will happen in both locations.
Lecture in Basel/Zürich: Monday 15-17h (BSA E46 / HG D16.2)
Tutorials in Zürich: Monday 17-18h (HG D 16.2)
Tutorials in Basel: Thursday 13-14h (BSA E60 exceptions: Sept. 28 and Oct. 5 in room Manser building 1078)
First lecture takes place Monday, Sept. 25 in room Manser building 1078 instead of BSA E46
3 hrs
Mon15-17BSA E 46 »
15-17HG D 16.2 »
17-18HG D 16.2 »
Thu13-14BSA E 60 »
06.11.17-18HG D 16.2 »
C. Magnus, T. Stadler, T. Vaughan
636-0017-00 AComputational Biology
Project Work (central element), no fixed presence required.
2 hrsC. Magnus, T. Stadler, T. Vaughan

Restrictions

There are no additional restrictions for the registration.

Offered in

ProgrammeSectionType
Biology MasterElective Compulsory Master CoursesWInformation
Biology MasterElective Compulsory Master CoursesWInformation
Biology MasterElective Compulsory Master CoursesWInformation
Biotechnology MasterElectivesWInformation
Certificate of Advanced Studies in Computer ScienceFocus Courses and ElectivesWInformation
Computational Biology and Bioinformatics MasterCore CoursesWInformation
Computational Biology and Bioinformatics MasterBioinformaticsWInformation
Health Sciences and Technology MasterElective Courses IIWInformation
Computer Science MasterFocus Elective Courses Computational ScienceWInformation
Mathematics MasterBiologyWInformation
Environmental Sciences MasterAdvanced Concept ClassesWInformation