626-0002-AAL  Bioinformatics

SemesterAutumn Semester 2016
LecturersJ. Stelling, N. Beerenwinkel
Periodicityevery semester recurring course
Language of instructionEnglish
CommentEnrolment ONLY for MSc students with a decree declaring this course unit as an additional admission requirement.

Any other students (e.g. incoming exchange students, doctoral students) CANNOT enrol for this course unit.

AbstractThe course introduces concepts of bioinformatics starting from first principles: DNA sequence alignment, phylogenetic tree inference, genome annotation, protein structure and function prediction. Key methods and algorithms are covered, including dynamic programming, Markov and Hidden Markov models, and molecular dynamics simulations. Practical applications and limitations are discussed.
ObjectiveThe course aims at introducing the fundamental concepts and methods of bioinformatics. Emphasis is given to a deep understanding of the methods' foundations and limitations to enable critical evaluations and applications of bioinformatics tools in areas such as biotechnology and systems biology.
ContentFrom "Understanding Bioinformatics":
Chapter 4: Producing and Analyzing Sequence Alignments
Chapter 5: Pairwise Sequence Alignment and Database Searching
Chapter 6: Patterns, Profiles, and Multiple Alignments
Chapter 7: Recovering Evolutionary History
Chapter 8: Building Phylogenetic Trees
Chapter 9: Revealing Genome Features
Chapter 10: Gene Detection and Genome Annotation
Chapter 11: Obtaining Secondary Structure from Sequence
Chapter 12: Predicting Secondary Structures
Chapter 13: Modeling Protein Structure
Chapter 14: Analyzing Structure-Function Relationships

From "Biological Sequence Analysis":
Sections 3.1, 3.2, 3.3, 4.1, 4.2, 4.4, 5.2, 5.3, 5.4, 6.5 (Markov Chains and Hidden Markov Models)

From "A First Course in Systems Biology":
Chapter 1: Biological Systems
Lecture notesCourse material will be made available at: http://www.csb.ethz.ch
LiteratureZvelebil M, Baum JO. Understanding Bioinformatics. Garland Science, 2008.
Durbin R, Eddy S, Krogh A, Mitchinson G. Biological Sequence Analysis. Cambridge University Press, 2004.
Voit EO. A First Course in Systems Biology. Garland Science, 2012.
Prerequisites / NoticeThere will be two opportunities for tutorials during the semester