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Bioinformatics
News
May 1
Our paper Reliable detection of subclonal
single-nucleotide variants in tumor cell populations appeared in Nature Communications today (see also ETH Life). In this work, we present the deepSNV algorithm and demonstrate its capability to detect subclonal mutations present in only 1/10,000 cells.
Gerstung et al. (2012) Nat Commun 3:811. DOI: 10.1038/ncomms1814.
| Abstract | The 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. |
| Objective | The 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. |
| Content | Lecture topics: (1) Background: DNA, proteins, databases; (2-4) Sequence alignments, dynamic programming; (5-7) Evolutionary processes, Markov models, phylogenetic trees; (8-9) Genome characteristics, Hidden Markov models, genome annotation; (10-12) Protein structure and function, molecular modeling; (13) Outlook: genomics and proteomics. |
| Literature |
Marketa Zvelebil, Jeremy O. Baum. Understanding Bioinformatics. Garland Science, 2008. http://www.garlandscience.co.uk/textbooks/0815340249.asp |
Course Details
Number and title: 626-002-00L Bioinformatics
|
Date |
Room |
|
| Lecture |
Monday, 13-15h |
BSA E 54 |
| Tutorial |
Monday, 15-16h |
BSA E 54 |
All lectures will be given in English and are accompanied
by a 1h tutorial. To each tutorial corresponds an assignment that will be given on the same day. The assignments imperatively have to be handed by the following Monday before 9a.m. The latter will be corrected and discussed on the same day. The assignments can be returned either electronically to
teaching.cbg(at)bsse.ethz.ch, or as a hardcopy to Gabriel Dissard, D-BSSE, Room 8.46. A 15 Min oral exam for each student will take place at the end of the semester. The final grade will be 50% assignments and 50% exam.
Schedule
|
Date |
Title |
Lecture |
Assignment |
Tutorial | |
|
1 |
Feb 22 |
Producing and Analyzing Sequence Alignments |
Introduction Lecture 1 |
Assignment 1 |
Introduction to Matlab Dealing with biological databases |
| 2 | Mar 1 | Pairwise Sequence Alignment and Database Searching | Lecture 2 |
Assignment 2 Hashing_chaining.m |
|
| 3 |
Mar 8 |
Markov Chains and Hidden Markov Models |
Lecture 3 |
Assignment 3 |
|
| 4 |
Mar 15 |
Patterns, Profiles, and Multiple Alignments |
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| 5 |
Mar 22 |
Recovering Evolutionary History |
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| 6 |
Mar 29 |
Building Phylogenetic Trees |
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