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Algorithms in Genome Research

392109/10 Stoye Fr 10:30-12:00/9:15-10:30 and 12:00-12:15 in U10-146

Contents

This class covers the basic algorithmic techniques used in the computational analysis of genome and post-genome data. This includes algorithms for genomic mapping and assembly, methods for functional genome annotation (gene finding and gene function prediction), algorithms for the analysis of DNA microarrays and mass spectra, methods and models for protein structure prediction, and algorithms for comparative genomics.

Literature

The page AlgGRLiterature contains many links to the original literature.

Time table

Date Topic Exercises
13.10.2017 Introduction, logistics –
20.10.2017 Physical mapping Exercises 01
27.10.2017 Genome assembly, re-sequencing Exercises 02
03.11.2017 Hybrid genome assembly Exercises 03
10.11.2017 Haplotype inference Exercises 04
17.11.2017 SNV-disease association mapping Exercises 05
24.11.2017 Gene finding (tRNAs, protein-coding genes) Exercises 06
01.12.2017 Finding patterns in non-coding regions Exercises 07
08.12.2017 RNA-seq Exercises 08
15.12.2017 Proteomics: analysis of mass spectra Exercises 09
22.12.2017 – –
X-mas break
12.01.2018 Subclonal composition reconstruction (Linda Sundermann) Motivation, Exercises 10
19.01.2018 Reconstruction of ancestral genomes (Roland Wittler) Intro to Genome Rearrangements (Pedro Feijão, slides 1--14), handout, Exercises 11
26.01.2018 Synteny Hierarchies, or: PQ-Tree construction with Generating Families of Common Intervals (Daniel Dörr) Exercises 12, Lecture Notes
02.02.2018 Finding Gene Clusters by Discovering Common Intervals in Strings (Daniel Dörr) Lecture Notes, Slides

Examination dates

Oral exams will be on 05.04.2018. Please make an appointment with the secretary in U10-151, Heike Samuel.

A second oral exam can be taken on May 28. Please contact Heike Samuel if you are interested.

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