Bioinformatics
General
Lecturer: Marc Hellmuth
Tutor: Nikolai Nøjgaard - nikolai.nojgaard@uni-greifswald.de
Stefanie König - stefaniekoenigymailcom
Previous Knowledge:
- Genomanalyse, Bioinformatisches Praktikum
- Familiarity with discrete mathematics
Certificate Requirements:
- 50% correctly solved problems in the exercises
- Active participation in tutorials
- Pass exam
Dates and News
- Lecture starts on Monday 4. April at 2.15pm - Franz-Mehring-Straße 47/48 - SR 4
- Tutorial starts on Thursday 14. April at 12.15pm - Franz-Mehring-Straße 47/48 - SR 4
- Oral Exam: 29. 07. 2015 in my office (Walther-Rathenau-Straße 47, R 5.05)
MatrNr Time // 140278 9.15am // 138681 10.00am // 128074 10.45am // 140058 11:30am
All registered participants that don't have an exam appointment so-far but want to be examined
should write me an email until July 22th.
04.04. - Auf Bitte der Studierenden: beginnen alle Vorlesung 14 Uhr und enden 15:30 Uhr, wird das Tutorium auf Montags 15:45 Uhr verlegt - Start 18.04.
11.04. - Korrigierte Version von Übung 2 online.
09.05 - Die Vorlesungen am 23. Mai und 30. Mai fallen aus und werden zu gegebener Zeit nachgeholt. Das Tutorial findet am Mo 23. Mai statt (2pm)
13.06 - Extra-Vorlesung am Do. 23. Juni - 12.15pm
Material Lectures
Lecture Slides Extra Material
Vorlesung 1: Orga
Vorlesung 1: WarmUp + Cracking the Genetic Code "Die schönste falsche Theorie der Biochemie"
Vorlesung 2-4: Shotgun Sequencing and Superstrings "Linear Approximation of Shortest Superstrings" Blum et al. 1994
"Genome Reconstruction: A Puzzle with a Billion Pieces" Compeau and Pevzner 2010
Vorlesung 5: String Matching and Alignment Quick Blast Tutorial
Vorlesung 6: Intro Graphs BFS-Exmpl
Vorlesung 7-9: RNA Structures Vienna RNA-Webserver
Vorlesung 9-10: Graph Products and Phenotypespace
Vorlesung 11-12: Phylogenetics "Phylogenomics with paralogs"
Material Exercises
(Exercise // Deadline // Extra Material)
Recommended Literature
- "Introduction to Computational Biology: Maps, Sequences and Genomes", Michael S. Waterman
- "Understanding Bioinformatics", Marketa J. Zvelebil
- "Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology", Dan Gusfield
- "RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods" Gorodkin, Jan, Ruzzo, Walter L. (Eds.)
- "Phylogenetics", Charles Semple and Mike Steel
- "Handbook of Product Graphs, Second Edition (Discrete Mathematics and Its Applications)", Richard Hammack, Wilfried Imrich and Sandi Klavzar