Bioinformatics

General

Modulbeschreibung

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

(Partial) Lecture Script

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 

                                Graph Products

Vorlesung 11-12:  Phylogenetics                                         "Phylogenomics with paralogs"  

                                                                                              "Phylogenomics from Event-Relations" 

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