Computational Biology, Winter 2008

An International Master's course arranged by Andrzej Lingas

Course plan

Lectures

Several basic algorithmic problems occurring in molecular biology are considered: e.g., string and sequence problem, protein folding, construction of evolutionary trees etc. The final lecture is devoted to DNA computing.

Goals

The purpose of the course is to give in-depth insight in the construction and analysis of algorithms for (primarily, molecular) biological applications.

Recommended for

The course is recommended for students having interest in algorithms/complexity theory or/and bioinformatics.

Examination

In order to pass the course, students are required to return acceptable solutions for a sufficient number of homework problems and present a relevant paper.

Prerequisites

Basic courses in algorithms and data structures, and discrete mathematics (e.g., corresponding to DAT107, DAT119 or DAT302).

Contents

The tentative plan of the course is as follows:

• 14.01.2008, 1 p.m. - 2 p.m., "Introduction" (E: 2216), Andrzej Lingas, Lund University.
• 14.01.2008, 2 p.m. - 3 p.m., "Pairwise alignment" (E: 2216), Andrzej Lingas, Lund University, slides.
• 21.01.2008, 1 p.m. - 3 p.m., "Multiple alignment" (E: 2116), Andrzej Lingas, Lund University, slides.
• 25.01.2008, 10 a.m. - 12 a.m. (E: 2405), "Exercises 1 & 2", Andrzej Lingas, Lund University.
• 28.01.2008, 1 p.m. - 3 p.m. (E: 2116), "Phylogenetic trees I", Jesper Jansson, INRIA Lille, slides.
• 29.01.2008, 3 p.m. - 5 p.m. (E: 2116), "Phylogenetic trees II", Jesper Jansson, INRIA Lille, slides.
• 8.02.2008, 10 a.m. - 12 a.m. (E: 2405), "Exercises 3 & 4", Jesper Jansson, INRIA Lille.
• 4.01.2008, 1 p.m. - 3 p.m., "Databases" (E: 2216), David Gisselsson, Lund University, slides ?
• 11.02.2008, 1 p.m. - 3 p.m. (E: 2116), "Physical mapping", Mia Persson, Blekinge University , slides.
• 12.02.2008, 3 p.m. - 5 p.m. (E: 2116), "Fragment assembly", "Introduction", Andrzej Lingas, Lund University, slides, "Shortest superstring", Martin Paluszewski, Copenhagen University slides.
• 15.02.2008, 10 a.m. - 11.30 a.m. (E: 2405), "Exercises 6" and distribution of papers for student presentations, Andrzej Lingas, Lund University.
• 18.02.2008, 1 p.m. - 3 p.m. (E: 2116), "Protein folding", Eva-Marta Lundell, Lund University, slides.
• 22.02.2008, 10 a.m. - 11 a.m. (E: 2405), "Exercises 7", Eva-Marta Lundell, Lund University.
• 25.02.2008, 1 p.m. - 3 p.m. (E: 2116), "DNA computing", Eva-Marta Lundell, Lund University, slides.
• 3.03.2008, 1 p.m. - 5 p.m. (E: 2405), Student presentations program.
• 4.03.2008, 3 p.m. - 5 p.m. (E: 2116), "Sorting by reversals", Mia Persson, Blekinge University, slides, compressed slides.
• 4.03.2008, 5 p.m. - 6 p.m. (E: 2116), "Exercises 5", Mia Persson, Blekinge University.
• 11.03.2008, 1 p.m. - 2 p.m. (E: 2405), "Exercises 8", Mia Persson, Blekinge University.

Preliminary results

For G at least 450, for VG at least 650.

• Antoniadis Antonios 740 VG (A)
• Rasmus B. Arling 765 VG (A)
• Haseeb Baluch 650 VG (B)
• Isen Begiri 623 G (C)
• Viswanathan Bhojan 483 G (E)
• Ehsan Bouhendi 590 G (D)
• Bereket Gichamo 695 VG (B)
• Roubesh Jhumun 463 G (E)
• Ahren Langschmidt 405+activity G (E)
• Hanna Mikhailava 665 VG (B)
• Paul Stapleton 900 VG (A, first place)
• John Wangoudu 600 G (C)
• Cenny Wenner 762 VG (A)
• Gudumundur Hereidersson 773 VG (A)
• Davide Zambo 683 VG (B)
• Sebastain Clauzel 623 G (C)
• Cui Di 190
• Sung Won Park 237

Last edited March 19, 2008 by Andrzej Lingas