The Seminar DNA String Algorithms
is intended for Master students in Computer Science.
Lectures are in English.
The seminar is organised by
dr. H.J. (Hendrik Jan) Hoogeboom
and
dr. W.A. (Walter) Kosters.
The seminar examines algorithms that deal with DNA,
viewed as a string.
Students should perhaps write programs and certainly study recent literature,
and present their results. Meetings are on a weekly basis.
Students can also suggest subjects. For a "full" list, see below.
Dates: Monday September 8, 2008 — Monday November 24, 2008
(12 sessions, see below);
time: 11.15-13.00; room: 407, Snellius.
Credit points: 7 ECTS (at some other locations "6 ECTS"
are mentioned, but it is 7 (seven)).
An extra session has been added in December.
There is no written exam.
========== PAST: ================
teams | |||||
✓ | Giovanni Bernardi | gbtito X gmail | A1 | C2 | |
✓ | Bertram Bourdrez | bertram X bourdrez.org | C1 | F2 | |
✓ | Ramon van Dam | ramonvandam X gmail | G1 | D2 | |
✓ | Bart van der Drift | bartvanderdrift X hotmail | G1 | E2 | |
✓ | Sjoerd van Egmond | sjoerdvanegmond X gmail | E1 | E2 | |
✓ | Johan Groenen | johan.groenen X gmail | E1 | G2 | |
- | Sjoerd Henstra | shenstra X liacs.nl | . | ||
✓ | Erik Jongsma | ejongsma X liacs.nl | F1 | G2 | |
✓ | Susan Laraghy | susan X running-gag.nl | F1 | D2 | |
✓ | Jori van Lier | jlier X liacs.nl | B1 | F2 | |
✓ | Edgar Reehuis | edgarreehuis X hotmail | D1 | C2 | |
✓ | Jan van Rijn | janvanrijn X gmail | A1 | B2 | |
Johan de Ruiter | johan.de.ruiter X gmail | C1 | A2 | ||
✓ | Marijn Swenne | marijn.swenne X gmail | D1 | B2 | |
- | Frank Takes | ftakes X liacs.nl | B1 | A2 |
Given a large piece of DNA, for example the (or a) human genome. How many unique substrings of length 25 does this string possess?To get some ideas, see
Prerequisites: Algorithms, Artificial intelligence, Data mining, Complexity, Datastructures (all at bachelor's level, see for instance the Dutch course pages Artificial intelligence and Complexity). And perhaps some Biology.
Students should
team | date | first | second | done | topic |
D1 (Edgar & Marijn) | 29.9 | WAK | HJH | ✓ | Fast Algorithms for Selecting ...
WABI'07, Davila doi |
A1 (Giovanni & Jan) | 6.10 | HJH | WAK | ✓ | Fixed Parameter Tractable ...
CPM'08, Möhl doi |
C1 (Bertram & JohandR) | 6.10 | HJH | WAK | ✓ | Indexing a Dictionary ...
SPIRE'07, Landau doi |
E1 (SjoerdvE & JohanG) | 13.10 | WAK | HJH | ✓ | Jump-Matching with Errors
SPIRE'07, Butman doi |
F1 (Erik & Susan) | 13.10 | WAK | HJH | ✓ | More Efficient Algorithms ...
RECOMB'08, Ma doi |
G1 (Ramon & Bart) | 20.10 | WAK | HJH | ✓ | Optimal Self-adjusting Trees ...
SPIRE'07, Ko doi |
B1 (Jori (& Frank)) | 10.11 | WAK | HJH | ✓ | Faster Algorithm for the Set ...
CPM'08, Gąsieniec doi |
B2 (Jan & Marijn) | 10.11 | HJH | WAK | ✓ | Efficient Text Proximity Search
SPIRE'07, Schenkel doi |
C2 (Giovanni & Edgar) | 17.11 | WAK | HJH | ✓ | A Faster Algorithm for RNA ...
WABI'08, Ziv-Ukelson doi |
G2 (Erik & JohanG) | 17.11 | WAK | HJH | ✓ | Searching for Gapped Palindromes
CPM 2008, Kolpakov doi |
D2 (Susan & Ramon) | 24.11 | WAK | HJH | ✓ | Tuning Approximate Boyer-Moore ...
SPIRE'07, Kalsi doi |
E2 (Bart & SjoerdvE) | 24.11 | WAK | HJH | ✓ | Minimum Common String Partition
WABI'08, Damaschke doi |
F2 (Jori & Bertram) | 1.12 | HJH | WAK | ✓ | CompostBin: A DNA Composition-Based ...
RECOMB 2008, Chatterji doi |
A2 ((Frank &) JohandR) | 1.12 | HJH | WAK | ✓ | Computation of Median Gene Clusters
RECOMB 2008, Böcker doi |
The columns "first" and "second"
denote the person handling your paper.
A period "." means that that person is still busy reading ;-).
And what's "done"✓ is done.
Conferences
Questions/remarks: kosters@liacs.nl.
21 June 2010 — http://www.liacs.nl/home/kosters/semdna/index.html