course computational molecular biology
Seminarium
Computational Molecular Biology
voorheen / previously
Seminarium Advanced BioComputing
Voorjaar 2004
Hendrik Jan Hoogeboom
en
Walter Kosters
begeleidden in 2002 en
2003 (deeltijd)
een
Seminarium Advanced BioComputing / Computational Molecular Biology.
Dit seminarium wordt ook in het voorjaar van 2004 aangeboden.
Het vak levert 5 'oude' studiepunten op.
spring 2004: Friday 9.15 to 11.00, room 403.
Vooraf aanmelden bij de docent.
Het aantal deelnemeners is beperkt.
Inhoud
Met het ontwarren van de DNA code komt een grote hoeveelheid
data beschikbaar. Voor de verwerking van deze gegevens is het
gebruik van computers onontbeerlijk. Het vakgebied van de
"computational biology" of "bioinformatics" ontwikkelt de
benodigde gereedschappen: complexe databases, geavanceerde
zoektechnieken, maar vooral efficiente algoritmen toegesneden
op het vergelijken en samenpassen van strings.
Het Seminarium CMB beoogt een aantal representatieve
algoritmen te bestuderen aan de hand van recente literatuur.
Topics: We are guided through a number of topics by
Shamir's Lecture
Notes, Tel Aviv University School of Computer Science.
Participants
mail sent: 03 Feb,
18 Feb,
20 Feb
.
List of participants.
The number of active participants is limited by the number of topics!
| name |
email (@ liacs.nl) |
| Hendrik Jan Hoogeboom |
hoogeboom |
| Taco Buitenhuis |
tbuitenh |
| Arjen de Mooij |
zipje_and_zopje (a) penguinpowered.nl |
| Klaske van Vuurden |
kvvuurde |
| Bas van Zon |
vanzon2000 (a) yahoo.com |
| Frederico Sangati |
s.fede (a) gmx.net |
| Yan Gao |
ygao |
| Guoxiang Liu |
liugx_2 (a) 163.com |
| Jinshuo Liu |
sureliu (a) yahoo.com.cn |
| Yun Bei |
ybei |
Schedule
| 30.1.04 |
1 |
Introductory Concepts |
Hendrik Jan |
|
| 13.2 |
2 |
Pairwise alignment |
Jinshuo Liu + Yan Gao |
Pevzner 6 |
| 20.2 |
8 |
Phylogeny |
Frederico Sangati + Guoxiang Liu |
'All about Eve' Clote 4 |
| 27.2 |
5 |
Hidden Markov Models |
Taco Buitenhuis + Klaske van Vuurden |
|
| 5.3 |
9 |
Physical Mapping |
Bas van Zon + Jinshuo Liu |
Pevzner 3 |
| 19.3 |
7 |
Gene Finding |
Yun Bei + Guoxiang Liu |
|
| 26.3 |
10 |
Genome Rearrangements |
Arjen de Mooij + Klaske van Vuurden |
Setubal 7 Pevzner 10 |
applet |
| 2.4 |
11 |
DNA Chips and Gene Networks |
Taco Buitenhuis + Yun Bei |
Pevzner 5 |
| 9.4 |
|
holiday: no meeting |
| 16.4 |
x |
Fourier Transform |
Frederico Sangati + Yan Gao |
|
| 23.4 |
12 |
Protein Structure |
Bas van Zon + Arjen de Mooij |
Clote 6 |
|
3 |
Sequence Alignment Heuristics |
|
|
|
4 |
Multiple Sequence Alignment |
|
Pevzner 7 |
|
6 |
Bioinformatics Tools |
|
Gibas |
| |
13 |
Linkage Analysis |
|
|
Format
Each topic is presented by a team of two
participants, each lecturing for 30 to 45 minutes.
Each participant contributes in two two topics,
with changing partners.
- Please contact the Teacher in advance, when you foresee
any problems.
Do not hesitate!
- Presentation, in English.
Don't forget the biological background and
motivation, but try to stress algorithms or mathematical models.
It is not necessary to cover the complete set of notes.
You can use other sources, or restrict the topic.
It is allowed to get inspiration from presentations found
on the internet, as long as you understand
what is happening.
Send me the presentation in advance, to put it on the laptop,
or bring your own.
If receeived on time, I can make sets of prints to distribute to class mates.
It is also possible to copy/print the slides on
transparencies if you prefer. University can provide those.
- Active participation: ask questions where needed.
- Written report of about 5 to 10 pages for
each participant, English or Dutch.
If possible you may combine the two parts of a given topic into
a single report.
Main Source
Our main source of information is the set of lecture notes written for
the lacture of R. Shamir from Tel Aviv University.
Ron Shamir,
Algorithms for
Molecular Biology.
Literatuur
Een selectie uit:
- Pierre Baldi and Søren Brunak,
Bioinformatics: The Machine Learning Approach,
MIT Press, 1998
- Peter Clote
»
and Rolf Backofen,
Computational Molecular Biology: An Introduction,
Wiley, 2000
- Richard Durbin, Sean Eddy, Anders Krogh and Graeme Mitchison,
Biological Sequence Analysis:
Probabilistic Models of Proteins and Nucleic Acids,
Cambridge University Press, 1998
- Cynthia Gibas»
and Per Jambeck,
Developing Bioinformatics Computer Skills,
O'Reilly, 2001
- Dan Gusfield,
Algorithms on Strings, Trees, and Sequences,
Cambridge University Press, 1997
- Pavel A. Pevzner
»,
Computational Molecular Biology,
An Algorithmic Approach,
The MIT Press, 2000
- João Setubal and João Meidanis,
Introduction to Computational Molecular Biology,
PWS Publishing Company, 1997
Conference proceedings
& Journals
»
Bioinformatics at DBLP Trier. Lists many journals, conferences,
etc.
-
»WABI
Algorithms in Bioinformatics, International Workshop
(Springer Lecture Notes in Computer Science / Bioinformatics)
-
»RECOMB
Annual Conference on Research in Computational Molecular Biology
⇒ACM,
- Lecture Notes in Bioinformatics (LNBI)
- ⇒
Bioinformatics, Journal, Oxford University Press.
⇒ULIB
- ⇒
IEEE/ACM Transactions on Computational Biology and Bioinformatics
-
»Journal of Computational Biology
Links
Nuttige link gevonden? Even doorgeven
(met een korte beschrijving van het gebodene).
Vragen en/of opmerkingen kunnen worden gestuurd
naar: hoogeboom@liacs.
20 apr 2004 - http://www.liacs.nl/home/hoogeboo/semabc/