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Advanced Bioinformatics 2006

Advanced Bioinformatics - #27614

Course Programme - Fall 2006

The course starts on September 05, 2006 at 13:00. Lectures will be held Tuesday afternoons and exercises Friday mornings.
Lectures and exercises will take place at the Center for Biological Sequence Analysis at the Technical University of Denmark,
building 208 in Lyngby. Tuesday's lecture will take place in aud. 54 in building 208, whereas Friday's exercises
will take place in aud. 51.
The additional reading material you can find here



Evaluation: written examination, 4 hours without books (pocket calculator is allowed). Scale of marks (0-13), internal examiner.


Please fill in the course evaluation on Campusnet
Some information about the exam ... (last changed 2006-12-10 23:45:38)



Tuesday, September 05

Alignments, Phylogeny and Database Searching Anders Gorm Pedersen


13.00-13.45

Introduction to bioinformatics with focus on the human, mouse and rat genomes



13.45-14.00

Coffee break


14.00-15.30

Pairwise sequence alignment and database searching: global and local alignments,
substitution matrices, gap penalties, statistical significance Handout (PDF), Lecture notes







Friday, September 08


09.00-12.00






Tuesday, September 12


13.00-16.00

Multiple alignment and phylogenetic reconstruction Handout (PDF) Lecture notes (PPT)






Friday, September 15


09.00-12.00





Tuesday, September 19


13.00-16.00

Maximum likelihood phylogenyHandout (PDF) Lecture notes (PPT)


Anders Gorm Pedersen





Friday, September 22


09.00-12.00






Tuesday, September 26

Gene Expression and DNA array technology Henrik Bjoern Nielsen


13.00-13.45

Introduction to DNA microarray technology


Array group


13.45-14.00

Coffee break


14.00-17.00

Data analysis: pre-processing and statistics slides (pdf)





Friday, September 29


09.00-10.00

Case story

10.00-12:00

Microarray discussion (group work) (answers to exercise)






Tuesday, October 03


---

As the Array block has been compressed to one week, there will be no lectures and exercises this week




Friday, October 06


---

no exercise





Tuesday, October 10

Protein Modelling, Drug Discovery and Fold recognition Ole Lund


13.00-13.45

Protein Secondary Structure: Classification and Prediction (slides)



13.45-14.00

Coffee break


14.00-14.45

Industry lecture: Computational decision support for drug discovery. Property profiling and virtual screening of small molecule libraries (slides)


Anne Marie Munk Jørgensen






Friday, October 13


09.00-12.00



Thomas N. Petersen, Thomas Blicher





Tuesday, October 17


13.00-13.45

Efterårsferie





Friday, October 20


09.00-12.00

Efterårsferie





Tuesday, October 24


13.00-13.45

Protein Structure (slides)



13.45-14.00

Coffee break


14.00-15.30

Fold Recognition



15.30-17.00

Homology modeling and model evaluation (slides)






Friday, October 27


09.00-12.00


Claus Lundegaard, Ole Lund





Tuesday, October 31

Datadriven Predictions and gene finding with Hidden Markov Models and Neural Networks Thomas Nordahl Petersen


13.00-13.45

Datadriven prediction methods and neural networks (slides)



13.45-14.00

Coffee break


14.00-15.30

Applications: learning from evolution to predict protein structure (slides)



15.30-17.00

Application: prediction of post-translational modifications and protein function






Friday, November 03


09.00-12.00





Tuesday, November 07


13.00-13.45

Immunological bioinformatics (slides)




13.45-14.00

Coffee break


14.00-15.30

Eukaryotic gene finding (slides)






Friday, November 10


09.00-12.00









Tuesday, November 14


13.00-13.45

The essential role of biological hypothesis in microarray based research - Meaningful data integration in high throughput biology



14.00-16.00

Industrial lecture: Genes and Patents (slides,Patent application,Medicon Valley Patent Guide)


Jens Viktor Noergaard





Friday, November 17


10.00-12.00

Finding sequence motifs: consensus sequences, weight matrices, information content,
sequence logos, and Hidden Markov models (slides)








Tuesday, November 21

Systems Biology and Comparative Genomics Dave Ussery


13.00-13.45

20 Methods to Compare Microbial Genomes (slides)



13.45-14.00

Coffee break


14.00-15.30

Global Regulation of Gene Expression in Microbial Genomes(slides)






Friday, November 24


09.00-09:45

Industrial lecture: Peder Worming, Astra (slides)



10.00-12.00






Tuesday, November 28


13.00-13.45

Introduction to Systems Biology(slides)



13.45-14.00

Coffee break


14.00-14.45

Proteomics technologies and protein-protein interaction(slides)



15.00-16.00

Disease gene finding(slides)






Friday, December 01


09.00-12.00


Carsten Friis





Tuesday, December 05


---

No lectures. The students are encouraged to go over last years exam and prepare ev. questions
to the teachers on Friday 8/12.





Friday, December 08


09.00-12.00

Questions to last year exam





Tuesday, December 19


15.00-19.00

Exam