Intelligent systems in bioinformatics Introduction to the course

Contact details Dr. Karen Page Computer Science - Room G50a Tel: (internal: 33683)

Lecture format Monday and Thursday afternoons (2- 5pm) – Pearson Lecture Theatre (Mon.) & Rm 229 (Thurs.) We will take one or two 10/15-minute breaks, so typically the lecture might be split: or

Coursework & Homework Coursework: –1 piece –15% of total mark –towards end of course Homework: –Each week (doesn’t contribute to course grade) –Attach cover sheet ( htm) htm –Give to JJ Giwa (G07) by 12pm on due date

Exam Written exam 15 th March 85% of total mark

Newsgroups/ Mailing list All communication concerning this course will be done via the list. Please join by sending an with Subject: join to or local.cs.gi10 or or local.cs.4c58

Useful Books Alberts et al- Molecular Biology of the Cell Stryer- Biochemistry Baldi and Brunak – Bioinformatics – a machine learning approach Durbin, Eddy, Krogh and Mitchison – Biological sequence analysis Kanehisa - Post genome informatics Lesk- Introduction to bioinformatics Orengo, Jones and Thornton - Bioinformatics

The Course- motivation for biological material Modern molecular biology and especially genomics has led to vast quantities of data: DNA/ protein sequence, gene expression. This mainly consists of vast strings/ matrices of letters/ numbers, which in their raw form are not very interesting. What’s needed now is synthesis of data and mining of data for patterns. Intelligent systems techniques are very good for extracting useful patterns.

Motivation In order to extract useful information, it is necessary to understand biological principles involved. In this course we will introduce some basic molecular biology/ genomics and look at ways in which computers can be used to analyse it (bioinformatics), with a particular focus on intelligent systems techniques.

Course material content I will give five three-hour blocks of lectures towards the start of the course. Prof. David Jones will give the rest of the lectures. Will now give a brief summary of the content of my lectures and a very brief one of his.

Content Block 1: Biology –Introduction to course –Basic molecular biology Cells, DNA, RNA, proteins, central dogma –Sequencing Block 2: Genomics –History of genomics –Introduction to bioinformatics –Gene prediction

Content Block 3: Microarrays –Microarray technology –Statistics –Analysis of microarray data Block 5: Guest lectures (Systems biology and Gene networks) –Intelligent systems and software for systems biology (Dr. Peter Saffrey, UCL) –Bayesian networks (Dr. Lorenz Wernisch, Birkbeck) –Reverse engineering of gene networks from microarray data (Dr. Lorenz Wernisch)

Content Block 8: Gene networks and Computational biology –Continuation of analysis of microarray data –Signalling pathways –Reverse engineering of networks from microarray data –Evolutionary games and evolutionary algorithms (if time)

Content Below is a rough outline of what Prof. Jones will cover: Blocks 4,6,7,9 & 10: –Gene finding and basic sequence comparisons –Sequence comparisons; Hidden Markov Models; proteins –Databases; agent technology –Protein structure; structure classification; structure prediction –Protein structure prediction; drug discovery