Lecturer	Jotun Hein
Degrees	Schedule B — MSc in Advanced Computer Science
Term	Michaelmas Term 2012  (16 lectures)

Overview

Modern molecular biology generates large amounts of data, such as sequences, structures and expression data, that needs different forms of statistical analysis and modelling to be properly interpreted. The fields of Bioinformatics and Computational Biology have this as their subject matter and there is no sharp boundary between them. Bioinformatics has an applied flavour while Computational Biology is viewed as the study of the models, statistical methodology and algorithms needed to do bioinformatics analysis. This course aims to present core topics of these fields with and emphasis on modelling and computation.

Learning outcomes

• understand some of the issues and challenges in contemporaryBioinformatics and Computational Biology (BCB)
• be able to specify and design algorithms solving BCB problems
• have an overview of BCB as a discipline over the last decades.

Prerequisites

Knowledge of elementary probability would be very helpful.

Synopsis

• Fundamental Data Structures in Biology: Sequences, Genes, Networks and RNA secondary structure.
•  Stochastic Models of Sequence and Genome Evolution including models of single nucleotide/amino acid/codon evolution.
• Phylogenies: enumerating phylogenies, the probability of sequences related by a specified  phylogeny, the minimal number of events needed to explain a data set (Parsimony).
• Likelihood and algorithms (Markov Chain Monte Carlo) for inference based on the likelihood. 
• Software packages for sample-based inference.
• Alignment Algorithms. Comparing 2 strings, an arbitrary number of strings, find segments of high similarity in 2 strings.
• Common Patterns in a set of Sequences.
• Network Inference and Network Evolution.
• Detection of Recombinations in Sequences

Method of Assessment

It is proposed to assess this course by mini-project.

Teaching material and exercises can be found at:

http://www.stats.ox.ac.uk/research/genome/compbiol08

Reading list

• C. Semple and M. Steel, Phylogenetics, Oxford University Press (2003).
• Durbin et al., Biological Sequence Analysis, Cambrigde University Press (1998).
• T. Jiang et al., (editors) Current Topics in Computational Biology, MIT Press, (2003).
• M. S. Waterman et al., Computational Genome Analysis: An Introduction, Springer (2004).

Feedback

Students are formally asked for feedback at the end of the course. Students can also submit feedback at any point here. Feedback received here will go to the Head of Academic Administration, and will be dealt with confidentially when being passed on further. All feedback is welcome.

Taking our courses

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Other matriculated University of Oxford students who are interested in taking this, or other, courses in the Department of Computer Science, must complete this online form by 17.00 on Friday of 0th week of term in which the course is taught. Late requests, and requests sent by email, will not be considered. All requests must be approved by the relevant Computer Science departmental committee and can only be submitted using this form.