Welcome Ammar!

A warm welcome to Ammar Malik who has joined the group as a PhD student. Ammar has a degree in Computer Engineering and brings with him a lot of experience in machine learning. Welcome!

Bayesian network preprint

A new preprint, “High-dimensional Bayesian network inference from systems genetics data using genetic node ordering”, is available on bioRxiv. Bayesian networks are statistical models for gene regulatory networks, and their inference from large-scale omics data is a major problem in systems genetics. In this paper we present an algorithm to solve this problem that uses causal inference, topological sorting and variable selection, and that is much more efficient than traditional Markov chain Monte Carlo algorithms. The algorithm is implemented in the Findr and lassopv software packages.

4 PhD positions in computer science

Four PhD positions in computer science are available at the Department of Informatics. These positions can be held in any of the department’s research areas (algorithms, bioinformatics, machine learning, optimization, programming theory, security, and visualization). Applicants with an interest in computational biology and machine learning are welcome to contact me prior to submitting their application.

For more details and application instructions, see here.

VSG Pacbio preprint

It’s been a long time in the making, but Sid’s work on using long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections has finally been posted on bioRxiv!

In this collaboration with Liam Morrison, we applied long read sequencing (PacBio) to VSG amplicons generated from blood extracted from mice infected with T. brucei. We found that long read sequencing is reliable for resolving allelic differences between VSGs, that there is significant expressed diversity (449 VSGs detected across 20 mice) and that there is a striking semi-reproducible pattern of expressed diversity across the timeframe of study.

Well done Sid and everyone else who contributed to this study!