Computational Evolution Group

The Genome Informatics conference (November 1 – 5, 2007) focused on the application of information technology and computational approaches to genomics. This field has become increasingly popular in recent years, due to the rapid increase in genomic data availability and the increasing throughput of genome sequencing. Because of the growth in data, there has been a need to develop more efficient methods of analysis, such as the automation of many tasks that were previously done manually. This meeting attempted to bring together the community of researchers that work in this field. Over 300 were in attendance from various universities, research institutes and companies. Delegates’ backgrounds ranged from pure biologists to more computationally savvy software developers.

The meeting talks were loosely divided into 6 categories: regulation, pathways and networks; pathogenic microbe genomics; assembly, annotation and resources; epigenomics; images, atlases and reconstruction; and comparative and evolutionary genomics. At the meeting, there was a major focus on the application of high-throughput sequencing technologies. Other topic focuses include patterns in genome evolution and software tools for genome studies.

The promise of new high-throughput sequencing technologies has stemmed great interest in the genomics community. New age sequencing machines, such as 454, Solexa and SOLiD, can rapidly and at a low cost sequence huge numbers of sequence fragments from a single genome. A major conundrum associated with these sequencing technologies is the lack of accurate methods to assemble a full genome from the short fragments that are outputted by the machine. At the meeting, there was research presented on recently developed methods of genome assembly from high-throughput short reads and also methods of improving existing genome assemblies using these fragments.

Studies of patterns and correlations attempt to further understand the genomic mechanics that govern the phenotype of an organism. An example shown at this conference is that regulatory elements in a genome can be identified by their evolutionary signature across species. This study was one of the many that outlined the importance of using between species comparisons (comparative genomics) to discover details about the biological structure of the studied organisms.

Amongst presented research were introductions of software tools designed to be used by other researchers to apply to their own studies. These include software tools for assembling, visualizing, summarizing, annotating and comparing genomes. In addition, delegates representing the major genome databases each presented updated methods for maintaining information in their databases, to ensure the data they are providing to the public is accurate.

I would like to thank my sponsors that provided funding for the trip: Travel allowance from Technology Industry Fellowships (TIF) funding through Biomatters Ltd. and The Foundation for Research, Science and Technology New Zealand (FRSTNZ) and also the Royal Society of New Zealand travel funds.

- Sibon Li