Systems Biology Brings Life Sciences Closer: —Report on the China-UK Systems Biology Workshop 2005

Chen, Ming

The workshop was opened by Jun Zhu with a welcome to the participants and an introduction to Zhejiang University. The morning session of the first day began with lectures of Bailin Hao (Fudan University, China) and John Findlay. Hao proposed a composition vector approach to analyze prokaryote phylogeny without sequence alignment. It is a systematic way of inferring evolutionary relatedness of microbial organisms from the oligopeptide content, that is, the frequency of amino acid K-strings in their complete proteomes. The method circumvents the ambiguity of choosing the genes for phylogenetic reconstruction and avoids the necessity of aligning sequences of essentially different lengths and gene contents. It can incorporate the effect of lateral gene transfer to some extent and leads to results comparable with the bacteriologists’ systematics as reflected in the Bergey’s Manual of Systematic Bacteriology. Findlay introduced a new tool for folding prediction and a new system for ligand delivery. He designed and used diagnostic amino acid residue fingerprints to predict protein structures and functions. The main interest of his laboratory is to examine the structure and mechanism of action of membrane proteins, particularly receptors and transport systems. The principle techniques used, dependent on the exact project, include protein chemistry, electrophysiology, molecular biology, protein mutation and expression, general membranology, and biophysical analysis (NMR, X-ray, and EM). In the second period, Guoping Zhao (Chinese Academy of Sciences, China) addressed the bioinformatics research and development in Shanghai in the recent years, from genomics research to new drug development. Their work on the evolution of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) was very much highlighted. Andy Brass (University of Manchester, UK) presented numerous computational challenges involved in developing a computational infrastructure to meet the needs of systems biology. The challenges range from the technical demands of capturing and sharing data and meta-data from genome, transcriptome, proteome, and metabolome experiments to how we can provide an environment in which researchers can formulate and explore hypotheses across different “-omics” data types. He explored these issues, and described some of the systems they were developing to meet these data capture and integration needs, focusing particularly on the areas of data standards, ontology, and e-Science.