Computational genomics of prokaryotes

PhD ceremony: E.J. Blom, 14.45 uur, Academiegebouw, Broerstraat 5, Groningen

Thesis: Computational genomics of prokaryotes

Promotor(s): prof. O.P. Kuipers, prof. J.B.T.M. Roerdink

Faculty: Mathematics and Natural Sciences

The use of DNA microarray-based transcription pro fi ling techniques is providing large quantities of genome-wide data on gene-expression patterns. This transcriptome data provide researchers with alternative ways to address and interpret biological questions in a functional and regulatory context. Although its application is ubiquitous in various areas of research, the analysis of the data that result from these experiments still remain a challenge.

The main research theme of the thesis of Evert-Jan Blom is the development of analytical software approaches and tools to analyze, visualize and exploit the information contained in global gene expression data. He has addressed the analysis of transcriptome data using various applications that were developed in-house; ranging from functional enrichment analyses, identi fi cation and visualization of regulatory elements, annotation of clustering results and the inference of putative gene functions using gene expression data.

His last experimental chapter describes the results of the analysis of a large time-resolved transcriptome dataset (40 time points) of the model bacterium B. subtilis using several of the earlier described tools. The most remarkable outcome of his analysis is the occurrence of stress during the transitions between the different growth phases. These stress responses are not induced by added external stimuli or arti fi cially induced starvation conditions, but are naturally occurring during the growth phases of B. subtilis.