Bioinformatics: Organisms from Venus, Technology from Jupiter, Algorithms from Mars

Bart De Moor, Kathleen Marchal, Janick Mathys, Yves Moreau
2003 European Journal of Control  
In this paper, we discuss datasets that are being generated by microarray technology, which makes it possible to measure in parallel the activity or expression of thousands of genes simultaneously. We discuss the basics of the technology, how to preprocess the data, and how classical and newly developed algorithms can be used to generate insight in the biological processes that have generated the data. Algorithms we discuss are Principal Component Analysis, clustering techniques such as
more » ... ical clustering and Adaptive Quality Based Clustering and statistical sampling methods, such as Monte Carlo Markov Chains and Gibbs sampling. We illustrate these algorithms with several real-life cases from diagnostics and class discovery in leukemia, functional genomics research on the mitotic cell cycle of yeast, and motif detection in Arabidopsis thaliana using DNA background models. We also discuss some bioinformatics software platforms. In the final part of the manuscript, we present some future perspectives on the development of bioinformatics, including some visionary discussions on technology, algorithms, systems biology and computational biomedicine. , the mathematics master Geert Fannes and the statistician Jos Debrabanter. This year 2003 marks the 50 th anniversary of the discovery of the double helix structure of DNA, the basic building structure of all living organisms, by Crick and Watson, in the 1 page landmark paper [Watson, 1953] 3 . Since then, over the past 50 years, the evolution of biotechnology has been remarkable and expontential, not in the least because of the recent merger of biology with advanced computation, into what is nowadays called bioinformatics. Computer science and mathematical engineering on the one hand, and biology on the other, are, at first blush, an unlikely pairing: abstract,
doi:10.3166/ejc.9.237-278 fatcat:w26h4jvugjg35abzgqctb2yubi