Guest Editor's Introduction to the Special Issue on Computational Biology and Bioinformatics - Part 1

In the last 10 years, bioinformatics has emerged as a necessary interdisciplinary science where different dis- ciplines contribute to the advancement of a common goal: establishing new paradigms for modern biology. This was prompted by the shift of interest in molecular biology when new powerful technologies made feasible fast and reliable sequencing of the whole DNA, protein, and RNA content of cells from different species, including Homo sapiens . A new era started, the so-called “omic” era, and an enormous amount of information has been piling up at a hyperbolic rate in the specific electronic data bases that represent the landmarks for these ongoing efforts. geno- mics, proteomics, transcriptomics, regulomics, metabolo- mics, and interactomics are emerging disciplines where experimental data are collected at large with the perspective of highlighting a global picture of all the possible molecular events and metabolic reactions at the basis of what we call a living system. Data detailed at a molecular level are then analyzed with new and powerful algorithms with the aim of integrating them to model the subtle and still elusive relations among genotype and phenotype in living organ- isms and concomitantly to highlight biodiversity among and within species. As an immediate consequence of all these efforts, the term ”molecular” is added to biological disciplines, including evolution, biochemistry, genetics, and even medicine, to stress the finding that, in many instances, processes can be described and modeled down at a molecular level. In this scenario, computational biology includes all the theoretical efforts of developing specialized algorithms to address relevant biological problems and finding possible heuristic solutions consistent with the presently available results. This requires a joint effort among theoreticians and biologists to cope with a new common way of exchanging information, such as is the goal of bioinformatics. The development of algorithms specifically addressing the most significant problems of computational biology and bioinformatics prompted the selection of the papers pub- lished in this special issue and in the special section to be published in the January-March 2007 issue. The authors were invited after considering new and powerful develop- ments among those presented at the Fifth International Workshop on Algorithms in Bioinformatics (WABI ’05, Mallorca, Spain, 3-6 October 2005) and soliciting a more extensive and/or a new description/implementation of their work. The submitted papers have been extensively reviewed and I would like to acknowledge all the colleagues (three per manuscript) who participated in the reviewing process and who, for journal policy reasons, need to remain anonymous. I am also indebted to Emidio Capriotti, postdoctoral fellow in our Biocomputing Group, at the University of Bologna for his invaluable technical help in handling the reviewing process.