Affiliations: Institute of Informatics, Warsaw University, Banacha 2, 02-097 Warsaw, Poland and European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. bartek@mimuw.edu.pl; Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden and Computational Life Science Cluster (CLiC), Umeå University, 901 87 Umeå, Sweden. torgeir.hvidsten@plantphys.umu.se
Note: [] Address for correspondence: Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
Abstract: Recent years have seen a wealth of computational methods applied to problems stemming from molecular biology. In particular, with the completion of many new full genome sequences, great advances have been made in studying the role of non-protein-coding parts of the genome, reshaping our understanding of the role of DNA sequences. Recent breakthroughs in experimental technologies allowing us to inspect the innards of cells on a genomic scale has provided us with unprecedented amounts of data, posing new computational challenges for scientists working to uncover the secrets of life. Due to the binary-like nature of the DNA code and switch-like behavior of many regulatory mechanisms, many of the questions that are currently in focus in biology are surprisingly related to problems that have been of long-term interest to computer scientists. In this review, we present a glimpse into the current state of research in computational methods applied to modeling the regulatory genome. Our aim is to cover current approaches to selected problems from molecular biology that we consider most interesting from the perspective of computer scientists as well as highlight new challenges that will most likely draw the attention of computational biologists in the coming years.
Keywords: computational biology, gene regulation, DNA motifs, regulatory elements
