title: Computational Modelling Approaches on Epigenetic Factors in Neurodegenerative and Autoimmune Diseases and Their Mechanistic Analysis.
abstract: Neurodegenerative as well as autoimmune diseases have unclear aetiologies, but an increasing number of evidences report for a combination of genetic and epigenetic alterations that predispose for the development of disease. This review examines the major milestones in epigenetics research in the context of diseases and various computational approaches developed in the last decades to unravel new epigenetic modifications. However, there are limited studies that systematically link genetic and epigenetic alterations of DNA to the aetiology of diseases. In this work, we demonstrate how disease-related epigenetic knowledge can be systematically captured and integrated with heterogeneous information into a functional context using Biological Expression Language (BEL). This novel methodology, based on BEL, enables us to integrate epigenetic modifications such as DNA methylation or acetylation of histones into a specific disease network. As an example, we depict the integration of epigenetic and genetic factors in a functional context specific to Parkinson's disease (PD) and Multiple Sclerosis (MS).
authors.affiliation: Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, 53754 Sankt Augustin, Germany ; Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universität Bonn, Dahlmannstrasse 2, 53113 Bonn, Germany.
authors.forename: Afroza
authors.initials: A
authors.lastname: Khanam Irin
authors.affiliation: Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, 53754 Sankt Augustin, Germany ; Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universität Bonn, Dahlmannstrasse 2, 53113 Bonn, Germany.
authors.forename: Alpha Tom
authors.initials: AT
authors.lastname: Kodamullil
authors.affiliation: Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, 53754 Sankt Augustin, Germany ; Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universität Bonn, Dahlmannstrasse 2, 53113 Bonn, Germany.
authors.forename: Michaela
authors.initials: M
authors.lastname: Gündel
authors.affiliation: Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, 53754 Sankt Augustin, Germany ; Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universität Bonn, Dahlmannstrasse 2, 53113 Bonn, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Hofmann-Apitius
mesh_terms: D000107:Acetylation; D000818:Animals; D001327:Autoimmune Diseases / Q000235:genetics*; D019295:Computational Biology; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D020022:Genetic Predisposition to Disease; D006657:Histones / Q000378:metabolism; D006801:Humans; D008954:Models, Biological; D009103:Multiple Sclerosis / Q000235:genetics*; D010300:Parkinson Disease / Q000235:genetics*
chemical_list: D006657:Histones