title: Deep learning for computational biology.
abstract: Technological advances in genomics and imaging have led to an explosion of molecular and cellular profiling data from large numbers of samples. This rapid increase in biological data dimension and acquisition rate is challenging conventional analysis strategies. Modern machine learning methods, such as deep learning, promise to leverage very large data sets for finding hidden structure within them, and for making accurate predictions. In this review, we discuss applications of this new breed of analysis approaches in regulatory genomics and cellular imaging. We provide background of what deep learning is, and the settings in which it can be successfully applied to derive biological insights. In addition to presenting specific applications and providing tips for practical use, we also highlight possible pitfalls and limitations to guide computational biologists when and how to make the most use of this new technology.
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge, UK.
authors.forename: Christof
authors.initials: C
authors.lastname: Angermueller
authors.affiliation: Department of Computer Science, University of Tartu, Tartu, Estonia Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Cambridge, UK.
authors.forename: Tanel
authors.initials: T
authors.lastname: Pärnamaa
authors.affiliation: Department of Computer Science, University of Tartu, Tartu, Estonia Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Cambridge, UK leopold.parts@sanger.ac.uk oliver.stegle@ebi.ac.uk.
authors.forename: Leopold
authors.initials: L
authors.lastname: Parts
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge, UK leopold.parts@sanger.ac.uk oliver.stegle@ebi.ac.uk.
authors.forename: Oliver
authors.identifier: 0000-0002-8818-7193
authors.initials: O
authors.lastname: Stegle
mesh_terms: D019295:Computational Biology / Q000379:methods*; D023281:Genomics / Q000379:methods; D006801:Humans; D000069550:Machine Learning; D008957:Models, Genetic
keywords: cellular imaging; computational biology; deep learning; machine learning; regulatory genomics