Quantitative Modelling Approaches

doi:10.1016/B978-0-12-809633-8.20454-8

Reference Module in Life Sciences

Encyclopedia of Bioinformatics and Computational Biology

Volume 2, 2019, Pages 874-883

https://doi.org/10.1016/B978-0-12-809633-8.20454-8 Get rights and content

Abstract

Computational biology aims at disentangling the complexity of biological phenomena by providing tools/algorithms to analyse experimental data or models to predict outcomes of the biological system based on experimental and clinical data. Bioinformatics tools are used to analyse and interpret large scale experimental data and to distil useful information necessary to set up mathematical/computational models. In turn, computational models replicate the dynamics of complex biological systems thus offering in silico evaluations of a hypothesis. Models can be used to predict changes in the behaviour of a system over time and further unravel the complexity of the phenomena under study. Together, these methodologies have the potential to reshape our understanding of biology at all levels of details eventually allowing the optimization of existing therapies or even the formulation of new ones. In this article, we present succinct and informal descriptions of the main approaches or frameworks underlying most mathematical and computational methods currently used in quantitative studies of biological systems.

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Filippo Castiglione is researcher at the Istituto per le Applicazioni del Calcolo of the National Research Council of Italy and adjunct professor of Computational Biology at the Department of Mathematics and Physics of Roma Tre University. He graduated in computer science at the University of Milan, Italy, and got a PhD in Scientific Computing at the University of Cologne, Germany. He has been PostDoc at the Institute for Medical Bio-Mathematics in Tel Aviv, Israel and visiting research fellow at the IBM - T.J. Watson Research Center, Yorktown Heights (NY), at the Department of Molecular Biology at Princeton University and at the Department of Cell Biology, Harvard Medical School, Boston. Filippo has published one book and about 100 reviewed research papers among journals, books and conferences proceedings. He is the main author of the C-ImmSim agent-based simulation model of the immune system. Filippo has been involved as principal investigator in two EU-funded projects of the ICT for Health of the 6th Framework Programme (FP6) and has coordinate a project of the FP7. His research interests range from the study of complex systems to the modeling of biological systems, machine learning and high-performance computing.

Emiliano Mancini is programme developer on Health Systems Complexity at the Institute for Advanced Study in Amsterdam, where he coordinates the research in various academic disciplines for interdisciplinary research projects. In this role, he also engages private companies and stakeholders for the valorisation and utilization of these academic projects as well as collaborate on the strategic plan for the growth of the Institute. Emiliano obtained his Master degree in Physics at University of Rome Tor Vergata and a PhD in Computational Science at University of Amsterdam simulating infectious diseases (HIV and H1N1) using agent-based modeling. As a postdoc Emiliano has worked between University of Amsterdam and the Nanyang Technological University in Singapore on modeling the dynamics of several complex biological systems. He worked as a consultant or team member of several start-up companies and has been involved in the development of a clinical decision support platform for HIV treatment and on a non-invasive continuous glucose meter funded by SMART-MIT. Emiliano was also responsible for the organization and supervision of several experiments on crowd dynamics for the Kumbh Mela Experiment: an Indo-Dutch project to study the Kumbh Mela, the largest religious event in the world.

Marco Pedicini is professor of Computer Science at the Department of Mathematics and Physics of Roma Tre University. He received his Ph.D. in Mathematics (Mathematical Logic and Theoretical Computer Science) from the University of Paris 7 in 1998. He was researcher at Italian National Research Council (CNR). Since his PhD thesis, Marco has developed ideas in TCS and his interests include logic in computer science, cryptography, computer security, parallel and distributed computing, computational methods for systems biology, computational number theory, and more recently quantum computing. Although his whole activity could be classifiable in TCS it finds in interdisciplinary research its own specificity. Interactions with other disciplines are the key to evaluate his scientific activity: in fact, he developed a very special kind of expertise while coping deep theoretical results with practical issues in advanced applications in collaboration with colleagues of different disciplines. Marco has published 30 scientific papers, many of them in leading international journals and selective peer reviewed conferences. In order to witness a broad area in Marco interests, these papers not only appeared on top conferences and journals in logic for computer science but also on top journals covering application of computer science to biology and medicine.

Abdul Salam Jarrah is a Professor of Mathematics and a faculty member of the Master of Science in Biomedical Engineering Programme at the American University of Sharjah (AUS) in the United Arab Emirates. Before joining the AUS in 2009, he was a senior research scientist at the Virginia Bioinformatics Institute and Affiliate Assistant Professor at the Department of Mathematics in Virginia Tech, USA. Prior to that, he was as an Assistant Professor of Applied Mathematics at East Tennessee State University, USA. In addition, Abdul was a member of the Mathematical Sciences Research Institute at Berkeley, USA from August 2016 to January 2018. He received his PhD in Mathematics from New Mexico State University in 2002. His current research interests span many areas of mathematics including discrete dynamical systems, discrete homology theory of graphs, computational algebra, and their applications in biology, especially the modeling and simulation of biological systems. He has made several contributions to these fields through many publications in international journals.

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