|Lab Phone:||410-455-8168 410-455-2279|
Postdoctoral, Tufts University, 2015
PhD, University of Malaga, 2010
MSc, University of Malaga, 2007
BSc, University of Seville, 2005
What are the dynamic regulatory mechanisms, the information processing, and the specific molecular elements that control complex biological processes? At the Lobo Lab we develop new computational systems and methods to automatically reverse-engineer quantitative dynamic models from experimental data, produce testable hypothesis, and find the best next set of novel experiments to test at the bench. Our computational systems biology approach aims to understand the regulatory dynamics controlling multidimensional biological phenomena such as development and regeneration, the formation of cancer and other diseases when this process goes awry, and their applications to systems and synthetic biology. To this end, we also create mathematical and computational models, high-performance in silico experiments and simulators, and novel formalisms, ontologies, and databases to centralize and unambiguously describe biological experiments and their results. their results, paving the way for scientific progress by both human and AI scientists.
Lobo, D., Levin, M., 2015. Inferring regulatory networks from experimental morphological phenotypes: a computational method reverse-engineers planarian regeneration. PLoS Computational Biology 11, e1004295.
Lobo, D., Feldman, E.B., Shah, M., Malone, T.J., Levin, M., 2014. Limbform: a functional ontology-based database of limb regeneration experiments. Bioinformatics 30, 3598-3600.
Lobo, D., Feldman, E.B., Shah, M., Malone, T.J., Levin, M., 2014. A bioinformatics expert system linking functional data to anatomical outcomes in limb regeneration. Regeneration 1, 37-56.
Lobo, D., Solano, M., Bubenik, G.A., Levin, M., 2014. A linear-encoding model explains the variability of the target morphology in regeneration. Journal of the Royal Society Interface 11.
Lobo, D., Malone, T.J., Levin, M., 2013. Planform: an application and database of graph-encoded planarian regenerative experiments. Bioinformatics 29, 1098-1100.
Lobo, D., Malone, T.J., Levin, M., 2013. Towards a bioinformatics of patterning: a computational approach to understanding regulative morphogenesis. Biology Open 2, 156-169.
Lobo, D., Fernández, J.D., Vico, F.J., 2013. Behavior-Finding: Morphogenetic Designs Shaped by Function, in: Doursat, R., Sayama, H., Michel, O. (Eds.), Morphogenetic Engineering. Springer Berlin Heidelberg, pp. 441-472.
Lobo, D., Beane, W.S., Levin, M., 2012. Modeling planarian regeneration: a primer for reverse-engineering the worm. PLoS Computational Biology 8, e1002481.
Lobo, D., Vico, F.J., Dassow, J., 2011. Graph grammars with string-regulated rewriting. Theoretical Computer Science 412, 6101-6111.
Lobo, D., Vico, F.J., 2010. Evolution of form and function in a model of differentiated multicellular organisms with gene regulatory networks. Biosystems 102, 112-123.
Lobo, D., Vico, F.J., 2010. Evolutionary development of tensegrity structures. Biosystems 101, 167-176.