8 papers · ranked by Valyu relevance
Oluwateniayo O. Ogunsan, Daniel Lobo
Mathematical models formally and precisely represent biological mechanisms with complex dynamics. To understand the possible behaviors of such systems, phase portrait diagrams can be used to visualize their overall global dynamics across a domain. However, producing these phase portrait diagrams is a laborious process…
Stuart J. E. Baird, Jan Petružela, Izar Jaroň, Pavel Škrabánek + 1 more
We extend classic allele counting measures of geneflow to the case of genomescale data. Using a deterministic data labelling, small numbers of diagnostic markers can be replaced by large numbers of markers, each with a diagnostic index. Individuals’ hybrid indices can then be calculated genome wide conditioned on…
Éléa Thibault Greugny, Nicolas Ratto, Loïc Etheve, Jean-Baptise Gourlet + 2 more
Mathematical modeling of disease and drug action is becoming an indispensable component of drug development, underscored by recent examples of models predicting trial results. To be able to rely on such approaches, decision-makers need to be able to verify those results independently with in silico confirmatory…
Matthew Hur, Patrick T. Hwu, Katherine L. Thompson-Peer, Eric D. Mjolsness
Dendrites develop branching patterns that are critical for their function, yet the mechanisms guiding arbor morphology remain incompletely understood, and quantitative models predicting how signals guide morphology remain limited. The ddaE neuron in Drosophila larvae is a proprioceptive sensory neuron with a…
Adam Šmelko, Miroslav Kratochvíl, Emmanuel Barillot, Vincent Noël
Computational models in systems biology are becoming more important with the advancement of experimental techniques to query the mechanistic details responsible for leading to phenotypes of interest. In particular, Boolean models are well fit to describe the complexity of signaling networks while being simple enough to…
Ayush Pandey, Inigo Incer, Alberto Sangiovanni-Vincentelli, Richard M. Murray
We provide a new perspective on using formal methods to model specifications and synthesize implementations for the design of biological circuits. In synthetic biology, design objectives are rarely described formally. We present an assume-guarantee contract framework to describe biological circuit design objectives as…
Georges Czaplicki, Serge Mazeres
Model validation depends on the agreement between the predicted and experimental data. However, finding solutions to problems, described by equations with many parameters, for which virtually nothing is known, is a difficult task. For example, the extraction of kinetic parameters from complex schemes representing the…
V. L. Kalmykov, L. V. Kalmykov
Mathematical black box models, which hide the structure and behavior of the subsystems, currently dominate science. Errors and paradoxes, such as the biodiversity paradox and the limiting similarity hypothesis, often arise from subjective interpretations of these hidden mechanisms. To address these problems, we have…