Computational modeling, formal analysis, and tools for systems biology

E Bartocci, P Lió - PLoS computational biology, 2016 - journals.plos.org
As the amount of biological data in the public domain grows, so does the range of modeling
and analysis techniques employed in systems biology. In recent years, a number of …

Verifiable biology

S Konur, M Gheorghe… - Journal of the Royal …, 2023 - royalsocietypublishing.org
The formalization of biological systems using computational modelling approaches as an
alternative to mathematical-based methods has recently received much interest because …

Attraction basins as gauges of robustness against boundary conditions in biological complex systems

J Demongeot, E Goles, M Morvan, M Noual, S Sené - PloS one, 2010 - journals.plos.org
One fundamental concept in the context of biological systems on which researches have
flourished in the past decade is that of the apparent robustness of these systems, ie, their …

Stable gene regulatory network modeling from steady-state data

JE Larvie, MG Sefidmazgi, A Homaifar, SH Harrison… - Bioengineering, 2016 - mdpi.com
Gene regulatory networks represent an abstract mapping of gene regulations in living cells.
They aim to capture dependencies among molecular entities such as transcription factors …

On the modelling and analysis of the regulatory network of dengue virus pathogenesis and clearance

B Aslam, J Ahmad, A Ali, RZ Paracha… - … Biology and Chemistry, 2014 - Elsevier
Dengue virus can ignite both protective and pathogenic responses in human. The
pathogenesis is related with modified functioning of our immune system during infection …

Formal modeling and analysis of the mal-associated biological regulatory network: insight into cerebral malaria

J Ahmad, U Niazi, S Mansoor, U Siddique, J Bibby - PloS one, 2012 - journals.plos.org
The discrete modeling formalism of René Thomas is a well known approach for the
modeling and analysis of Biological Regulatory Networks (BRNs). This formalism uses a set …

Sur la bio-informatique des réseaux d'automates

S Sené - 2012 - theses.hal.science
Ce travail présente des contributions théoriques et appliquées dans le contexte des
systèmes dynamiques discrets vus comme modèles des réseaux de régulation biologique …

[PDF][PDF] Attraction basins as gauges of environmental robustness in biological complex systems

J Demongeot, E Goles, M Morvan, M Noual, S Sené - networks, 2010 - researchgate.net
One fundamental concept in the context of biological systems on which researches have
flourished since a decade is that of the apparent robustness of these systems, ie, their ability …

EcoMata: Un logiciel d'aide à la décision pour améliorer la gestion des écosystèmes

Y Zhao, C Largouët, MO Cordier - … des Sciences et Technologies de l' …, 2011 - hal.science
Les modèles de simulation sont reconnus, en particulier dans le domaine de l'écologie,
comme un moyen de mieux comprendre les liens complexes existant entre les actions …

Incorporating time delays in process hitting framework for dynamical modeling of large biological regulatory networks

IA Sheikh, J Ahmad, M Magnin, O Roux - Frontiers in Physiology, 2019 - frontiersin.org
Modeling and simulation of molecular systems helps in understanding the behavioral
mechanism of biological regulation. Time delays in production and degradation of …