112 citations
Counting papers with at most 25 authors, so collaboration author lists do not stand in for the people here.
- Consejo Superior de Investigaciones CientíficasES11 papers
- Hungarian Academy of SciencesHU2 papers
- Adaptation et Diversité en Milieu MarinFR1 paper
- CEA GrenobleFR1 paper
- Centre National de la Recherche ScientifiqueFR1 paper
- Commissariat à l'Énergie Atomique et aux Énergies AlternativesFR1 paper
- ETH ZurichCH1 paper
- Friedrich Schiller University JenaDE1 paper
- GenoscopeFR1 paper
- GEOMAR Helmholtz Centre for Ocean Research KielDE1 paper
- Ghent UniversityBE1 paper
- Harvard UniversityUS1 paper
12 papers
Identifiability-aware neural ordinary differential equations for parsimonious and reliable dynamic modelling
Núria Campo-Manzanares, Eva Balsa-Canto
Neural ordinary differential equations (NODE) and hybrid NODE models provide flexible continuous-time representations of complex dynamic systems, but their expressive capacity can…
PEtab -- interoperable specification of parameter estimation problems in systems biology
Leonard Schmiester, Yannik Schälte, Frank T. Bergmann +26
Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been -- so far -- no broadly supported format for the specification of p…
A community perspective on the concept of marine holobionts: state-of-the-art, challenges, and future directions
Simon Dittami, Enrique Arboleda, Jean-Christophe Auguet +28
Host-microbe interactions play crucial roles in marine ecosystems, but we still have very little understanding of the mechanisms that govern these relationships, the evolutionary p…
MPA network design based on graph network theory and emergent properties of larval dispersal
Andres Ospina-Alvarez, Silvia de Juan, Josep Alós +5
Despite the recognised effectiveness of networks of Marine Protected Areas (MPAs) as a biodiversity conservation instrument, nowadays MPA network design frequently disregards the i…
Transient hysteresis and inherent stochasticity in gene regulatory networks
Manuel Pájaro, Irene Otero-Muras, Carlos Vázquez +1
Cell fate determination, the process through which cells commit to differentiated states is commonly mediated by gene regulatory motifs with mutually exclusive expression states. T…
Exponential equilibration of genetic circuits using entropy methods
José A. Cañizo, José A. Carrillo, Manuel Pájaro
We analyse a continuum model for genetic circuits based on a partial integro-differential equation initially proposed in Friedman, Cai \& Xie (2006) as an approximation of a chemic…
Dynamical compensation and structural identifiability: analysis, implications, and reconciliation
Alejandro F. Villaverde, Julio R. Banga
The concept of dynamical compensation has been recently introduced to describe the ability of a biological system to keep its output dynamics unchanged in the face of varying param…
Dynamical compensation in biological systems as a particular case of structural non-identifiability
Alejandro F. Villaverde, Julio R. Banga
Dynamical compensation (DC) has been recently defined as the ability of a biological system to keep its output dynamics unchanged in the face of varying parameters. This concept is…
Uniqueness of feasible equilibria for mass action law (MAL) kinetic systems
Antonio A. Alonso, Gabor Szederkenyi
This paper studies the relations among system parameters, uniqueness, and stability of equilibria, for kinetic systems given in the form of polynomial ODEs. Such models are commonl…
Multicriteria global optimization for biocircuit design
Irene Otero-Muras, Julio R. Banga
One of the challenges in Synthetic Biology is to design circuits with increasing levels of complexity. While circuits in Biology are complex and subject to natural tradeoffs, most…
Biological mechanism and identifiability of a class of stationary conductance model for Voltage-gated Ion channels
Febe Francis, Míriam R. García, Oliver Mason +1
The physiology of voltage gated ion channels is complex and insights into their gating mechanism is incomplete. Their function is best represented by Markov models with relatively…
A Linear Programming Approach to Weak Reversibility and Linear Conjugacy of Chemical Reaction Networks
Matthew D. Johnston, David Siegel, Gábor Szederkényi
A numerically effective procedure for determining weakly reversible chemical reaction networks that are linearly conjugate to a known reaction network is proposed in this paper. Th…