[PDF] Top 20 Synthesis of Boolean Networks from Biological Dynamical Constraints using Answer-Set Programming
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Synthesis of Boolean Networks from Biological Dynamical Constraints using Answer-Set Programming
... support from ITMO Cancer and from the French Agence Nationale pourla Recherche (ANR), in the context of ANR- FNR project AlgoReCell ANR-16-CE12-0034 according to a collection of Boolean ... Voir le document complet
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Reasoning on the response of logical signaling networks with answer set programming
... particularly Boolean networks and slight variations ...layers of complexity yielding more precise descriptions [Wittmann et ...case of poorly understood biological systems where kinetic ... Voir le document complet
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Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision
... synthesizing Boolean model ensembles satisfying a set of biologically relevant constraints and b) rea- soning on the dynamics of the ensembles of ...The synthesis is ... Voir le document complet
18
Reasoning on the response of logical signaling networks with Answer Set Programming
... levels of causation pose indeed a long-term goal in the ...signaling networks: state of the art and current challenges Among various discrete dynamical systems, Boolean networks ... Voir le document complet
47
Formal Derivation of Qualitative Dynamical Models from Biochemical Networks
... the constraints accounting for limiting resources, since not only there must be enough resources so that the number of instances of a given chemical species may reach a given sampling interval, but ... Voir le document complet
101
Biological organisation as closure of constraints.
... functional constraints, prima facie, appear (see footnote 18 above) to transmit energy, we hold that they do in fact channel an energy transfer while being ...example of the heart which, according to the ... Voir le document complet
29
Computation of Lyapunov Functions under State Constraints using Semidefinite Programming Hierarchies
... tion of the differential equation with the nonlinearity η is interpreted as a Lur’e ...the constraints imposed on the state trajectories of system ...constraint set being the positive orthant, ... Voir le document complet
13
Concurrency in Boolean networks
... Abstract Boolean networks (BNs) are widely used to model the qualitative dynamics of biological ...tion of each component with respect to the state of its regulators, the ... Voir le document complet
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Temporal Reprogramming of Boolean Networks
... node of the original transition graph have multiple copies, given how many perturbations are used to reach it: thus, a state of the perturbation transition graph is composed of the state of ... Voir le document complet
18
Bridging boolean and quantitative synthesis using smoothed proof search
... expectation of P c (x) is guaranteed to fall within I. Given this mapping from c 7→ (p, I), our goal is to find a value of c that leads to low values of p as well as ...value of c that ... Voir le document complet
15
Dynamical Boolean Modeling of Immunogenic Cell Death
... frame of E-Rare-2, the ERA-Net for Research on Rare Diseases; Association pour la recherche sur le cancer (ARC); Cancéropôle Ile-de-France; Chancellerie des universités de Paris (Legs Poix), Fondation pour la ... Voir le document complet
13
Constraints Programming for Unifying Gene Regulatory Networks Modeling Approaches
... additional constraints-based techniques usually applied for analyzing meta- bolic ...models of genetic regulatory networks: [3, ...patterns of the derivatives of concentrations levels ... Voir le document complet
11
Most Permissive Semantics of Boolean Networks
... downloaded from http: ...Models of differentiation processes from literature We show on several case studies from literature that MPBNs, although potentially predicting more behaviors than ... Voir le document complet
26
Pseudo-Boolean Programming for Partially Ordered Genomes
... Impact of width for CI-1PO. 16Gb of memory running Linux was required for 14 of the ...out of 70), but without specific gene distribution (21 times ...ranges from 5 to 22 and is on ... Voir le document complet
13
Sequential Reprogramming of Boolean Networks Made Practical
... kinds of perturbations and targeted dynamical ...[1,19,12] using quite different approaches: Abou- Jaoud´ e et ...a set of perturbations can reprogram the cell correctly, using ... Voir le document complet
18
Identification of Biological Regulatory Networks from Process Hitting models
... dynamics of the ...derived from two different ...expression of its regulators. Some of the informa- tion included in the IG and the parametrization may appear as slightly redun- ...additional ... Voir le document complet
40
Logical Differential Constraints Based on Interval Boolean Tests
... approximation of the true system S, especially for continuous-time systems defined by ordinary differential equations (ODEs), where some unknown data have to be ...sition of a mobile robot is usually known ... Voir le document complet
6
Using hybrid concurrent constraint programming to model dynamic biological systems
... L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignemen[r] ... Voir le document complet
16
Fixing monotone Boolean networks asynchronously
... in networks f which can be fixed in polynomial time, ...F of n-component ...members of F are ...length of a shortest word fixing ...result of this kind was given in [15], where it is ... Voir le document complet
22
Speech synthesis using recurrent neural networks
... collection of all 32 Beethoven’s piano sonatas publicly available on ...hours of non-vocal ...demonstration of examples from datasets and generated ...are using a 16 kHz sample rate and ... Voir le document complet
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