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6 Publications visible to you, out of a total of 6
Automated inference of Boolean models from molecular interaction maps using CaSQ

Abstract

Not specified

Authors: Sara Sadat Aghamiri, Vidisha Singh, Aurélien Naldi, Tomáš Helikar, Sylvain Soliman, Anna Niarakis

Date Published: 15th Aug 2020

Publication Type: Journal

Iterative community-driven development of a SARS-CoV-2 tissue simulator

Abstract

Not specified

Authors: Michael Getz, Yafei Wang, Gary An, Maansi Asthana, Andrew Becker, Chase Cockrell, Nicholson Collier, Morgan Craig, Courtney L. Davis, James R. Faeder, Ashlee N. Ford Versypt, Tarunendu Mapder, Juliano F. Gianlupi, James A. Glazier, Sara Hamis, Randy Heiland, Thomas Hillen, Dennis Hou, Mohammad Aminul Islam, Adrianne L. Jenner, Furkan Kurtoglu, Caroline I. Larkin, Bing Liu, Fiona Macfarlane, Pablo Maygrundter, Penelope A Morel, Aarthi Narayanan, Jonathan Ozik, Elsje Pienaar, Padmini Rangamani, Ali Sinan Saglam, Jason Edward Shoemaker, Amber M. Smith, Jordan J.A. Weaver, Paul Macklin

Date Published: 5th Apr 2020

Publication Type: Journal

Conceptual and computational framework for logical modelling of biological networks deregulated in diseases.

Abstract (Expand)

Mathematical models can serve as a tool to formalize biological knowledge from diverse sources, to investigate biological questions in a formal way, to test experimental hypotheses, to predict the … effect of perturbations and to identify underlying mechanisms. We present a pipeline of computational tools that performs a series of analyses to explore a logical model's properties. A logical model of initiation of the metastatic process in cancer is used as a transversal example. We start by analysing the structure of the interaction network constructed from the literature or existing databases. Next, we show how to translate this network into a mathematical object, specifically a logical model, and how robustness analyses can be applied to it. We explore the visualization of the stable states, defined as specific attractors of the model, and match them to cellular fates or biological read-outs. With the different tools we present here, we explain how to assign to each solution of the model a probability and how to identify genetic interactions using mutant phenotype probabilities. Finally, we connect the model to relevant experimental data: we present how some data analyses can direct the construction of the network, and how the solutions of a mathematical model can also be compared with experimental data, with a particular focus on high-throughput data in cancer biology. A step-by-step tutorial is provided as a Supplementary Material and all models, tools and scripts are provided on an accompanying website: https://github.com/sysbio-curie/Logical_modelling_pipeline.

Authors: A. Montagud, P. Traynard, L. Martignetti, E. Bonnet, E. Barillot, A. Zinovyev, L. Calzone

Date Published: 19th Jul 2019

Publication Type: Journal

PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling

Abstract

Not specified

Authors: Gaelle Letort, Arnau Montagud, Gautier Stoll, Randy Heiland, Emmanuel Barillot, Paul Macklin, Andrei Zinovyev, Laurence Calzone

Date Published: 1st Apr 2019

Publication Type: Journal

MaBoSS 2.0: an environment for stochastic Boolean modeling.

Abstract (Expand)

Motivation: Modeling of signaling pathways is an important step towards the understanding and the treatment of diseases such as cancers, HIV or auto-immune diseases. MaBoSS is a software that allows … to simulate populations of cells and to model stochastically the intracellular mechanisms that are deregulated in diseases. MaBoSS provides an output of a Boolean model in the form of time-dependent probabilities, for all biological entities (genes, proteins, phenotypes, etc.) of the model. Results: We present a new version of MaBoSS (2.0), including an updated version of the core software and an environment. With this environment, the needs for modeling signaling pathways are facilitated, including model construction, visualization, simulations of mutations, drug treatments and sensitivity analyses. It offers a framework for automated production of theoretical predictions. Availability and Implementation: MaBoSS software can be found at https://maboss.curie.fr , including tutorials on existing models and examples of models. Contact: gautier.stoll@upmc.fr or laurence.calzone@curie.fr. Supplementary information: Supplementary data are available at Bioinformatics online.

Authors: G. Stoll, B. Caron, E. Viara, A. Dugourd, A. Zinovyev, A. Naldi, G. Kroemer, E. Barillot, L. Calzone

Date Published: 15th Jul 2017

Publication Type: Journal

Continuous time Boolean modeling for biological signaling: application of Gillespie algorithm.

Abstract (Expand)

UNLABELLED: Mathematical modeling is used as a Systems Biology tool to answer biological questions, and more precisely, to validate a network that describes biological observations and predict the … effect of perturbations. This article presents an algorithm for modeling biological networks in a discrete framework with continuous time. BACKGROUND: There exist two major types of mathematical modeling approaches: (1) quantitative modeling, representing various chemical species concentrations by real numbers, mainly based on differential equations and chemical kinetics formalism; (2) and qualitative modeling, representing chemical species concentrations or activities by a finite set of discrete values. Both approaches answer particular (and often different) biological questions. Qualitative modeling approach permits a simple and less detailed description of the biological systems, efficiently describes stable state identification but remains inconvenient in describing the transient kinetics leading to these states. In this context, time is represented by discrete steps. Quantitative modeling, on the other hand, can describe more accurately the dynamical behavior of biological processes as it follows the evolution of concentration or activities of chemical species as a function of time, but requires an important amount of information on the parameters difficult to find in the literature. RESULTS: Here, we propose a modeling framework based on a qualitative approach that is intrinsically continuous in time. The algorithm presented in this article fills the gap between qualitative and quantitative modeling. It is based on continuous time Markov process applied on a Boolean state space. In order to describe the temporal evolution of the biological process we wish to model, we explicitly specify the transition rates for each node. For that purpose, we built a language that can be seen as a generalization of Boolean equations. Mathematically, this approach can be translated in a set of ordinary differential equations on probability distributions. We developed a C++ software, MaBoSS, that is able to simulate such a system by applying Kinetic Monte-Carlo (or Gillespie algorithm) on the Boolean state space. This software, parallelized and optimized, computes the temporal evolution of probability distributions and estimates stationary distributions. CONCLUSIONS: Applications of the Boolean Kinetic Monte-Carlo are demonstrated for three qualitative models: a toy model, a published model of p53/Mdm2 interaction and a published model of the mammalian cell cycle. Our approach allows to describe kinetic phenomena which were difficult to handle in the original models. In particular, transient effects are represented by time dependent probability distributions, interpretable in terms of cell populations.

Authors: G. Stoll, E. Viara, E. Barillot, L. Calzone

Date Published: 29th Aug 2012

Publication Type: Journal

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