8 documents found, page 1 of 1
FROG analysis ensures the reproducibility of genome scale metabolic models
Raman, Karthik; Kratochvil, Miroslav; Olivier, Brett G.; Konig, Matthias; Sengupta, Pratyay; Baskaran, Dinesh Kumar Kuppa; Nguyen, Tung V NGenome scale metabolic models (GEMs) and other constraint-based models (CBMs) play a pivotal role in understanding biological phenotypes and advancing research in areas like metabolic engineering, human disease modelling, drug discovery, and personalized medicine. Despite their growing application, a significant challenge remains in ensuring the reproducibility of GEMs, primarily due to inconsistent reporting a...
Impact of changing cell-cell communication network in models of epithelial patt...
Varela, Pedro L.; Monteiro, Pedro T.; Chaouiya, ClaudineWhen modelling multi-cellular systems, one has to account for cell-cell signalling in addition to the molecular networks driving cell behaviours. Here, we aim at exploring how the topology of the cell-cell communication network impacts the behaviour of the whole multicellular system. More precisely, we focus on epithelial pattern formation, on which our question can be rephrased in terms of cell sizes and shape...
EpiLog: A software for the logical modelling of epithelial dynamics
Varela, Pedro L.; Ramos, Camila V.; Monteiro, Pedro T.; Chaouiya, ClaudineCellular responses are governed by regulatory networks subject to external signals from surrounding cells and to other micro-environmental cues. The logical (Boolean or multi-valued) framework proved well suited to study such processes at the cellular level, by specifying qualitative models of involved signalling pathways and gene regulatory networks. Here, we describe and illustrate the main features of EpiL...
Estimating Attractor Reachability in Asynchronous Logical Models
Mendes, Nuno D.; Henriques, Rui; Remy, Elisabeth; Carneiro, Jorge; Monteiro, Pedro T.; Chaouiya, ClaudineLogical models are well-suited to capture salient dynamical properties of regulatory networks. For networks controlling cell fate decisions, cell fates are associated with model attractors (stable states or cyclic attractors) whose identification and reachability properties are particularly relevant. While synchronous updates assume unlikely instantaneous or identical rates associated with component changes, th...
Logical Modeling and Dynamical Analysis of Cellular Networks
Abou-Jaoudé, Wassim; Traynard, Pauline; Monteiro, Pedro T.; Saez-Rodriguez, Julio; Helikar, Tomáš; Thieffry, Denis; Chaouiya, ClaudineThe logical (or logic) formalism is increasingly used to model regulatory and signaling networks. Complementing these applications, several groups contributed various methods and tools to support the definition and analysis of logical models. After an introduction to the logical modeling framework and to several of its variants, we review here a number of recent methodological advances to ease the analysis of l...
Model Checking to Assess T-Helper Cell Plasticity
Abou-Jaoudé, Wassim; Monteiro, Pedro T.; Naldi, Aurélien; Grandclaudon, Maximilien; Soumelis, Vassili; Chaouiya, Claudine; Thieffry, DenisComputational modeling constitutes a crucial step toward the functional understanding of complex cellular networks. In particular, logical modeling has proven suitable for the dynamical analysis of large signaling and transcriptional regulatory networks. In this context, signaling input components are generally meant to convey external stimuli, or environmental cues. In response to such external signals, cells ...
Not seeing the forest for the trees: size of the minimum spanning trees (MSTs) ...
Teixeira, Andreia Sofia; Monteiro, Pedro T.; Carrico, Joao Andre; Ramirez, Mário; Francisco, Alexandre P.Trees, including minimum spanning trees (MSTs), are commonly used in phylogenetic studies. But, for the research community, it may be unclear that the presented tree is just a hypothesis, chosen from among many possible alternatives. In this scenario, it is important to quantify our confidence in both the trees and the branches/edges included in such trees. In this paper, we address this problem for MSTs by int...
PHYLOViZ: phylogenetic inference and data visualization for sequence based typi...
Francisco, Alexandre P.; Vaz, Cátia; Monteiro, Pedro T.; Melo-Cristino, José; Ramirez, Mario; Carrico, JoaoBackground: With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results needed for a global scale bacterial population analysis, while retaining their usefulness for local epidemiological surveys. Online databases that collect the generated allelic profiles and associat...