14 papers · ranked by Valyu relevance
Vincent Noël, Marco Ruscone, Gautier Stoll, Eric Viara + 3 more
'Andrei Zinovyev' 'Emmanuel Barillot' 'Laurence Calzone'] WebMaBoSS is an easy-to-use web interface for conversion, storage, simulation and analysis of Boolean models that allows to get insight from these models without any specific knowledge of modeling or coding. It relies on an existing software, MaBoSS, which…
Ahmed Abdelmonem Hemedan, Anna Niarakis, Reinhard Schneider, Marek Ostaszewski
'Marek Ostaszewski'] Title: Graphical abstract
Nadine Ben Boina, Brigitte Mossé, Anaïs Baudot, Elisabeth Remy + 1 more
Set $B={0,1}$ and $n$ an integer $>0$. A Boolean Model (BM) of dimension $n$ is a map $f=(f_{1},…,f_{n}) : Bn \rightarrowBn,$ where each Boolean state $x=(x_{1},…,x_{n})\inBn$ specifies the activity level of $n$ components of the model $g_{1}$, …, $g_{n}$. The values of the logical regulatory function $f_{i}(x)\inB$…
Bryan J. Glazer, Jonathan T. Lifferth, Carlos F. Lopez
Many important processes in biology, such as signaling and gene regulation, can be described using logic models. These logic models are typically built to behaviorally emulate experimentally observed phenotypes, which are assumed to be steady states of a biological system. Most models are built by hand and therefore…
Marco Fariñas, Eirini Tsirvouli, John Zobolas, Tero Aittokallio + 2 more
Boolean models are a powerful resource for studying dynamic processes of biological systems. However, their inherent discrete nature limits their ability to capture continuous aspects of signal transduction, such as signal strength or protein activation levels. Although existing tools provide some path exploration…
Domenico Sgariglia, Alessandra Jordano Conforte, Carlos Eduardo Pedreira, Luis Alfredo Vidal de Carvalho + 3 more
'Carlos Eduardo Pedreira' 'Luis Alfredo Vidal de Carvalho' 'Flavia Raquel Gonçalves Carneiro' 'Nicolas Carels' 'Fabricio Alves Barbosa\xa0da Silva'] Cancer is a genomic disease involving various intertwined pathways with complex cross-communication links. Conceptually, this complex interconnected system forms a…
Ahmed Abdelmonem Hemedan, Reinhard Schneider, Marek Ostaszewski
Computational modeling has emerged as a critical tool in investigating the complex molecular processes involved in biological systems and diseases. In this study, we apply Boolean modeling to uncover the molecular mechanisms underlying Parkinson’s disease (PD), one of the most prevalent neurodegenerative disorders. Our…
Van-Giang Trinh, Kyu Hyong Park, Samuel Pastva, Jordan C Rozum + 1 more
Here, we first give an overview of key Boolean modeling concepts and notation. More formal details are given in [sup1]. Then, we give an overview of the methods implemented by biobalm. Details, pseudo-code, and proofs are given in [sup1]. An asynchronous Boolean network (ABN) of dimension n, denoted B, is a…
Stéphanie Chevalier, Julia Becker, Yujuan Gui, Vincent Noël + 9 more
Boolean networks provide robust, explainable, and predictive models of cellular dynamics, especially for cellular differentiation and fate decision processes. Yet, the construction of such models is extremely challenging, as it requires integrating prior knowledge with experimental observation of the transcriptome…
Minsoo Kim, Eunjung Kim
Background In cell signaling pathways, proteins interact with each other to determine cell fate in response to either cell-extrinsic (micro-environmental) or intrinsic cues. One of the well-studied pathways, the mitogen-activated protein kinase (MAPK) signaling pathway, regulates cell processes such as differentiation…
Mohammad Taheri-Ledari, Sayed-Amir Marashi, Kaveh Kavousi, Sofia Forslund
Boolean networks (BNs) are mathematical models representing complex systems as a collection of binary variables connected through Boolean logic interactions, called update rules. BN modeling plays an important role in the study of complex biological systems, capturing essential interactions and dynamics. BN models have…
Biruck Woldai Abraha, Mario Andrea Marchisio
In 2008, we were among the first to propose a method for the visual design and modular modeling of synthetic gene circuits, mimicking the way electronic circuits are realized in silico. Basic components were DNA sequences that could be composed, first, into transcription units (TUs) and, then, circuits by exchanging…
Deyun Zhong, Ju Zhang, Liguan Wang, Lin Bi
In this paper, we implement an automatic modeling method for narrow vein type ore bodies based on Boolean combination constraints. Different from the direct interpolation approach, we construct the implicit functions of the hanging wall and foot wall surfaces, respectively. And then the combined implicit function is…
Malgorzata Kardynska, Daria Kogut, Marcin Pacholczyk, Jaroslaw Smieja
'Jaroslaw Smieja'] Regulatory networks structure and signaling pathways dynamics are uncovered in time- and resource consuming experimental work. However, it is increasingly supported by modeling, analytical and computational techniques as well as discrete mathematics and artificial intelligence applied to to extract…