Learning Boolean logic models of signaling networks with ASP

DOI10.1016/J.TCS.2014.06.022zbMATH Open1330.92050DBLPjournals/tcs/VidelaGETGNSSS15OpenAlexW2013942866WikidataQ56755016 ScholiaQ56755016MaRDI QIDQ498928FDOQ498928

Authors Santiago Videla, Carito Guziolowski, Federica Eduati, Sven Thiele, Martin Gebser, Jacques Nicolas, Julio Saez-Rodriguez, Torsten Schaub, Anne Siegel 

Publication date 29 September 2015

Published in Theoretical Computer Science (Search for Journal in Brave)

Full work available at URL https://hal.inria.fr/hal-01058610/file/paper.pdf

zbMATH Keywords

answer set programmingsystems biologyBoolean logic modelscombinatorial multi-objective optimizationsignaling transduction networks

Mathematics Subject Classification ID

Systems biology, networks (92C42) Logic programming (68N17)

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Cites work

• scientific article; zbMATH DE number 3957109 (Why is no real title available?)
• Analyzing pathways using ASP-based approaches
• Automatic network reconstruction using ASP
• Completing networks using observed data
• Complex optimization in answer set programming
• Contributions to the Theory of Logic Programming
• Detecting inconsistencies in large biological networks with answer set programming
• Directed hypergraphs and applications
• Extending the metabolic network of Ectocarpus siliculosus using answer set programming
• Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework
• Identification of genetic networks by strategic gene disruptions and gene overexpressions under a Boolean model.
• Knowledge Representation, Reasoning and Declarative Problem Solving
• Minimal intervention strategies in logical signaling networks with ASP
• Multi-threaded ASP solving with clasp
• Opportunities for combinatorial optimization in computational biology
• Static Analysis of Boolean Networks Based on Interaction Graphs: A Survey
• Survey of multi-objective optimization methods for engineering
• Transactions on Computational Systems Biology VI

Cited in

(14)

• “Don’t Care” Modeling: A Logical Framework for Developing Predictive System Models
• Modelling Biological Networks by Action Languages Via Answer Set Programming
• Learning Boolean controls in regulated metabolic networks: a case-study
• Minimal intervention strategies in logical signaling networks with ASP
• Bilevel integer programming on a Boolean network for discovering critical genetic alterations in cancer development and therapy
• Analyzing pathways using ASP-based approaches
• Logical modeling of biological systems
• Interpolative Boolean networks
• Comparing probabilistic and logic programming approaches to predict the effects of enzymes in a neurodegenerative disease model
• Automatic network reconstruction using ASP
• Modeling biological networks by action languages via answer set programming
• Logical modelling, some recent methodological advances illustrated
• Computing diverse Boolean networks from phosphoproteomic time series data
• A logic-based framework leveraging neural networks for studying the evolution of neurological disorders

Describes a project that uses

Uses Software

• Gringo
• clasp
• KEGG
• Cellnoptr
• Pathway Commons
• REVEAL

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