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Modeling Protein Interaction Networks with Answer Set Programming

Timur Fayruzov, Martine De Cock, Chris Cornelis, Dirk Vermeir
2009 2009 IEEE International Conference on Bioinformatics and Biomedicine  
In this paper we propose the use of answer set programming (ASP) to model protein interaction networks.  ...  set program.  ...  BUILDING A NETWORK MODEL IN ASP In this section, we set up the framework for describing protein interaction networks as answer set programs.  ... 
doi:10.1109/bibm.2009.9 dblp:conf/bibm/FayruzovCCV09 fatcat:seeeayizwbeqvmac6ypo6bqaaq

Modelling gene and protein regulatory networks with Answer Set Programming

Timur Fayruzov, Jeroen Janssen, Dirk Vermeir, Chris Cornelis, Martine De Cock
2011 International Journal of Data Mining and Bioinformatics  
In this paper we propose an answer set programming (ASP) based approach to model interaction networks.  ...  We build a general ASP framework that describes the network semantics and allows to model specific networks with little effort.  ...  Dynamical networks A dynamical network of protein interactions, such as a boolean network, captures interactions between proteins in the form of a directed graph G = (V, E) with V a set of nodes and E  ... 
doi:10.1504/ijdmb.2011.039178 pmid:21544955 fatcat:beo22vcca5gjpbs5nkg2jqdmry

Extending boolean regulatory network models with answer set programming

Timur Fayruzov, Jeroen Janssen, Chris Cornelis, Dirk Vermeir, Martine De Cock
2010 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)  
In this paper we develop an answer set programming (ASP) framework that supports threshold boolean network semantics and extends it with the capability to model meta interactions.  ...  Moreover, readily available answer set solvers can be used to find the steady states of the network.  ...  If the minimal model S of the naf-free program P coincides with S, then S is an answer set of the original program P . Example 2 A program with negation-as-failure can have more than one answer set.  ... 
doi:10.1109/bibmw.2010.5703800 fatcat:z4hqjoscvbd7xiwkloj3wx47we

Toward Synthesizing Executable Models in Biology

Jasmin Fisher, Nir Piterman, Rastislav Bodik
2014 Frontiers in Bioengineering and Biotechnology  
We describe synthesis of biological models from curated mutation experiment data, inferring network connectivity models from phosphoproteomic data, and synthesis of Boolean networks from gene expression  ...  If the observed behavior of the program agrees with the observed biological behavior, then the program explains the phenomena.This approach has proven beneficial for gaining new biological insights and  ...  Each such cell model will be composed of multiple proteins that will interact with proteins inside the cell as well as proteins (receptors) on neighboring cells.  ... 
doi:10.3389/fbioe.2014.00075 pmid:25566538 pmcid:PMC4271700 fatcat:6kfal2qk6jfetfsxjaasg4kwl4

Post-Proceedings of the First International Workshop on Learning and Nonmonotonic Reasoning [article]

Katsumi Inoue, Chiaki Sakama
2013 arXiv   pre-print
Nonmonotonic logic programming (NMLP) and Answer Set Programming (ASP) provide formal languages for representing and reasoning with commonsense knowledge and realize declarative problem solving in AI.  ...  Cross-fertilization between learning and nonmonotonic reasoning can also occur in such as the use of answer set solvers for ILP, speed-up learning while running answer set solvers, learning action theories  ...  We showed with one short example that axioms used to analyze signalling networks could be expressed in this formalism.  ... 
arXiv:1311.4639v1 fatcat:ofrlbpdsg5hmrlpluhx3z3vkdy

Introduction to Network Analysis in Systems Biology

A. Ma'ayan
2011 Science Signaling  
This Teaching Resource provides lecture notes, slides, and a problem set for a set of three lectures from a course entitled "Systems Biology: Biomedical Modeling."  ...  The second lecture surveys milestones and key concepts in network analysis by introducing topological measures, random networks, growing network models, and topological observations from molecular biological  ...  Make the nodes appear in two colors, viral proteins in one color, and human proteins in another color. Answer the following two questions: Which host proteins interact with many HCV proteins?  ... 
doi:10.1126/scisignal.2001965 pmid:21917719 pmcid:PMC3196357 fatcat:uohhuzayo5cftkyapp3sueglui

Hypothesizing about signaling networks

Nam Tran, Chitta Baral
2009 Journal of Applied Logic  
We illustrate the applicability of our system with an example of hypothesis formation in the signaling network of the p53 protein.  ...  These formalisms are mostly monotonic and are now known to be not quite suitable for knowledge representation, especially in dealing with the inherently incomplete knowledge about signaling networks.  ...  A set S of atoms is a consistent answer set of Π iff S = X ∪ Y for some solution X, Y to Π with respect to A.  ... 
doi:10.1016/j.jal.2008.10.001 fatcat:4uhxzthvsrgwlg5ibekm5leglu

A knowledge based approach for representing and reasoning about signaling networks

C. Baral, K. Chancellor, N. Tran, N.L. Tran, A. Joy, M. Berens
2004 Bioinformatics  
Some of the advantages of our approach are, we can use recent advances in reasoning with incomplete and partial information to deal with gaps in signal network knowledge; and can perform various kinds  ...  Results: Using our approach we have developed the system BioSigNet-RR for representation and reasoning about signaling networks.  ...  with the answer set semantics-simply referred to as AnsProlog in Baral (2003) .  ... 
doi:10.1093/bioinformatics/bth918 pmid:15262776 fatcat:mn3vcmof4jbyraqqhueifke2tu

INTERACT: an object oriented protein-protein interaction database

K Eilbeck, A Brass, N Paton, C Hodgman
1999 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
Protein-protein interactions provide vital information concerning the function of proteins, complexes and networks. Currently there is no widely accepted repository of this interaction information.  ...  An object oriented database has been created which provides scientists with a resource for examining existing protein-protein interactions and inferring possible interactions from the data stored.  ...  As an example of analysis, a clustering program further analyzes the interactions reported for yeast to obtain networks of interacting proteins.  ... 
pmid:10786290 fatcat:7vlhbmih7bc7belhvgx35nr3wu

Constraint-based models for dominating protein interaction networks

Adel A Alofairi, Emad Mabrouk, Ibrahim E Elsemman
2021 IET Systems Biology  
The MDSet has been successfully applied to extract proteins that control protein-protein interaction (PPI) networks and to reveal the correlation between structural analysis and biological functions.  ...  In MOIA, they provide three models; the first one generates two MDSets with a minimum number of shared proteins, the second model generates constrained multiple MDSets ( k -MDSets), and the third model  ...  | Bioplex protein interaction network Two versions of the protein interaction data set of the BioPlex network [39] were used.  ... 
doi:10.1049/syb2.12021 pmid:34048146 fatcat:tq7hn6adljbtlbtxm5lx3vofbu

Accurate and Scalable Techniques for the Complex/Pathway Membership Problem in Protein Networks

Orhan Çamoğlu, Tolga Can, Ambuj K. Singh
2009 Advances in Bioinformatics  
A protein network shows physical interactions as well as functional associations. An important usage of such networks is to discover unknown members of partially known complexes and pathways.  ...  Network flow technique with clustering is able to optimize meaningful threshold queries and answer them with high efficiency compared to a similar method that uses Monte Carlo simulation.  ...  Discussion In this paper we analyzed two classes of techniques for the analysis of protein interaction networks.  ... 
doi:10.1155/2009/787128 pmid:20182643 pmcid:PMC2826754 fatcat:2ietnaorh5emjfr6khfewts37i

NetR and AttR, Two New Bioinformatic Tools to Integrate Diverse Datasets into Cytoscape Network and Attribute Files

Halajyan, Weingart, Yeahia, Loza-Coll
2019 Genes  
NetR also allows users to import protein and genetic interaction data from InterMine, which can further enrich a network model based on curated information.  ...  with Cytoscape to display hypothetical networks that result from combining individual datasets, as well as a series of published attributes related to the genes or proteins in the network.  ...  Stan Metzenberg, who introduced Armen to Python coding and who inspired us all in our department to boldly pursue biological modelling in our research efforts.  ... 
doi:10.3390/genes10060423 pmid:31159440 pmcid:PMC6628208 fatcat:jjupeegy3bdmldr6kipukwabmm

Logical Modeling and Analysis of Regulatory Genetic Networks in a Non Monotonic Framework [chapter]

Nicolas Mobilia, Alexandre Rocca, Samuel Chorlton, Eric Fanchon, Laurent Trilling
2015 Lecture Notes in Computer Science  
Keywords: computational systems biology · gene networks · discrete modeling · AIoriented declarative approach · non monotonic logic · Answer Set Programming structure and its dynamics (e.g., existence  ...  For this purpose, we use the logic programming technology ASP (Answer Set Programming) whose related logic is non monotonic. Our aim is twofold.  ...  A set X ⊆ A is an answer set (AS) or stable model of a program P if X is the minimal model 3 4 of the reduct P X = {head(r)←body + (r)|r∈P, body − (r) ∩ X = ∅}.  ... 
doi:10.1007/978-3-319-16483-0_58 fatcat:qt5dke4h5bhvjhvttokqzgpbh4

CytoASP: a Cytoscape app for qualitative consistency reasoning, prediction and repair in biological networks

Aristotelis Kittas, Amélie Barozet, Jekaterina Sereshti, Niels Grabe, Sophia Tsoka
2015 BMC Systems Biology  
It allows easy integration of qualitative modelling, combining the functionality of BioASP with the visualisation and processing capability in Cytoscape, and thereby greatly simplifying qualitative network  ...  Qualitative reasoning frameworks, such as the Sign Consistency Model (SCM), enable modelling regulatory networks to check whether observed behaviour can be explained or if unobserved behaviour can be predicted  ...  The BioASP software collection 1 implements methods for modelling metabolic and gene regulatory networks [3] , using logical rules with Answer Set Programming (ASP) [4] .  ... 
doi:10.1186/s12918-015-0179-6 pmid:26163265 pmcid:PMC4499222 fatcat:dj2jhvwgrvcifamqb7j37gfeoi

Using Biological Pathway Data with Paxtools

Emek Demir, Özgün Babur, Igor Rodchenkov, Bülent Arman Aksoy, Ken I. Fukuda, Benjamin Gross, Onur Selçuk Sümer, Gary D. Bader, Chris Sander, Andreas Prlic
2013 PLoS Computational Biology  
significantly altered portions of the cellular network in a disease state and building predictive models that can be used for precision medicine.  ...  Due to its complexity and fragmented nature, however, working with pathway data is still difficult.  ...  In this scenario, a user writes a small Java program that loads the cellular process network curated by a pathway database.  ... 
doi:10.1371/journal.pcbi.1003194 pmid:24068901 pmcid:PMC3777916 fatcat:ts6lhfv64va6lm5bioyqw4a4y4
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