{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,30]],"date-time":"2025-05-30T08:22:47Z","timestamp":1748593367633},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Given a large-scale biological network represented as an influence graph, in this article we investigate possible decompositions of the network aimed at highlighting specific dynamical properties.<\/jats:p>\n               <jats:p>Results: The first decomposition we study consists in finding a maximal directed acyclic subgraph of the network, which dynamically corresponds to searching for a maximal open-loop subsystem of the given system. Another dynamical property investigated is strong monotonicity. We propose two methods to deal with this property, both aimed at decomposing the system into strongly monotone subsystems, but with different structural characteristics: one method tends to produce a single large strongly monotone component, while the other typically generates a set of smaller disjoint strongly monotone subsystems.<\/jats:p>\n               <jats:p>Availability: Original heuristics for the methods investigated are described in the article.<\/jats:p>\n               <jats:p>Contact: \u00a0altafini@sissa.it<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr620","type":"journal-article","created":{"date-parts":[[2011,11,10]],"date-time":"2011-11-10T06:32:04Z","timestamp":1320906724000},"page":"76-83","source":"Crossref","is-referenced-by-count":9,"title":["Decompositions of large-scale biological systems based on dynamical properties"],"prefix":"10.1093","volume":"28","author":[{"given":"Nicola","family":"Soranzo","sequence":"first","affiliation":[{"name":"1 CRS4 Bioinformatica, Loc. Piscina Manna, 09010 Pula (CA), Italy, 2Max-Planck-Institut f\u00fcr Informatik, Stuhlsatzenhausweg 85, 66123 Saarbr\u00fccken, Germany and 3SISSA, via Bonomea 265, 34136 Trieste, Italy"}]},{"given":"Fahimeh","family":"Ramezani","sequence":"additional","affiliation":[{"name":"1 CRS4 Bioinformatica, Loc. Piscina Manna, 09010 Pula (CA), Italy, 2Max-Planck-Institut f\u00fcr Informatik, Stuhlsatzenhausweg 85, 66123 Saarbr\u00fccken, Germany and 3SISSA, via Bonomea 265, 34136 Trieste, Italy"}]},{"given":"Giovanni","family":"Iacono","sequence":"additional","affiliation":[{"name":"1 CRS4 Bioinformatica, Loc. Piscina Manna, 09010 Pula (CA), Italy, 2Max-Planck-Institut f\u00fcr Informatik, Stuhlsatzenhausweg 85, 66123 Saarbr\u00fccken, Germany and 3SISSA, via Bonomea 265, 34136 Trieste, Italy"}]},{"given":"Claudio","family":"Altafini","sequence":"additional","affiliation":[{"name":"1 CRS4 Bioinformatica, Loc. Piscina Manna, 09010 Pula (CA), Italy, 2Max-Planck-Institut f\u00fcr Informatik, Stuhlsatzenhausweg 85, 66123 Saarbr\u00fccken, Germany and 3SISSA, via Bonomea 265, 34136 Trieste, Italy"}]}],"member":"286","published-online":{"date-parts":[[2011,11,9]]},"reference":[{"key":"2023061011552324800_B1","first-page":"1700","article-title":"Graph-theoretic topological control of biological genetic networks","volume-title":"Proceedings of the American Control Conference.","author":"Aswani","year":"2009"},{"key":"2023061011552324800_B2","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/j.biosystems.2006.08.001","article-title":"Algorithmic and complexity results for decompositions of biological networks into monotone subsystems","volume":"90","author":"DasGupta","year":"2007","journal-title":"Biosystems"},{"key":"2023061011552324800_B3","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-642-82625-2","volume-title":"Positive Feedback in Natural Systems.","author":"Deangelis","year":"1986"},{"key":"2023061011552324800_B4","volume-title":"Graph Theory with Applications to Engineering and Computer Science.","author":"Deo","year":"1974"},{"key":"2023061011552324800_B5","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1007\/978-3-540-68413-8_7","article-title":"From reaction models to influence graphs and back: A theorem","volume-title":"Formal Methods in Systems Biology","author":"Fages","year":"2008"},{"key":"2023061011552324800_B6","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1007\/978-1-4757-3023-4_4","article-title":"Feedback set problems","volume-title":"Handbook of Combinatorial Optimization","author":"Festa","year":"1999"},{"key":"2023061011552324800_B7","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1145\/504210.504214","article-title":"Algorithm 815: FORTRAN subroutines for computing approximate solutions of feedback set problems using GRASP","volume":"27","author":"Festa","year":"2001","journal-title":"ACM Trans. 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