Parameter space exploration within dynamic simulations of signaling networks
We started offering an introduction to very basic aspects of molecular biology, for the reader coming from computer sciences, information technology, mathematics. Similarly we offered a minimum of information about pathways and networks in graph theory, for a reader coming from the bio-medical secto...
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| Format: | Article |
| Language: | English |
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AIMS Press
2012-11-01
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| Series: | Mathematical Biosciences and Engineering |
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| Online Access: | https://www.aimspress.com/article/doi/10.3934/mbe.2013.10.103 |
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| author | Cristina De Ambrosi Annalisa Barla Lorenzo Tortolina Nicoletta Castagnino Raffaele Pesenti Alessandro Verri Alberto Ballestrero Franco Patrone Silvio Parodi |
| author_facet | Cristina De Ambrosi Annalisa Barla Lorenzo Tortolina Nicoletta Castagnino Raffaele Pesenti Alessandro Verri Alberto Ballestrero Franco Patrone Silvio Parodi |
| author_sort | Cristina De Ambrosi |
| collection | DOAJ |
| description | We started offering an introduction to very basic aspects of molecular biology, for the reader coming from computer sciences, information technology, mathematics. Similarly we offered a minimum of information about pathways and networks in graph theory, for a reader coming from the bio-medical sector. At the crossover about the two different types of expertise, we offered some definition about Systems Biology. The core of the article deals with a Molecular Interaction Map (MIM), a network of biochemical interactions involved in a small signaling-network sub-region relevant in breast cancer. We explored robustness/sensitivity to random perturbations. It turns out that our MIM is a non-isomorphic directed graph. For non physiological directions of propagation of the signal the network is quite resistant to perturbations. The opposite happens for biologically significant directions of signal propagation. In these cases we can have no signal attenuation, and even signal amplification. Signal propagation along a given pathway is highly unidirectional, with the exception of signal-feedbacks, that again have a specific biological role and significance. In conclusion, even a relatively small network like our present MIM reveals the preponderance of specific biological functions over unspecific isomorphic behaviors. This is perhaps the consequence of hundreds of millions of years of biological evolution. |
| format | Article |
| id | doaj-art-85442e67b5224f9cb56d8374285ffd73 |
| institution | Kabale University |
| issn | 1551-0018 |
| language | English |
| publishDate | 2012-11-01 |
| publisher | AIMS Press |
| record_format | Article |
| series | Mathematical Biosciences and Engineering |
| spelling | doaj-art-85442e67b5224f9cb56d8374285ffd732025-01-24T02:25:25ZengAIMS PressMathematical Biosciences and Engineering1551-00182012-11-0110110312010.3934/mbe.2013.10.103Parameter space exploration within dynamic simulations of signaling networksCristina De Ambrosi0Annalisa Barla1Lorenzo Tortolina2Nicoletta Castagnino3Raffaele Pesenti4Alessandro Verri5Alberto Ballestrero6Franco Patrone7Silvio Parodi8DIBRIS Department of Informatics, Bioengineering, Robotics and Systems Engineering, Università degli Studi di Genova - Via Balbi, 5 - 16126 GenovaDIBRIS Department of Informatics, Bioengineering, Robotics and Systems Engineering, Università degli Studi di Genova - Via Balbi, 5 - 16126 GenovaDIBRIS Department of Informatics, Bioengineering, Robotics and Systems Engineering, Università degli Studi di Genova - Via Balbi, 5 - 16126 GenovaDIBRIS Department of Informatics, Bioengineering, Robotics and Systems Engineering, Università degli Studi di Genova - Via Balbi, 5 - 16126 GenovaDIBRIS Department of Informatics, Bioengineering, Robotics and Systems Engineering, Università degli Studi di Genova - Via Balbi, 5 - 16126 GenovaDIBRIS Department of Informatics, Bioengineering, Robotics and Systems Engineering, Università degli Studi di Genova - Via Balbi, 5 - 16126 GenovaDIBRIS Department of Informatics, Bioengineering, Robotics and Systems Engineering, Università degli Studi di Genova - Via Balbi, 5 - 16126 GenovaDIBRIS Department of Informatics, Bioengineering, Robotics and Systems Engineering, Università degli Studi di Genova - Via Balbi, 5 - 16126 GenovaDIBRIS Department of Informatics, Bioengineering, Robotics and Systems Engineering, Università degli Studi di Genova - Via Balbi, 5 - 16126 GenovaWe started offering an introduction to very basic aspects of molecular biology, for the reader coming from computer sciences, information technology, mathematics. Similarly we offered a minimum of information about pathways and networks in graph theory, for a reader coming from the bio-medical sector. At the crossover about the two different types of expertise, we offered some definition about Systems Biology. The core of the article deals with a Molecular Interaction Map (MIM), a network of biochemical interactions involved in a small signaling-network sub-region relevant in breast cancer. We explored robustness/sensitivity to random perturbations. It turns out that our MIM is a non-isomorphic directed graph. For non physiological directions of propagation of the signal the network is quite resistant to perturbations. The opposite happens for biologically significant directions of signal propagation. In these cases we can have no signal attenuation, and even signal amplification. Signal propagation along a given pathway is highly unidirectional, with the exception of signal-feedbacks, that again have a specific biological role and significance. In conclusion, even a relatively small network like our present MIM reveals the preponderance of specific biological functions over unspecific isomorphic behaviors. This is perhaps the consequence of hundreds of millions of years of biological evolution.https://www.aimspress.com/article/doi/10.3934/mbe.2013.10.103parameter space exploration.dynamicsimulationsmolecular interaction mapssystems biologysignaling networks |
| spellingShingle | Cristina De Ambrosi Annalisa Barla Lorenzo Tortolina Nicoletta Castagnino Raffaele Pesenti Alessandro Verri Alberto Ballestrero Franco Patrone Silvio Parodi Parameter space exploration within dynamic simulations of signaling networks Mathematical Biosciences and Engineering parameter space exploration. dynamicsimulations molecular interaction maps systems biology signaling networks |
| title | Parameter space exploration within dynamic simulations of signaling networks |
| title_full | Parameter space exploration within dynamic simulations of signaling networks |
| title_fullStr | Parameter space exploration within dynamic simulations of signaling networks |
| title_full_unstemmed | Parameter space exploration within dynamic simulations of signaling networks |
| title_short | Parameter space exploration within dynamic simulations of signaling networks |
| title_sort | parameter space exploration within dynamic simulations of signaling networks |
| topic | parameter space exploration. dynamicsimulations molecular interaction maps systems biology signaling networks |
| url | https://www.aimspress.com/article/doi/10.3934/mbe.2013.10.103 |
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