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Analysis of institutional authors

Rodriguez-Paton, AlfonsoAuthorPaun, AndreiCorresponding Author

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June 9, 2019
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DISCRETE NONDETERMINISTIC MODELING OF THE FAS PATHWAY

Publicated to: INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE. 19 (5): 1147-1162 - 2008-01-01 19(5), DOI: 10.1142/S0129054108006194

Authors:

Jack, John; Rodriguez-Paton, Alfonso; IBarra, Oscar H.; Paun, Andrei;
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Affiliations

Louisiana Tech Univ, IFM, Dept Comp Sci, Ruston, LA 71272 USA - Author
Natl Inst Res & Dev Biol Sci, Bioinformat Dept, Bucharest, Romania - Author
Univ Calif Santa Barbara, Dept Comp Sci, Santa Barbara, CA 93106 USA - Author
Univ Politecn Madrid, Fac Informat, E-28660 Madrid, Spain - Author
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Abstract

Computer modeling of molecular signalling cascades can provide useful insight into the underlying complexities of biological systems. We present a refined approach for the discrete modeling of protein interaction within the environment of a single cell. The technique we offer utilizes the Membrane Systems paradigm which, due to its hierarchical structure, lends itself readily to mimic the behavior of cells. Since our approach terministic ordinary differential equations techniques. We argue that our approach may outperform ordinary differential equations when modeling systems with relatively low numbers of molecules - a frequent occurrence in cellular signaling cascades. Refinements over our previous modeling efforts include the addition of nondeterminism for handling reaction competition over limited reactants, increased efficiency in the storing and storing of reaction waiting times, and modifications of the model reactions. Results of our discrete simulation of the type I and type II Fas-mediated apoptotic signaling cascade are illustrated and compared with two approaches: one based on ordinary differential equations and another based on the well-known Gillespie algorithm.
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Keywords

ApoptosisBaxBcl-2DeathDiscrete simulationHiv-1Membrane systemsNondeterministic simulationNondeterministic stimulationOdeProteinSignal transduction pathwaySimulation of pathways

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE due to its progression and the good impact it has achieved in recent years, according to the agency Scopus (SJR), it has become a reference in its field. In the year of publication of the work, 2008, it was in position , thus managing to position itself as a Q1 (Primer Cuartil), in the category Computer Science (Miscellaneous). Notably, the journal is positioned above the 90th percentile.

Independientemente del impacto esperado determinado por el canal de difusión, es importante destacar el impacto real observado de la propia aportación.

Según las diferentes agencias de indexación, el número de citas acumuladas por esta publicación hasta la fecha 2026-04-24:

  • WoS: 5
  • Scopus: 5
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Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2026-04-24:

  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 3 (PlumX).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.
  • Assignment of a Handle/URN as an identifier within the deposit in the Institutional Repository: https://oa.upm.es/2261/

As a result of the publication of the work in the institutional repository, statistical usage data has been obtained that reflects its impact. In terms of dissemination, we can state that, as of

  • Views: 572
  • Downloads: 592
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Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: Oman; United States of America.

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: Last Author (PAUN, PAUL ANDREI).

the author responsible for correspondence tasks has been PAUN, PAUL ANDREI.

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