Clustering Nodes in Large-Scale Biological Networks Using External Memory Algorithms

Arefin, Ahmed Shamsul; Inostroza-Ponta, Mario; Mathieson, Luke; Berretta, Regina; Moscato, Pablo

doi:10.1007/978-3-642-24669-2_36

Cited by 12 publications

(2 citation statements)

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“…It is also used to extract features and knowledge from data as well as to reduce dimensions and classify data, having been mostly applied in medical sciences helping with the explanation and diagnosis of disease. For example, it was applied to some cancer types [19][20][21][22], Alzheimer's disease [23][24][25], and epilepsy [26]. As far as we know, this is the first time that it is applied to plant biology, namely to the cork oak-P. cinnamomi interaction.…”

Section: Introductionmentioning

confidence: 99%

Protein Markers for the Identification of Cork Oak Plants Infected with Phytophthora cinnamomi by Applying an (α, β)-k-Feature Set Approach

Coelho

Schütz

2022

Forests

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Cork oak decline in Mediterranean forests is a complex phenomenon, observed with remarkable frequency in the southern part of the Iberian Peninsula, causing the weakening and death of these woody plants. The defoliation of the canopy, the presence of dry peripheral branches, and exudations on the trunk are visible symptoms used for the prognosis of decline, complemented by the presence of Phytophthora cinnamomi identified in the rhizosphere of the trees and adjacent soils. Recently, a large proteomic dataset obtained from the leaves of cork oak plants inoculated and non-inoculated with P. cinnamomi has become available. We explored it to search for an optimal set of proteins, markers of the biological pattern of interaction with the oomycete. Thus, using published data from the cork oak leaf proteome, we mathematically modelled the problem as an α, β-k-Feature Set Problem to select molecular markers. A set of proteins (features) that represent dominant effects on the host metabolism resulting from pathogen action on roots was found. These results contribute to an early diagnosis of biochemical changes occurring in cork oak associated with P. cinnamomi infection. We hypothesize that these markers may be decisive in identifying trees that go into decline due to interactions with the pathogen, assisting the management of cork oak forest ecosystems.

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Section: Introductionmentioning

confidence: 99%

Protein Markers for the Identification of Cork Oak Plants Infected with Phytophthora cinnamomi by Applying an (α, β)-k-Feature Set Approach

Coelho

Schütz

2022

Forests

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“…Large networks are hard to analyze mathematically, both from discrete and from continuous point of view [15], [17]. Usually in such cases a model reduction technique is applied [13], [17], [18], [19].…”

Section: Problem Statementmentioning

confidence: 99%

Coupled cell networks: Boolean perspective

Swirydowicz

2017

BIOMATH

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Abstract-In this paper we use Boolean framework to redefine coupled cell networkss, originally described in [2]. We also analyze some of the important properties of Boolean coupled cell networkss.In the second part of this paper we focus on properties of a quotient networks. We redefine the concept of a quotient to suit Boolean network framework. Next, we investigate in details the networks in which two-cell bidirectional ring and three-cell bidirectional ring arise as quotients.

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