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Dataset | Modeling method | Tool/technique software/database | References |
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Saccharomyces cerevisiae (yeast) | Fuzzy logic + clustering | Preprocessing algorithm coded in MATLAB | Ram et al. [9] |
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Saccharomyces cerevisiae (yeast) cell cycle | Fuzzy rules | GeneChip + SAGE | Woolf and Wang [12] |
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Saccharomyces cerevisiae | Fuzzy logic + clustering | DSOM approach + ART | Ressom et al. [20] |
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Breast cancer (cancerous cells in human) | AFEGRN | AFEGRN framework |
Sehgal et al. [6] |
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10 different cancer datasets (cancerous cells in human) | Coalesce GRN (CGRN) | Cross platform GRN fusion | Sehgal et al. [21, 22] |
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Bacterium Escherichia coli | FRBPN | FRBPN technique | Hamed [19] |
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Saccharomyces cerevisiae | Combined fuzzy clustering and Bayesian networks (FCBN) | Software platform MATLAB and BNT package | Wang et al. [11] |
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Lac operon in Escherichia coli | Combined ODEs models and FIS | Simulink, fuzzy logic Toolbox and Optimization Toolbox in MATLAB | Muñoz et al. [17] |
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Arabidopsis thaliana plants, Affymetrix Arabidopsis ATH1 genome with 22K genes | Fuzzy cognitive map (FCM) model + clustering | FCModeler tool | Du et al. [13] |
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Escherichia coli bacteria SOS DNA consisting of 30 genes | Fuzzy logic + artificial bee colony (ABC) | ABC- and DE-based simulations, on Pentium | Das et al. [15] |
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Saccharomyces cerevisiae | Fuzzy Petri net (FPN) | FPN graphical tool | Hamed et al. [18] |
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Saccharomyces cerevisiae | Fuzzy logic based modeling | Fuzzy data mining technique | Ma and Chan [3] |
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Escherichia coli and Saccharomyces cerevisiae (210 time points in 100-gene networks), 10 DREAM-4 datasets | Fuzzy cognitive maps (FCMs) model and ant colony optimization (ACO) | Simulation using stochastic differential equations, DREAM project | Chen et al. [2] |
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Saccharomyces cerevisiae microarray time series (three datasets) | Activator-repressor regulatory model, SRS biological model | SRS program, regulatory-fit scoring method | Volkert and Malhis [14] |
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Saccharomyces cerevisiae genes time series gene expression data (about 800 cell cycle regulated genes) | Fuzzy data mining model | C4.5, SVM, and FID, 10-fold cross validation strategy | Ma and Chan [16] |
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Yeast cell cycle (cell-synchronized datasets with 14 time points) | Fuzzy logic genetic search algorithm model | KEGG database,
k-nearest-neighbor (kNN) algorithm | Brock et al. [4] |
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