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| !!!Genome Analysis (6) |
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| * [HMC]: Haplotype inference tool based on Markov Chain model |
| * [PTG]: Pasimonious tree-grow method for haplotype inference |
| * [LOHCRP]: LOH inference and segmentation tool based on conditional random field model |
| * [CKSAAP-Palm]: A tool for predicting palmitoylation sites from protein sequences |
| * [PTMPred]: A tool for predicting post-transcriptional modification sites from protein sequences |
| * [PRNA]: Prediction of protein-RNA binding sites by a random forest method with combined features |
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| !!!Molecular Networks (9) |
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| !!Gene Regulatory Networks Inference (2) |
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| * [GNTInfer]: Gene network reconstruction tool with compound targets by integrating multiple microarray datasets and prior information |
| * [GRNInfer]: Gene regulatory network inference tool from multiple microarray datasets |
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| !!PPI Networks Inference (3) |
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| * [MDCInfer]: PPI prediction tool based on multiple domain cooperation analysis |
| * [DeterminePPI]: Inferring protein-protein interactions by parsimony principle |
| * [InferPPI]: Predicting protein interactions based on parsimony tendency of domain interactions |
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| !!Network Module Analysis (2) |
| * [PPICPM]: Identification of functional modules in PPI network by clique percolation clustering |
| * [ModularityOptimization]: Modularity optimization in community identification of complex networks |
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| !!Network Alignment (2) |
| * [MNAligner]: Alignment of molecular networks by quadratic programming |
| * [PPINA]: Alignment of protein interaction networks by integer quadratic programming |
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| !!!Structure Biology (5) |
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| * [Samo]: Protein structure alignment tool based on multiple objective optimization |
| * [SANA]: Protein Structure Alignment by Neighborhood Alignment |
| * [SABIC]: protein Structure Alignment Based on Internal Coordinates |
| * [StruComp]: Evaluating protein similarity from coarse structures |
| * [PSN]: Protein pocket similarity networks |
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| !!!Systems Biology (3) |
| * [ADR]: Detecting and analyzing differentially activated pathways in brain regions of Alzheimer's disease patients |
| * [MCDGPA]: Modularized Candidate Disease Genes Prioritization Algorithm |
| * [NRWRH]: Network-based Random Walk with Restart on the Heterogeneous network |
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