Applications of domain-domain interactions in pathway study
Computational Biology and Chemistry
Large-scale Protein-Protein Interaction prediction using novel kernel methods
International Journal of Data Mining and Bioinformatics
Integrative Neural Network Approach for Protein Interaction Prediction from Heterogeneous Data
ADMA '08 Proceedings of the 4th international conference on Advanced Data Mining and Applications
Brief communication: Effect of example weights on prediction of protein-protein interactions
Computational Biology and Chemistry
Prediction of protein protein interactions from primary sequences
International Journal of Data Mining and Bioinformatics
Advances in Artificial Intelligence - Special issue on artificial intelligence in neuroscience and systems biology: lessons learnt, open problems, and the road ahead
Prediction of protein-protein interactions using subcellular and functional localizations
LSMS/ICSEE'10 Proceedings of the 2010 international conference on Life system modeling and simulation and intelligent computing, and 2010 international conference on Intelligent computing for sustainable energy and environment: Part III
On Position-Specific Scoring Matrix for Protein Function Prediction
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
DS'06 Proceedings of the 9th international conference on Discovery Science
Using a stochastic adaboost algorithm to discover interactome motif pairs from sequences
ICIC'06 Proceedings of the 2006 international conference on Computational Intelligence and Bioinformatics - Volume Part III
RECOMB'12 Proceedings of the 16th Annual international conference on Research in Computational Molecular Biology
Mining from protein–protein interactions
Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery
Predicting functional protein-protein interactions based on computational methods
LSMS'07 Proceedings of the 2007 international conference on Life System Modeling and Simulation
Classifying Very High-Dimensional Data with Random Forests Built from Small Subspaces
International Journal of Data Warehousing and Mining
Domain information based prediction of protein-protein interactions of glucosinolate biosynthesis
International Journal of Computer Applications in Technology
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Motivation: Protein interactions are of biological interest because they orchestrate a number of cellular processes such as metabolic pathways and immunological recognition. Domains are the building blocks of proteins; therefore, proteins are assumed to interact as a result of their interacting domains. Many domain-based models for protein interaction prediction have been developed, and preliminary results have demonstrated their feasibility. Most of the existing domain-based methods, however, consider only single-domain pairs (one domain from one protein) and assume independence between domain--domain interactions. Results: In this paper, we introduce a domain-based random forest of decision trees to infer protein interactions. Our proposed method is capable of exploring all possible domain interactions and making predictions based on all the protein domains. Experimental results on Saccharomyces cerevisiae dataset demonstrate that our approach can predict protein--protein interactions with higher sensitivity (79.78%) and specificity (64.38%) compared with that of the maximum likelihood approach. Furthermore, our model can be used to infer interactions not only for single-domain pairs but also for multiple domain pairs. Contact: xwchen@ku.edu Availability: Source code is written in Java and is available upon request from the authors. Supplementary information: http://www.ittc.ku.edu/~xwchen/PPI/random_forest_PPI