A survey of computational methods in protein–protein interaction networks
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DOI: 10.1007/s10479-018-2956-2
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- Guilherme T Valente & Marcio L Acencio & Cesar Martins & Ney Lemke, 2013. "The Development of a Universal In Silico Predictor of Protein-Protein Interactions," PLOS ONE, Public Library of Science, vol. 8(5), pages 1-11, May.
- Ravi S. Kamath & Andrew G. Fraser & Yan Dong & Gino Poulin & Richard Durbin & Monica Gotta & Alexander Kanapin & Nathalie Le Bot & Sergio Moreno & Marc Sohrmann & David P. Welchman & Peder Zipperlen &, 2003. "Systematic functional analysis of the Caenorhabditis elegans genome using RNAi," Nature, Nature, vol. 421(6920), pages 231-237, January.
- H. Jeong & B. Tombor & R. Albert & Z. N. Oltvai & A.-L. Barabási, 2000. "The large-scale organization of metabolic networks," Nature, Nature, vol. 407(6804), pages 651-654, October.
- Benjamin A Shoemaker & Anna R Panchenko, 2007. "Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners," PLOS Computational Biology, Public Library of Science, vol. 3(4), pages 1-7, April.
- Anuj Kumar & Michael Snyder, 2002. "Protein complexes take the bait," Nature, Nature, vol. 415(6868), pages 123-124, January.
- Anton J. Enright & Ioannis Iliopoulos & Nikos C. Kyrpides & Christos A. Ouzounis, 1999. "Protein interaction maps for complete genomes based on gene fusion events," Nature, Nature, vol. 402(6757), pages 86-90, November.
- Pattillo, Jeffrey & Youssef, Nataly & Butenko, Sergiy, 2013. "On clique relaxation models in network analysis," European Journal of Operational Research, Elsevier, vol. 226(1), pages 9-18.
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- Camur, Mustafa C. & Sharkey, Thomas C. & Vogiatzis, Chrysafis, 2023. "The stochastic pseudo-star degree centrality problem," European Journal of Operational Research, Elsevier, vol. 308(2), pages 525-539.
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Keywords
Protein–protein interaction networks; Modularity; Clustering; Centrality; Protein essentiality;All these keywords.
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