Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach
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* Corresponding author: David Eisenberg david@mbi.ucla.edu
Genome Biology 2003, 4:R59 doi:10.1186/gb-2003-4-9-r59
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BioMed Central: 12 citations
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Research article
Ignacio Rodriguez-Llorente, Miguel A Caviedes, Mohammed Dary, Antonio J Palomares, Francisco M Cánovas, José M Peregrín-Alvarez BMC Systems Biology 2009, 3:63 (16 June 2009) |
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Research article
Tao Cui, Lei Zhang, Xizhou Wang, Zheng-Guo He BMC Genomics 2009, 10:118 (19 March 2009) |
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Research article
Predicting protein linkages in bacteria: Which method is best depends on task Anis Karimpour-Fard, Sonia M Leach, Ryan T Gill, Lawrence E Hunter BMC Bioinformatics 2008, 9:397 (24 September 2008) |
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Research article
Anis Karimpour-Fard, Sonia M Leach, Lawrence E Hunter, Ryan T Gill BMC Genomics 2008, 9:313 (30 June 2008) |
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Research article
Anis Karimpour-Fard, Lawrence Hunter, Ryan T Gill BMC Genomics 2007, 8:393 (29 October 2007) |
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Methodology article
Jingchun Sun, Yan Sun, Guohui Ding, Qi Liu, Chuan Wang, Youyu He, Tieliu Shi, Yixue Li, Zhongming Zhao BMC Bioinformatics 2007, 8:414 (26 October 2007) |
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Method
Cross-species cluster co-conservation: a new method for generating protein interaction networks Anis Karimpour-Fard, Corrella S Detweiler, Kimberly D Erickson, Lawrence Hunter, Ryan T Gill Genome Biology 2007, 8:R185 (5 September 2007) Cluster Co-Conservation (CCC) has been extended to a method for developing protein interaction networks based on co-conservation between protein pairs across multiple species, Cross-Species Cluster Co-Conservation (CS-CCC). |
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Research article
False positive reduction in protein-protein interaction predictions using gene ontology annotations Mahmoud A Mahdavi, Yen-Han Lin BMC Bioinformatics 2007, 8:262 (23 July 2007) |
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Research article
Raja Jothi, Teresa M Przytycka, L Aravind BMC Bioinformatics 2007, 8:173 (23 May 2007) |
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Research article
Phylogenetic detection of conserved gene clusters in microbial genomes Yu Zheng, Brian P Anton, Richard J Roberts, Simon Kasif BMC Bioinformatics 2005, 6:243 (3 October 2005) |
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Research
Galina V Glazko, Arcady R Mushegian Genome Biology 2004, 5:R32 (27 April 2004) A hierarchy of 3,688 phyletic patterns was characterized encompassing more than 5,000 known protein-coding genes from 66 complete microbial genomes. The results indicate that gene loss and displacement has occurred in the evolution of most pathways. |
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Software
Prolinks: a database of protein functional linkages derived from coevolution Peter M Bowers, Matteo Pellegrini, Mike J Thompson, Joe Fierro, Todd O Yeates, David Eisenberg Genome Biology 2004, 5:R35 (16 April 2004) Four methods that infer protein function and linkages have been combined in a single database, Prolinks, which spans 83 organisms and includes 10 million high-confidence links. |