TY - JOUR AU - Galperin, M. Y. AU - Koonin, E. V. PY - 2000 DA - 2000// TI - Who's your neighbor? New computational approaches for functional genomics JO - Nat Biotechnol VL - 18 UR - https://doi.org/10.1038/76443 DO - 10.1038/76443 ID - Galperin2000 ER - TY - JOUR AU - Koonin, E. V. PY - 2000 DA - 2000// TI - Bridging the gap between sequence and function JO - Trends Genet VL - 16 UR - https://doi.org/10.1016/S0168-9525(99)01927-7 DO - 10.1016/S0168-9525(99)01927-7 ID - Koonin2000 ER - TY - JOUR AU - Altschul, S. F. AU - Madden, T. L. AU - Schaffer, A. A. AU - Zhang, J. AU - Zhang, Z. PY - 1997 DA - 1997// TI - Gapped BLAST and PSI-BLAST: a new generation of protein database search programs JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.17.3389 DO - 10.1093/nar/25.17.3389 ID - Altschul1997 ER - TY - STD TI - The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res. 2009, 37: D169-174. ID - ref4 ER - TY - JOUR AU - Gomez, A. AU - Cedano, J. AU - Espadaler, J. AU - Hermoso, A. AU - Pinol, J. PY - 2008 DA - 2008// TI - Prediction of protein function improving sequence remote alignment search by a fuzzy logic algorithm JO - Protein J VL - 27 UR - https://doi.org/10.1007/s10930-007-9116-x DO - 10.1007/s10930-007-9116-x ID - Gomez2008 ER - TY - JOUR AU - Deng, M. AU - Zhang, K. AU - Mehta, S. AU - Chen, T. AU - Sun, F. PY - 2003 DA - 2003// TI - Prediction of protein function using protein-protein interaction data JO - J Comput Biol VL - 10 UR - https://doi.org/10.1089/106652703322756168 DO - 10.1089/106652703322756168 ID - Deng2003 ER - TY - JOUR AU - Devos, D. AU - Valencia, A. PY - 2000 DA - 2000// TI - Practical limits of function prediction JO - Proteins VL - 41 UR - https://doi.org/3.0.CO;2-S DO - 3.0.CO;2-S ID - Devos2000 ER - TY - JOUR AU - Devos, D. AU - Valencia, A. PY - 2001 DA - 2001// TI - Intrinsic errors in genome annotation JO - Trends Genet VL - 17 UR - https://doi.org/10.1016/S0168-9525(01)02348-4 DO - 10.1016/S0168-9525(01)02348-4 ID - Devos2001 ER - TY - JOUR AU - Chua, H. N. AU - Sung, W. K. AU - Wong, L. PY - 2006 DA - 2006// TI - Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl145 DO - 10.1093/bioinformatics/btl145 ID - Chua2006 ER - TY - CHAP AU - Jaeger, S. AU - Leser, U. PY - 2007 DA - 2007// TI - High-Precision Function Prediction using Conserved Interaction BT - Proc of the German Conference on Bioinformatics ID - Jaeger2007 ER - TY - JOUR AU - Samanta, M. P. AU - Liang, S. PY - 2003 DA - 2003// TI - Predicting protein functions from redundancies in large-scale protein interaction networks JO - Proc Natl Acad Sci USA VL - 100 UR - https://doi.org/10.1073/pnas.2132527100 DO - 10.1073/pnas.2132527100 ID - Samanta2003 ER - TY - JOUR AU - Wu, H. AU - Su, Z. AU - Mao, F. AU - Olman, V. AU - Xu, Y. PY - 2005 DA - 2005// TI - Prediction of functional modules based on comparative genome analysis and Gene Ontology application JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki573 DO - 10.1093/nar/gki573 ID - Wu2005 ER - TY - JOUR AU - Couto, F. M. AU - Silva, M. J. AU - Lee, V. AU - Dimmer, E. AU - Camon, E. PY - 2006 DA - 2006// TI - GOAnnotator: linking protein GO annotations to evidence text JO - J Biomed Discov Collab VL - 1 UR - https://doi.org/10.1186/1747-5333-1-19 DO - 10.1186/1747-5333-1-19 ID - Couto2006 ER - TY - JOUR AU - Tao, Y. AU - Sam, L. AU - Li, J. AU - Friedman, C. AU - Lussier, Y. A. PY - 2007 DA - 2007// TI - Information theory applied to the sparse gene ontology annotation network to predict novel gene function JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm195 DO - 10.1093/bioinformatics/btm195 ID - Tao2007 ER - TY - JOUR AU - Chua, H. N. AU - Sung, W. K. AU - Wong, L. PY - 2007 DA - 2007// TI - Using indirect protein interactions for the prediction of Gene Ontology functions JO - BMC Bioinformatics VL - 8 Suppl 4 UR - https://doi.org/10.1186/1471-2105-8-S4-S8 DO - 10.1186/1471-2105-8-S4-S8 ID - Chua2007 ER - TY - JOUR AU - Arnaud, M. B. AU - Costanzo, M. C. AU - Shah, P. AU - Skrzypek, M. S. AU - Sherlock, G. PY - 2009 DA - 2009// TI - Gene Ontology and the annotation of pathogen genomes: the case of Candida albicans JO - Trends Microbiol VL - 17 UR - https://doi.org/10.1016/j.tim.2009.04.007 DO - 10.1016/j.tim.2009.04.007 ID - Arnaud2009 ER - TY - JOUR AU - Giglio, M. G. AU - Collmer, C. W. AU - Lomax, J. AU - Ireland, A. PY - 2009 DA - 2009// TI - Applying the Gene Ontology in microbial annotation JO - Trends Microbiol VL - 17 UR - https://doi.org/10.1016/j.tim.2009.04.003 DO - 10.1016/j.tim.2009.04.003 ID - Giglio2009 ER - TY - JOUR AU - Pesquita, C. AU - Faria, D. AU - Bastos, H. AU - Ferreira, A. E. AU - Falcao, A. O. PY - 2008 DA - 2008// TI - Metrics for GO based protein semantic similarity: a systematic evaluation JO - BMC Bioinformatics VL - 9 Suppl 5 UR - https://doi.org/10.1186/1471-2105-9-S5-S4 DO - 10.1186/1471-2105-9-S5-S4 ID - Pesquita2008 ER - TY - JOUR AU - Wang, J. Z. AU - Du, Z. AU - Payattakool, R. AU - Yu, P. S. AU - Chen, C. F. PY - 2007 DA - 2007// TI - A new method to measure the semantic similarity of GO terms JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm087 DO - 10.1093/bioinformatics/btm087 ID - Wang2007 ER - TY - JOUR AU - Newman, M. E. PY - 2006 DA - 2006// TI - Modularity and community structure in networks JO - Proc Natl Acad Sci USA VL - 103 UR - https://doi.org/10.1073/pnas.0601602103 DO - 10.1073/pnas.0601602103 ID - Newman2006 ER - TY - JOUR AU - Hartwell, L. H. AU - Hopfield, J. J. AU - Leibler, S. AU - Murray, A. W. PY - 1999 DA - 1999// TI - From molecular to modular cell biology JO - Nature VL - 402 UR - https://doi.org/10.1038/35011540 DO - 10.1038/35011540 ID - Hartwell1999 ER - TY - JOUR AU - Sharan, R. AU - Ulitsky, I. AU - Shamir, R. PY - 2007 DA - 2007// TI - Network-based prediction of protein function JO - Mol Syst Biol VL - 3 UR - https://doi.org/10.1038/msb4100129 DO - 10.1038/msb4100129 ID - Sharan2007 ER - TY - JOUR AU - Fraser, C. M. AU - Gocayne, J. D. AU - White, O. AU - Adams, M. D. AU - Clayton, R. A. PY - 1995 DA - 1995// TI - The minimal gene complement of Mycoplasma genitalium JO - Science VL - 270 UR - https://doi.org/10.1126/science.270.5235.397 DO - 10.1126/science.270.5235.397 ID - Fraser1995 ER - TY - JOUR AU - Glass, J. I. AU - Assad-Garcia, N. AU - Alperovich, N. AU - Yooseph, S. AU - Lewis, M. R. PY - 2006 DA - 2006// TI - Essential genes of a minimal bacterium JO - Proc Natl Acad Sci USA VL - 103 UR - https://doi.org/10.1073/pnas.0510013103 DO - 10.1073/pnas.0510013103 ID - Glass2006 ER - TY - JOUR AU - Dybvig, K. AU - Voelker, L. L. PY - 1996 DA - 1996// TI - Molecular biology of mycoplasmas JO - Annu Rev Microbiol VL - 50 UR - https://doi.org/10.1146/annurev.micro.50.1.25 DO - 10.1146/annurev.micro.50.1.25 ID - Dybvig1996 ER - TY - CHAP AU - von Mering, C. ED - Ron, A. p. p. e. l. ED - Ernest, F. e. y. t. m. a. n. s. ED - Lausanne, L. PY - 2008 DA - 2008// BT - Protein-Protein Interaction Networks: Assembly and Analysis ID - von Mering2008 ER - TY - JOUR AU - Alexeyenko, A. AU - Sonnhammer, E. L. PY - 2009 DA - 2009// TI - Global networks of functional coupling in eukaryotes from comprehensive data integration JO - Genome Res VL - 19 UR - https://doi.org/10.1101/gr.087528.108 DO - 10.1101/gr.087528.108 ID - Alexeyenko2009 ER - TY - JOUR AU - Gabow, A. P. AU - Leach, S. M. AU - Baumgartner, W. A. AU - Hunter, L. E. AU - Goldberg, D. S. PY - 2008 DA - 2008// TI - Improving protein function prediction methods with integrated literature data JO - BMC Bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-198 DO - 10.1186/1471-2105-9-198 ID - Gabow2008 ER - TY - JOUR AU - Hu, P. AU - Janga, S. C. AU - Babu, M. AU - Diaz-Mejia, J. J. AU - Butland, G. PY - 2009 DA - 2009// TI - Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins JO - PLoS Biol VL - 7 UR - https://doi.org/10.1371/journal.pbio.1000096 DO - 10.1371/journal.pbio.1000096 ID - Hu2009 ER - TY - JOUR AU - Lee, S. A. AU - Chan, C. H. AU - Tsai, C. H. AU - Lai, J. M. AU - Wang, F. S. PY - 2008 DA - 2008// TI - Ortholog-based protein-protein interaction prediction and its application to inter-species interactions JO - BMC Bioinformatics VL - 9 Suppl 12 UR - https://doi.org/10.1186/1471-2105-9-S12-S11 DO - 10.1186/1471-2105-9-S12-S11 ID - Lee2008 ER - TY - JOUR AU - Mavromatis, K. AU - Chu, K. AU - Ivanova, N. AU - Hooper, S. D. AU - Markowitz, V. M. PY - 2009 DA - 2009// TI - Gene context analysis in the Integrated Microbial Genomes (IMG) data management system JO - PLoS One VL - 4 UR - https://doi.org/10.1371/journal.pone.0007979 DO - 10.1371/journal.pone.0007979 ID - Mavromatis2009 ER - TY - JOUR AU - Couto, F. M. AU - Coutinho, P. M. AU - Silva, M. J. PY - 2007 DA - 2007// TI - Measuring semantic similarity between Gene Ontology terms JO - Data & Knowledge Engineering VL - 61 UR - https://doi.org/10.1016/j.datak.2006.05.003 DO - 10.1016/j.datak.2006.05.003 ID - Couto2007 ER - TY - JOUR AU - Jensen, L. J. AU - Kuhn, M. AU - Stark, M. AU - Chaffron, S. AU - Creevey, C. PY - 2009 DA - 2009// TI - STRING 8--a global view on proteins and their functional interactions in 630 organisms JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkn760 DO - 10.1093/nar/gkn760 ID - Jensen2009 ER - TY - JOUR AU - Sharan, R. AU - Ideker, T. PY - 2006 DA - 2006// TI - Modeling cellular machinery through biological network comparison JO - Nat Biotechnol VL - 24 UR - https://doi.org/10.1038/nbt1196 DO - 10.1038/nbt1196 ID - Sharan2006 ER - TY - JOUR AU - Sharan, R. AU - Suthram, S. AU - Kelley, R. M. AU - Kuhn, T. AU - McCuine, S. PY - 2005 DA - 2005// TI - Conserved patterns of protein interaction in multiple species JO - Proc Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0409522102 DO - 10.1073/pnas.0409522102 ID - Sharan2005 ER - TY - JOUR AU - Barrell, D. AU - Dimmer, E. AU - Huntley, R. P. AU - Binns, D. AU - O'Donovan, C. PY - 2009 DA - 2009// TI - The GOA database in 2009--an integrated Gene Ontology Annotation resource JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkn803 DO - 10.1093/nar/gkn803 ID - Barrell2009 ER - TY - JOUR AU - Camon, E. AU - Magrane, M. AU - Barrell, D. AU - Lee, V. AU - Dimmer, E. PY - 2004 DA - 2004// TI - The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh021 DO - 10.1093/nar/gkh021 ID - Camon2004 ER - TY - JOUR AU - Chen, F. AU - Mackey, A. J. AU - Stoeckert, C. J. AU - Roos, D. S. PY - 2006 DA - 2006// TI - OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkj123 DO - 10.1093/nar/gkj123 ID - Chen2006 ER - TY - JOUR AU - Lord, P. W. AU - Stevens, R. D. AU - Brass, A. AU - Goble, C. A. PY - 2003 DA - 2003// TI - Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg153 DO - 10.1093/bioinformatics/btg153 ID - Lord2003 ER - TY - JOUR AU - McCarthy, F. M. AU - Bridges, S. M. AU - Burgess, S. C. PY - 2007 DA - 2007// TI - GOing from functional genomics to biological significance. Cytogenet JO - Genome Res VL - 117 UR - https://doi.org/10.1159/000103189 DO - 10.1159/000103189 ID - McCarthy2007 ER - TY - CHAP AU - Resnik, P. PY - 1995 DA - 1995// TI - Using information content to evaluate semantic similarity in a taxonomy BT - Proceedings of the 14th International Joint conference on Artificial Intelligence ID - Resnik1995 ER - TY - CHAP AU - Lin, D. PY - 1998 DA - 1998// TI - An information-theoretic definition of similarity BT - Proceedings of the 15th International Conference on Machine Learning ID - Lin1998 ER - TY - CHAP AU - Jiang, J. AU - Conrath, D. PY - 1997 DA - 1997// TI - Semantic similarity based on corpus statistics and lexical taxonomy BT - Proceedings of the 10th International Conference on Research on Computational linguistics ID - Jiang1997 ER -