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RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs

BACKGROUND: When analyzing protein sequences using sequence similarity searches, orthologous sequences (that diverged by speciation) are more reliable predictors of a new protein's function than paralogous sequences (that diverged by gene duplication). The utility of phylogenetic information in...

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Detalhes bibliográficos
Main Authors:	Zmasek, Christian M, Eddy, Sean R, Chakraborty, Subhra, Sarmah, Bhaskarjyoti, Chakraborty, Niranjan, Datta, Asis, Fraternali, Franca, Cavallo, Luigi, Cserpán, Imre, Katona, Róbert, Praznovszky, Tünde, Novák, Edit, Rózsavölgyi, Márta, Csonka, Erika, Mórocz, Mónika, Fodor, Katalin, Hadlaczky, Gyula, Biswas, Esther E., Chen, Pei-Hua, Biswas, Subhasis B., Schulman, Deborah B., Setzer, David R., Cañestro, Cristian, Gonzàlez-Duarte, Roser, Albalat, Ricard, Finn, Patrick J., Sun, Lei, Nampalli, Satyam, Xiao, Haiguang, Nelson, John R., Mamone, J. Anthony, Grossmann, Greg, Flick, Parke K., Fuller, Carl W., Kumar, Shiv, Sabatti, Chiara, Rohlin, Lars, Oh, Min-Kyu, Liao, James C., Nulf, Christopher J., Corey, David R., De Haro, Luciano, Janknecht, Ralf, Achaz, G., Rocha, E. P. C., Netter, P., Coissac, E., Graziewicz, Maria A., Day, Brian J., Copeland, William C., Georgakilas, Alexandros G., Bennett, Paula V., Sutherland, Betsy M., Zhang, Yi, Li, Zhijie, Pilch, Daniel S., Leibowitz, Michael J., Chen, Jun, Zhang, Liang Ren, Min, Ji Mei, Zhang, Li He, Wei, Chao, Skopp, Rose, Takata, Minoru, Takeda, Shunichi, Price, Carolyn M., Liu, Li, Cheng, Shuqiu, van Brabant, Anja J., Kmiec, Eric B., Daniel, Juliet M., Spring, Christopher M., Crawford, Howard C., Reynolds, Albert B., Baig, Akeel, Rüfer, Andreas W., Sauer, Brian, Dang, Duyen T., Zhao, Weidong, Mahatan, Channing S., Geiman, Deborah E., Yang, Vincent W., Chen, Ying, Sharma, Rajiv P., Costa, Robert H., Costa, Erminio, Grayson, Dennis R., McPike, Mark P., Sullivan, Julie M., Goodisman, Jerry, Dabrowiak, James C., Vens, Conchita, Dahmen-Mooren, Els, Verwijs-Janssen, Manon, Blyweert, Wim, Graversen, Lise, Bartelink, Harry, Begg, Adrian C., Amarantos, Ioannis, Zarkadis, Ioannis K., Kalpaxis, Dimitrios L., Stehlikova, Kristyna, Kostrhunova, Hana, Kasparkova, Jana, Brabec, Viktor, Gygi, Melanie P., Ferguson, Mark D., Mefford, Heather C., Lund, Kevin P., O’Day, Christine, Zhou, Peiwen, Friedman, Cynthia, van den Engh, Ger, Stolowitz, Mark L., Trask, Barbara J., Dan, Ippeita, Watanabe, Norinobu M., Kajikawa, Eriko, Ishida, Takafumi, Pandey, Akhilesh, Kusumi, Akihiro, Shiroki, Kazuko, Ohsawa, Chieko, Sugi, Natuki, Wakiyama, Motoaki, Miura, Kin-ichiro, Watanabe, Manabu, Suzuki, Yutaka, Sugano, Sumio, Berge, Torunn, Jenkins, Nigel S., Hopkirk, Richard B., Waring, Michael J., Edwardson, J. Michael, Henderson, Robert M., Gu, Liya, Wu, Jianxin, Zhu, Bei-Bei, Li, Guo-Min, Mayer, Christine, RajBhandary, Uttam L., Renneberg, Dorte, Bouliong, Emilie, Reber, Ulrich, Schümperli, Daniel, Leumann, Christian J., Kim, Perry M., Paffett, Kimberly S., Solinger, Jachen A., Heyer, Wolf-Dietrich, Nickoloff, Jac A., Shedden, Kerby, Cooper, Stephen, Nagel, J. H. A., Gultyaev, A. P., Öistämö, K. J., Gerdes, K., Pleij, C. W. A., Van Dongen, Stefan, Lens, Luc, Rekart, Michael L., Krajden, Mel, Cook, Darrel, McNabb, Gail, Rees, Tony, Isaac-Renton, Judy, Harris, Marianne, Montaner, Julio, Basinski, Antoni, Lee, Shoo K., Sankaran, Koravangattu, Chien, Li-Yin, Walker, Robin, Seshia, Mary, Ohlsson, Arne, Lomas, Jonathan, Barer, Morris, Sehmer, John, Leung, Gabriel M., Lam, Tai-Hing, Ho, Lai-Ming, Thach, Thuan Q., Farrell, Scott A., Ridde, Valéry, Schneeweiss, Sebastian, Soumerai, Stephen B., Maclure, Malcolm, Anis, Aslam H.
Formato:	Artigo
Idioma:	English English English English English English English English English English English English English English English English English English English English English English English English English English English English English English English English English English English English English English English English English English English English English English English English English English
Publicado em:	BioMed Central 2002
Assuntos:	Methodology article Article NAR Methods Online Research Article Editorial Highlights of This Issue Letters
Acesso em linha:	https://ncbi.nlm.nih.gov/pmc/articles/PMC116988/ https://ncbi.nlm.nih.gov/pubmed/12028595 https://ncbi.nlm.nih.govhttp://dx.doi.org/10.1186/1471-2105-3-14 https://ncbi.nlm.nih.gov/pmc/articles/PMC117036/ https://ncbi.nlm.nih.gov/pubmed/12087180 https://ncbi.nlm.nih.gov/pmc/articles/PMC117037/ https://ncbi.nlm.nih.gov/pubmed/12087181 https://ncbi.nlm.nih.gov/pmc/articles/PMC117038/ https://ncbi.nlm.nih.gov/pubmed/12087175 https://ncbi.nlm.nih.gov/pmc/articles/PMC117039/ https://ncbi.nlm.nih.gov/pubmed/12087164 https://ncbi.nlm.nih.gov/pmc/articles/PMC117040/ https://ncbi.nlm.nih.gov/pubmed/12087160 https://ncbi.nlm.nih.gov/pmc/articles/PMC117041/ https://ncbi.nlm.nih.gov/pubmed/12087171 https://ncbi.nlm.nih.gov/pmc/articles/PMC117042/ https://ncbi.nlm.nih.gov/pubmed/12087172 https://ncbi.nlm.nih.gov/pmc/articles/PMC117043/ https://ncbi.nlm.nih.gov/pubmed/12087173 https://ncbi.nlm.nih.gov/pmc/articles/PMC117044/ https://ncbi.nlm.nih.gov/pubmed/12087161 https://ncbi.nlm.nih.gov/pmc/articles/PMC117045/ https://ncbi.nlm.nih.gov/pubmed/12087183 https://ncbi.nlm.nih.gov/pmc/articles/PMC117046/ https://ncbi.nlm.nih.gov/pubmed/12087185 https://ncbi.nlm.nih.gov/pmc/articles/PMC117047/ https://ncbi.nlm.nih.gov/pubmed/12087165 https://ncbi.nlm.nih.gov/pmc/articles/PMC117048/ https://ncbi.nlm.nih.gov/pubmed/12087163 https://ncbi.nlm.nih.gov/pmc/articles/PMC117049/ https://ncbi.nlm.nih.gov/pubmed/12087182 https://ncbi.nlm.nih.gov/pmc/articles/PMC117050/ https://ncbi.nlm.nih.gov/pubmed/12087187 https://ncbi.nlm.nih.gov/pmc/articles/PMC117051/ https://ncbi.nlm.nih.gov/pubmed/12087170 https://ncbi.nlm.nih.gov/pmc/articles/PMC117052/ https://ncbi.nlm.nih.gov/pubmed/12087156 https://ncbi.nlm.nih.gov/pmc/articles/PMC117053/ https://ncbi.nlm.nih.gov/pubmed/12087177 https://ncbi.nlm.nih.gov/pmc/articles/PMC117054/ https://ncbi.nlm.nih.gov/pubmed/12087159 https://ncbi.nlm.nih.gov/pmc/articles/PMC117055/ https://ncbi.nlm.nih.gov/pubmed/12087155 https://ncbi.nlm.nih.gov/pmc/articles/PMC117056/ https://ncbi.nlm.nih.gov/pubmed/12087179 https://ncbi.nlm.nih.gov/pmc/articles/PMC117057/ https://ncbi.nlm.nih.gov/pubmed/12087166 https://ncbi.nlm.nih.gov/pmc/articles/PMC117058/ https://ncbi.nlm.nih.gov/pubmed/12087186 https://ncbi.nlm.nih.gov/pmc/articles/PMC117059/ https://ncbi.nlm.nih.gov/pubmed/12087167 https://ncbi.nlm.nih.gov/pmc/articles/PMC117060/ https://ncbi.nlm.nih.gov/pubmed/12087174 https://ncbi.nlm.nih.gov/pmc/articles/PMC117061/ https://ncbi.nlm.nih.gov/pubmed/12087162 https://ncbi.nlm.nih.gov/pmc/articles/PMC117062/ https://ncbi.nlm.nih.gov/pubmed/12087176 https://ncbi.nlm.nih.gov/pmc/articles/PMC117063/ https://ncbi.nlm.nih.gov/pubmed/12087169 https://ncbi.nlm.nih.gov/pmc/articles/PMC117064/ https://ncbi.nlm.nih.gov/pubmed/12087184 https://ncbi.nlm.nih.gov/pmc/articles/PMC117065/ https://ncbi.nlm.nih.gov/pubmed/12087158 https://ncbi.nlm.nih.gov/pmc/articles/PMC117066/ https://ncbi.nlm.nih.gov/pubmed/12087168 https://ncbi.nlm.nih.gov/pmc/articles/PMC117067/ https://ncbi.nlm.nih.gov/pubmed/12087157 https://ncbi.nlm.nih.gov/pmc/articles/PMC117068/ https://ncbi.nlm.nih.gov/pubmed/12087154 https://ncbi.nlm.nih.gov/pmc/articles/PMC117069/ https://ncbi.nlm.nih.gov/pubmed/12087178 https://ncbi.nlm.nih.gov/pmc/articles/PMC117070/ https://ncbi.nlm.nih.gov/pubmed/12087188 https://ncbi.nlm.nih.gov/pmc/articles/PMC117071/ https://ncbi.nlm.nih.gov/pubmed/12086592 https://ncbi.nlm.nih.govhttp://dx.doi.org/10.1186/1471-2148-2-11 https://ncbi.nlm.nih.gov/pmc/articles/PMC117072/ https://ncbi.nlm.nih.gov/pubmed/12160109 https://ncbi.nlm.nih.gov/pmc/articles/PMC117073/ https://ncbi.nlm.nih.gov/pmc/articles/PMC117074/ https://ncbi.nlm.nih.gov/pubmed/12160110 https://ncbi.nlm.nih.gov/pmc/articles/PMC117075/ https://ncbi.nlm.nih.gov/pubmed/12160111 https://ncbi.nlm.nih.gov/pmc/articles/PMC117076/ https://ncbi.nlm.nih.gov/pmc/articles/PMC117077/ https://ncbi.nlm.nih.gov/pubmed/12160112 https://ncbi.nlm.nih.gov/pmc/articles/PMC117078/ https://ncbi.nlm.nih.gov/pmc/articles/PMC117079/ https://ncbi.nlm.nih.gov/pubmed/12160113 https://ncbi.nlm.nih.gov/pmc/articles/PMC117080/ https://ncbi.nlm.nih.gov/pubmed/12160114 https://ncbi.nlm.nih.gov/pmc/articles/PMC117081/ https://ncbi.nlm.nih.gov/pmc/articles/PMC117082/ https://ncbi.nlm.nih.gov/pubmed/12162294 https://ncbi.nlm.nih.gov/pmc/articles/PMC117083/ https://ncbi.nlm.nih.gov/pubmed/12160115 https://ncbi.nlm.nih.gov/pmc/articles/PMC117084/
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