Brasch, M.A., Hartley, J.L. and Vidal, M. (2004) ORFeome cloning and systems biology: standardized mass production of the parts from the parts-list. Genome Res., 14, 2001-2009.
Uetz, P., Rajagopala, S.V., Dong, Y.A. and Haas, J. (2004) From ORFeomes to protein interaction maps in viruses. Genome Res., 14, 2029-2033.
Navratil, V., de Chassey, B., Meyniel, L., Delmotte, S., Gautier, C., Andre, P., Lotteau, V. and Rabourdin-Combe, C. (2009) VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks. Nucleic Acids Res., 37, D661-D668.
Reboul, J., Vaglio, P., Rual, J.F., Lamesch, P., Martinez, M., Armstrong, C.M., Li, S., Jacotot, L., Bertin, N., Janky, R. et al. (2003) C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat. Genet., 34, 35-41.
Rual, J.F., Hirozane-Kishikawa, T., Hao, T., Bertin, N., Li, S., Dricot, A., Li, N., Rosenberg, J., Lamesch, P., Vidalain, P.O. et al. (2004) Human ORFeome version 1.1: a platform for reverse proteomics. Genome Res., 14, 2128-2135.
Dricot, A., Rual, J.F., Lamesch, P., Bertin, N., Dupuy, D., Hao, T., Lambert, C., Hallez, R., Delroisse, J.M., Vandenhaute, J. et al. (2004) Generation of the Brucella melitensis ORFeome version 1.1. Genome Res., 14, 2201-2206.
Schroeder, B.K., House, B.L., Mortimer, M.W., Yurgel, S.N., Maloney, S.C., Ward, K.L. and Kahn, M.L. (2005) Development of a functional genomics platform for Sinorhizobium meliloti: construction of an ORFeome. Appl. Environ. Microbiol., 71, 5858-5864.
Matsuyama, A., Arai, R., Yashiroda, Y., Shirai, A., Kamata, A., Sekido, S., Kobayashi, Y., Hashimoto, A., Hamamoto, M., Hiraoka, Y. et al. (2006) ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe. Nat. Biotechnol., 24, 841-847.
Brandner, C.J., Maier, R.H., Henderson, D.S., Hintner, H., Bauer, J.W. and Onder, K. (2008) The ORFeome of Staphylococcus aureus v 1.1. BMC Genomics, 9, 321.
Calderwood, M.A., Venkatesan, K., Xing, L., Chase, M.R., Vazquez, A., Holthaus, A.M., Ewence, A.E., Li, N., Hirozane-Kishikawa, T., Hill, D.E. et al. (2007) Epstein-Barr virus and virus human protein interaction maps. Proc. Natl Acad. Sci. USA, 104, 7606-7611.
von Brunn, A., Teepe, C., Simpson, J.C., Pepperkok, R., Friedel, C.C., Zimmer, R., Roberts, R., Baric, R. and Haas, J. (2007) Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome. PLoS ONE, 2, e459.
de Chassey, B., Navratil, V., Tafforeau, L., Hiet, M.S., Aublin-Gex, A., Agaugue, S., Meiffren, G., Pradezynski, F., Faria, B.F., Chantier, T. et al. (2008) Hepatitis C virus infection protein network. Mol. Syst. Biol., 4, 230.
Zhang, L., Villa, N.Y., Rahman, M.M., Smallwood, S., Shattuck, D., Neff, C., Dufford, M., Lanchbury, J.S., Labaer, J. and McFadden, G. (2009) Analysis of vaccinia virus-host protein-protein interactions: validations of yeast two-hybrid screenings. J. Proteome Res., 8, 4311-4318.
Vignuzzi, M., Wendt, E. and Andino, R. (2008) Engineering attenuated virus vaccines by controlling replication fidelity. Nat. Med., 14, 154-161.
Breakwell, L., Dosenovic, P., Karlsson Hedestam, G.B., D'Amato, M., Liljestrom, P., Fazakerley, J. and McInerney, G.M. (2007) Semliki Forest virus nonstructural protein 2 is involved in suppression of the type I interferon response. J. Virol., 81, 8677-8684.
Jenuth, J.P. (2000) The NCBI. Publicly available tools and resources on the Web. Methods Mol. Biol., 132, 301-312.
Sayers, E.W., Barrett, T., Benson, D.A., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., DiCuccio, M., Edgar, R., Federhen, S. et al. (2009) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 37, D5-D15.
Buchen-Osmond, C. (1997) Further progress in ICTVdB, a universal virus database. Arch. Virol., 142, 1734-1739.
Hubbard, T.J., Aken, B.L., Ayling, S., Ballester, B., Beal, K., Bragin, E., Brent, S., Chen, Y., Clapham, P., Clarke, L. et al. (2009) Ensembl 2009. Nucleic Acids Res., 37, D690-D697.
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A. et al. (2002) The generic genome browser: a building block for a model organism system database. Genome Res., 12, 1599-1610.
Hillier, L. and Green, P. (1991) OSP: a computer program for choosing PCR and DNA sequencing primers. PCR Methods Appl., 1, 124-128.
Ewing, B., Hillier, L., Wendl, M.C. and Green, P. (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res., 8, 175-185.
Notredame, C., Higgins, D.G. and Heringa, J. (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302, 205-217.
Laakkonen, P., Auvinen, P., Kujala, P. and Kaariainen, L. (1998) Alphavirus replicase protein NSP1 induces filopodia and rearrangement of actin filaments. J. Virol., 72, 10265-10269.
Wang, S.H., Syu, W.J., Huang, K.J., Lei, H.Y., Yao, C.W., King, C.C. and Hu, S.T. (2002) Intracellular localization and determination of a nuclear localization signal of the core protein of dengue virus. J. Gen. Virol., 83, 3093-3102.
Mori, Y., Okabayashi, T., Yamashita, T., Zhao, Z., Wakita, T., Yasui, K., Hasebe, F., Tadano, M., Konishi, E., Moriishi, K. et al. (2005) Nuclear localization of Japanese encephalitis virus core protein enhances viral replication. J. Virol., 79, 3448-3458.
Garmashova, N., Gorchakov, R., Volkova, E., Paessler, S., Frolova, E. and Frolov, I. (2007) The Old World and New World alphaviruses use different virus-specific proteins for induction of transcriptional shutoff. J. Virol., 81, 2472-2484.
Rice, C.M., Levis, R., Strauss, J.H. and Huang, H.V. (1987) Production of infectious RNA transcripts from Sindbis virus cDNA clones: mapping of lethal mutations, rescue of a temperaturesensitive marker, and in vitro mutagenesis to generate defined mutants. J. Virol., 61, 3809-3819.
Fontana, J.M., Bankamp, B. and Rota, P.A. (2008) Inhibition of interferon induction and signaling by paramyxoviruses. Immunol. Rev., 225, 46-67.
Pellet, J., Meyniel, L., Vidalain, P.O., de Chassey, B., Tafforeau, L., Lotteau, V., Rabourdin-Combe, C. and Navratil, V. (2009) pISTil: a pipeline for yeast two-hybrid Interaction Sequence Tags identification and analysis. BMC Res. Notes, 2, 220.