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Volumn 14, Issue 10 B, 2004, Pages 2001-2009

ORFeome cloning and systems biology: Standardized mass production of the parts from the parts-list

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

EID: 7444233131     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.2769804     Document Type: Article
Times cited : (71)

References (96)
  • 2
    • 0034649566 scopus 로고    scopus 로고
    • Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
    • Arabidopsis Genome Initiative
    • Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
    • (2000) Nature , vol.408 , pp. 796-815
  • 3
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization
    • Barabasi, A.L. and Oltvai, Z.N. 2004. Network biology: Understanding the cell's functional organization. Nat. Rev. Genet. 5: 101-113.
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 101-113
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 4
    • 0029741707 scopus 로고    scopus 로고
    • Positive selection of recombinant DNA by ccdB
    • Bernard, P. 1996. Positive selection of recombinant DNA by ccdB. Biotechniques 21: 320-323.
    • (1996) Biotechniques , vol.21 , pp. 320-323
    • Bernard, P.1
  • 8
    • 0842309871 scopus 로고    scopus 로고
    • Genome-wide RNAi analysis of growth and viability in Drosophila cells
    • Heidelberg Fly Array Consortium
    • Boutros, M., Kiger, A.A., Armknecht, S., Kerr, K., Hild, M., Koch, B., Haas, S.A., Heidelberg Fly Array Consortium, Paro, R., and Perrimon, N. 2004. Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science 303: 832-835.
    • (2004) Science , vol.303 , pp. 832-835
    • Boutros, M.1    Kiger, A.A.2    Armknecht, S.3    Kerr, K.4    Hild, M.5    Koch, B.6    Haas, S.A.7    Paro, R.8    Perrimon, N.9
  • 9
    • 0032509302 scopus 로고    scopus 로고
    • Genome sequence of the nematode C. elegans: A platform for investigating biology
    • elegans Sequencing Consortium
    • The C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282: 2012-2018.
    • (1998) Science , vol.282 , pp. 2012-2018
    • The, C.1
  • 10
    • 23444431611 scopus 로고
    • Green fluorescent protein as a marker for gene expression
    • Chalfie, M., Tu, Y., Euskirchen, G., Ward, W.W., and Prasher, D.C. 1994. Green fluorescent protein as a marker for gene expression. Science 263: 802-805.
    • (1994) Science , vol.263 , pp. 802-805
    • Chalfie, M.1    Tu, Y.2    Euskirchen, G.3    Ward, W.W.4    Prasher, D.C.5
  • 12
    • 7444261393 scopus 로고    scopus 로고
    • WormBase as an integrated platform for the C. elegans ORFeome
    • (this issue)
    • Chen, N., Lawson, D., Bradnam, K., Harris, T.W., and Stein, L.D. 2004. WormBase as an integrated platform for the C. elegans ORFeome. Genome Res. (this issue).
    • (2004) Genome Res.
    • Chen, N.1    Lawson, D.2    Bradnam, K.3    Harris, T.W.4    Stein, L.D.5
  • 13
    • 7444236455 scopus 로고    scopus 로고
    • Concerted assembly and cloning of multiple DNA segments using in vitro site-specific recombination: Functional analysis of multi-segment expression clones
    • (this issue)
    • Cheo, D.L., Titus, S.A., Byrd, D.R.N., Hartley, J.L., Temple, G.F., and Brasch, M.A. 2004. Concerted assembly and cloning of multiple DNA segments using in vitro site-specific recombination: Functional analysis of multi-segment expression clones. Genome Res. (this issue).
    • (2004) Genome Res.
    • Cheo, D.L.1    Titus, S.A.2    Byrd, D.R.N.3    Hartley, J.L.4    Temple, G.F.5    Brasch, M.A.6
  • 14
    • 0033968614 scopus 로고    scopus 로고
    • The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): Comprehensive resources for the organization and comparison of model organism protein information
    • Costanzo, M.C., Hogan, J.D., Cusick, M.E., Davis, B.P., Fancher, A.M., Hodges, P.E., Kondu, P., Lengieza, C., Lew-Smith, J.E., Lingner, C., et al. 2000. The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): Comprehensive resources for the organization and comparison of model organism protein information. Nucleic Acids Res. 28: 73-76.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 73-76
    • Costanzo, M.C.1    Hogan, J.D.2    Cusick, M.E.3    Davis, B.P.4    Fancher, A.M.5    Hodges, P.E.6    Kondu, P.7    Lengieza, C.8    Lew-Smith, J.E.9    Lingner, C.10
  • 17
    • 3242677639 scopus 로고    scopus 로고
    • siRNAs: Applications in functional genomics and potential as therapeutics
    • Dorsett, Y. and Tuschl, T. 2004. siRNAs: Applications in functional genomics and potential as therapeutics. Nat. Rev. Drug Discov. 3: 318-329.
    • (2004) Nat. Rev. Drug Discov. , vol.3 , pp. 318-329
    • Dorsett, Y.1    Tuschl, T.2
  • 19
    • 0034688173 scopus 로고    scopus 로고
    • A synthetic oscillatory network of transcriptional regulators
    • Elowitz, M.B. and Leibler, S. 2000. A synthetic oscillatory network of transcriptional regulators. Nature 403: 335-338.
    • (2000) Nature , vol.403 , pp. 335-338
    • Elowitz, M.B.1    Leibler, S.2
  • 20
    • 0036270934 scopus 로고    scopus 로고
    • Integrated version of reverse two-hybrid system for the postproteomic era
    • Endoh, H., Vincent, S., Jacob, Y., Real, E., Walhout, A.J., and Vidal, M. 2002. Integrated version of reverse two-hybrid system for the postproteomic era. Methods Enzymol. 350: 525-545.
    • (2002) Methods Enzymol. , vol.350 , pp. 525-545
    • Endoh, H.1    Vincent, S.2    Jacob, Y.3    Real, E.4    Walhout, A.J.5    Vidal, M.6
  • 21
    • 0032545933 scopus 로고    scopus 로고
    • Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans
    • Fire, A., Xu, S., Montgomery, M.K., Kostas, S.A., Driver, S.E., and Mello, C.C. 1998. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806-811.
    • (1998) Nature , vol.391 , pp. 806-811
    • Fire, A.1    Xu, S.2    Montgomery, M.K.3    Kostas, S.A.4    Driver, S.E.5    Mello, C.C.6
  • 22
  • 23
    • 0034688174 scopus 로고    scopus 로고
    • Construction of a genetic toggle switch in Escherichia coli
    • Gardner, T.S., Cantor, C.R., and Collins, J.J. 2000. Construction of a genetic toggle switch in Escherichia coli. Nature 403: 339-342.
    • (2000) Nature , vol.403 , pp. 339-342
    • Gardner, T.S.1    Cantor, C.R.2    Collins, J.J.3
  • 25
    • 0141561891 scopus 로고    scopus 로고
    • Integrating 'omic' information: A bridge between genomics and systems biology
    • Ge, H., Walhout, A.J., and Vidal, M. 2003. Integrating 'omic' information: A bridge between genomics and systems biology. Trends Genet. 19: 551-560.
    • (2003) Trends Genet. , vol.19 , pp. 551-560
    • Ge, H.1    Walhout, A.J.2    Vidal, M.3
  • 31
    • 0037165942 scopus 로고    scopus 로고
    • Combinatorial synthesis of genetic networks
    • Guet, C.C., Elowitz, M.B., Hsing, W., and Leibler, S. 2002. Combinatorial synthesis of genetic networks. Science 296: 1466-1470.
    • (2002) Science , vol.296 , pp. 1466-1470
    • Guet, C.C.1    Elowitz, M.B.2    Hsing, W.3    Leibler, S.4
  • 33
    • 0033676098 scopus 로고    scopus 로고
    • DNA cloning using in vitro site-specific recombination
    • Hartley, J.L., Temple, G.F., and Brasch, M.A. 2000. DNA cloning using in vitro site-specific recombination. Genome Res. 10: 1788-1795.
    • (2000) Genome Res. , vol.10 , pp. 1788-1795
    • Hartley, J.L.1    Temple, G.F.2    Brasch, M.A.3
  • 39
    • 7444265274 scopus 로고    scopus 로고
    • Feasibility of genome-scale construction of promoter::Reporter gene fusions for expression in Caenorhabditis elegans using a MultiSite Gateway recombination system
    • (this issue)
    • Hope, I.A., Stevens, J., Garner, A., Hayes, J., Cheo, D., Brasch, M.A., and Vidal, M. 2004. Feasibility of genome-scale construction of promoter::reporter gene fusions for expression in Caenorhabditis elegans using a MultiSite Gateway recombination system. Genome Res. (this issue).
    • (2004) Genome Res.
    • Hope, I.A.1    Stevens, J.2    Garner, A.3    Hayes, J.4    Cheo, D.5    Brasch, M.A.6    Vidal, M.7
  • 42
    • 0035836765 scopus 로고    scopus 로고
    • A comprehensive two-hybrid analysis to explore the yeast protein interactome
    • Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., and Sakaki, Y. 2001. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. 98: 4569-4574.
    • (2001) Proc. Natl. Acad. Sci. , vol.98 , pp. 4569-4574
    • Ito, T.1    Chiba, T.2    Ozawa, R.3    Yoshida, M.4    Hattori, M.5    Sakaki, Y.6
  • 43
  • 44
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • Jeong, H., Mason, S.P., Barabasi, A.L., and Oltvai, Z.N. 2001. Lethality and centrality in protein networks. Nature 411: 41-42.
    • (2001) Nature , vol.411 , pp. 41-42
    • Jeong, H.1    Mason, S.P.2    Barabasi, A.L.3    Oltvai, Z.N.4
  • 48
    • 0024386798 scopus 로고
    • Dynamic, structural, and regulatory aspects of λ site-specific recombination
    • Landy, A. 1989. Dynamic, structural, and regulatory aspects of λ site-specific recombination. Annu. Rev. Biochem. 58: 913-949.
    • (1989) Annu. Rev. Biochem. , vol.58 , pp. 913-949
    • Landy, A.1
  • 51
    • 0032481104 scopus 로고    scopus 로고
    • The univector plasmid-fusion system, a method for rapid construction of recombinant DNA without restriction enzymes
    • Liu, Q., Li, M.Z., Leibham, D., Cortez, D., and Elledge, S.J. 1998. The univector plasmid-fusion system, a method for rapid construction of recombinant DNA without restriction enzymes. Curr. Biol. 8: 1300-1309.
    • (1998) Curr. Biol. , vol.8 , pp. 1300-1309
    • Liu, Q.1    Li, M.Z.2    Leibham, D.3    Cortez, D.4    Elledge, S.J.5
  • 53
    • 0037470952 scopus 로고    scopus 로고
    • Identification of Hedgehog pathway components by RNAi in Drosophila cultured cells
    • Lum, L., Yao, S., Mozer, B., Rovescalli, A., Von Kessler, D., Nirenberg, M., and Beachy, P.A. 2003. Identification of Hedgehog pathway components by RNAi in Drosophila cultured cells. Science 299: 2039-2045.
    • (2003) Science , vol.299 , pp. 2039-2045
    • Lum, L.1    Yao, S.2    Mozer, B.3    Rovescalli, A.4    Von Kessler, D.5    Nirenberg, M.6    Beachy, P.A.7
  • 54
    • 0023615620 scopus 로고
    • Plasmid construction by homologous recombination in yeast
    • Ma, H., Kunes, S., Schatz, P.J., and Botstein, D. 1987. Plasmid construction by homologous recombination in yeast. Gene 58: 201-216.
    • (1987) Gene , vol.58 , pp. 201-216
    • Ma, H.1    Kunes, S.2    Schatz, P.J.3    Botstein, D.4
  • 55
    • 0035128859 scopus 로고    scopus 로고
    • Large-scale analysis of gene function in Caenorhabditis elegans by high-throughput RNAi
    • Maeda, I., Kohara, Y., Yamamoto, M., and Sugimoto, A. 2001. Large-scale analysis of gene function in Caenorhabditis elegans by high-throughput RNAi. Curr. Biol. 11: 171-176.
    • (2001) Curr. Biol. , vol.11 , pp. 171-176
    • Maeda, I.1    Kohara, Y.2    Yamamoto, M.3    Sugimoto, A.4
  • 56
    • 7444229263 scopus 로고    scopus 로고
    • Many paths to many clones: A comparative look at high-throughput cloning methods
    • (this issue)
    • Marsischky, G. and LaBaer, J. 2004. Many paths to many clones: A comparative look at high-throughput cloning methods. Genome Res. (this issue).
    • (2004) Genome Res.
    • Marsischky, G.1    LaBaer, J.2
  • 58
    • 0034581516 scopus 로고    scopus 로고
    • Monitoring protein conformations and interactions by fluorescence resonance energy transfer between mutants of green fluorescent protein
    • Miyawaki, A. and Tsien, R.Y. 2000. Monitoring protein conformations and interactions by fluorescence resonance energy transfer between mutants of green fluorescent protein. Methods Enzymol. 327: 472-500.
    • (2000) Methods Enzymol. , vol.327 , pp. 472-500
    • Miyawaki, A.1    Tsien, R.Y.2
  • 60
    • 0030873221 scopus 로고    scopus 로고
    • Recombination-mediated PCR-directed plasmid construction in vivo in yeast
    • Oldenburg, K.R., Vo, K.T., Michaelis, S., and Paddon, C. 1997. Recombination-mediated PCR-directed plasmid construction in vivo in yeast. Nucleic Acids Res. 25: 451-452.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 451-452
    • Oldenburg, K.R.1    Vo, K.T.2    Michaelis, S.3    Paddon, C.4
  • 61
    • 0020689374 scopus 로고
    • Genetic applications of yeast transformation with linear and gapped plasmids
    • Orr-Weaver, T.L., Szostak, J.W., and Rothstein, R.J. 1983. Genetic applications of yeast transformation with linear and gapped plasmids. Methods Enzymol. 101: 228-245.
    • (1983) Methods Enzymol. , vol.101 , pp. 228-245
    • Orr-Weaver, T.L.1    Szostak, J.W.2    Rothstein, R.J.3
  • 63
    • 0034649570 scopus 로고    scopus 로고
    • RNAi analysis of genes expressed in the ovary of Caenorhabditis elegans
    • Piano, F., Schetter, A.J., Mangone, M., Stein, L., and Kemphues, K.J. 2000. RNAi analysis of genes expressed in the ovary of Caenorhabditis elegans. Curr. Biol. 10: 1619-1622.
    • (2000) Curr. Biol. , vol.10 , pp. 1619-1622
    • Piano, F.1    Schetter, A.J.2    Mangone, M.3    Stein, L.4    Kemphues, K.J.5
  • 66
    • 0038708337 scopus 로고    scopus 로고
    • C. elegans ORFeome Version 1.1: Experimental verification of the genome annotation and resource for proteome-scale protein expression
    • 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.
    • (2003) Nat. Genet. , vol.34 , pp. 35-41
    • Reboul, J.1    Vaglio, P.2    Rual, J.F.3    Lamesch, P.4    Martinez, M.5    Armstrong, C.M.6    Li, S.7    Jacotot, L.8    Bertin, N.9    Janky, R.10
  • 68
    • 1042287135 scopus 로고    scopus 로고
    • ORFeome projects: Gateway between genomics and omics
    • Rual, J.F., Hill, D.E., and Vidal, M. 2004b. ORFeome projects: Gateway between genomics and omics. Curr. Opin. Chem. Biol. 8: 20-25.
    • (2004) Curr. Opin. Chem. Biol. , vol.8 , pp. 20-25
    • Rual, J.F.1    Hill, D.E.2    Vidal, M.3
  • 70
    • 0036188159 scopus 로고    scopus 로고
    • Exploring the pathway structure of metabolism: Decomposition into subnetworks and application to Mycoplasma pneumoniae
    • Schuster, S., Pfeiffer, T., Moldenhauer, F., Koch, I., and Dandekar, T. 2002. Exploring the pathway structure of metabolism: Decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinformatics 18: 351-361.
    • (2002) Bioinformatics , vol.18 , pp. 351-361
    • Schuster, S.1    Pfeiffer, T.2    Moldenhauer, F.3    Koch, I.4    Dandekar, T.5
  • 71
    • 0036578795 scopus 로고    scopus 로고
    • Network motifs in the transcriptional regulation network of Escherichia coli
    • Shen-Orr, S.S., Milo, R., Mangan, S., and Alon, U. 2002. Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 31: 64-68.
    • (2002) Nat. Genet. , vol.31 , pp. 64-68
    • Shen-Orr, S.S.1    Milo, R.2    Mangan, S.3    Alon, U.4
  • 73
    • 0034280113 scopus 로고    scopus 로고
    • Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing
    • Simpson, J.C., Wellenreuther, R., Poustka, A., Pepperkok, R., and Wiemann, S. 2000. Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. EMBO Rep. 1: 287-292.
    • (2000) EMBO Rep. , vol.1 , pp. 287-292
    • Simpson, J.C.1    Wellenreuther, R.2    Poustka, A.3    Pepperkok, R.4    Wiemann, S.5
  • 75
    • 0033968037 scopus 로고    scopus 로고
    • Heritable and inducible genetic interference by double-stranded RNA encoded by transgenes
    • Tavernarakis, N., Wang, S.L., Dorovkov, M., Ryazanov, A., and Driscoll, M. 2000. Heritable and inducible genetic interference by double-stranded RNA encoded by transgenes. Nat. Genet. 24: 180-183.
    • (2000) Nat. Genet. , vol.24 , pp. 180-183
    • Tavernarakis, N.1    Wang, S.L.2    Dorovkov, M.3    Ryazanov, A.4    Driscoll, M.5
  • 78
    • 0031663369 scopus 로고    scopus 로고
    • The green fluorescent protein
    • Tsien, R.Y. 1998. The green fluorescent protein. Annu. Rev. Biochem. 67: 509-544.
    • (1998) Annu. Rev. Biochem. , vol.67 , pp. 509-544
    • Tsien, R.Y.1
  • 82
    • 0035830505 scopus 로고    scopus 로고
    • A biological atlas of functional maps
    • Vidal, M. 2001. A biological atlas of functional maps. Cell 104: 333-339.
    • (2001) Cell , vol.104 , pp. 333-339
    • Vidal, M.1
  • 83
    • 0029809862 scopus 로고    scopus 로고
    • Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions
    • Vidal, M., Brachmann, R.K., Fattaey, A., Harlow, E., and Boeke, J.D. 1996. Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions. Proc. Natl. Acad. Sci. 93: 10315-10320.
    • (1996) Proc. Natl. Acad. Sci. , vol.93 , pp. 10315-10320
    • Vidal, M.1    Brachmann, R.K.2    Fattaey, A.3    Harlow, E.4    Boeke, J.D.5
  • 84
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S.G., Fields, S., and Bork, P. 2002. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417: 399-403.
    • (2002) Nature , vol.417 , pp. 399-403
    • von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Fields, S.6    Bork, P.7
  • 85
    • 0034854563 scopus 로고    scopus 로고
    • High-throughput yeast two-hybrid assays for large-scale protein interaction mapping
    • Walhout, A.J. and Vidal, M. 2001a. High-throughput yeast two-hybrid assays for large-scale protein interaction mapping. Methods 24: 297-306.
    • (2001) Methods , vol.24 , pp. 297-306
    • Walhout, A.J.1    Vidal, M.2
  • 86
    • 0035222942 scopus 로고    scopus 로고
    • Protein interaction maps for model organisms
    • Walhout, A.J. and Vidal, M. 2001b. Protein interaction maps for model organisms. Nat. Rev. Mol. Cell. Biol. 2: 55-62.
    • (2001) Nat. Rev. Mol. Cell Biol. , vol.2 , pp. 55-62
    • Walhout, A.J.1    Vidal, M.2
  • 89
  • 93
    • 0141493447 scopus 로고    scopus 로고
    • BTB proteins are substrate-specific adaptors in an SCF-like modular ubiquitin ligase containing CUL-3
    • Xu, L., Wei, Y., Reboul, J., Vaglio, P., Shin, T.H., Vidal, M., Elledge, S.J., and Harper, J.W. 2003. BTB proteins are substrate-specific adaptors in an SCF-like modular ubiquitin ligase containing CUL-3. Nature 425: 316-321.
    • (2003) Nature , vol.425 , pp. 316-321
    • Xu, L.1    Wei, Y.2    Reboul, J.3    Vaglio, P.4    Shin, T.H.5    Vidal, M.6    Elledge, S.J.7    Harper, J.W.8
  • 94
    • 0030745291 scopus 로고    scopus 로고
    • Two classes of human papillomavirus type 16 E1 mutations suggest pleiotropic conformational constraints affecting E1 multimerization, E2 interaction, and interaction with cellular proteins
    • Yasugi, T., Vidal, M., Sakai, H., Howley, P.M., and Benson, D. 1997. Two classes of human papillomavirus type 16 E1 mutations suggest pleiotropic conformational constraints affecting E1 multimerization, E2 interaction, and interaction with cellular proteins. J. Virol. 71: 5942-5951.
    • (1997) J. Virol. , vol.71 , pp. 5942-5951
    • Yasugi, T.1    Vidal, M.2    Sakai, H.3    Howley, P.M.4    Benson, D.5
  • 96
    • 0031664853 scopus 로고    scopus 로고
    • A new logic for DNA engineering using recombination in Escherichia coli
    • Zhang, Y., Buchholz, F., Muyrers, J.P., and Stewart, A.F. 1998. A new logic for DNA engineering using recombination in Escherichia coli. Nat. Genet. 20: 123-128.
    • (1998) Nat. Genet. , vol.20 , pp. 123-128
    • Zhang, Y.1    Buchholz, F.2    Muyrers, J.P.3    Stewart, A.F.4


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