Citing PLEX
  • Date, S. V & Marcotte, E. M.  Protein function prediction using the Protein Link Explorer (PLEX). (to appear in Bioinformatics).
PLEX acknowledges the following:
  1. Blattner,F.R. et al. (1997) The complete genome sequence of Escherichia coli K-12. Science, 277, 1453-1474.
  2. Dandekar,T., Snel,B., Huynen,M. and Bork,P. (1998) Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci., 23, 324-328.
  3. Date,S.V. and Marcotte,E.M. (2003) Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nature Biotechnol., 21, 1055-1062.
  4. Enright,A.J., Iliopoulos,I., Kyrpides,N.C. and Ouzounis,C.A. (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature 402, 86-90.
  5. Fischer,D. and Eisenberg,D. (1999) Finding families for genomic ORFans. Bioinformatics, 15, 759-62.
  6. Gardner et al. (2002) Genome sequence of the human malaria parasite Plasmodium falciparum. Nature, 419, 498-511.
  7. Goffeau,A. et al. (1997) The Yeast Genome Directory. Nature, 387, Supplement.
  8. Huynen,M., Dandekar,T. and Bork,P. (1998) Differential genome analysis applied to the species-specific features of Helicobacter pylori. FEBS Letters 426, 1-5.
  9. Koonin, E.V, Wolf,Y.I. and Aravind,L. (2001) Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach. Genome Res. 11, 240-252.
  10. Korbel,J.O., Jensen,L.J., von Mering,C. and Bork,P. (2004) Analysis of genomic context: prediction of functional associations from conserved bi-directionally transcribed gene pairs. Nat Biotechnol., 22, 911-7.
  11. Marcotte,E.M., Pellegrini,M., Thompson,M.J., Yeates,T. and Eisenberg,D. (1999a) A combined algorithm for genome-wide prediction of protein function. Nature, 402, 83-86.
  12. Marcotte,E.M., Pellegrini,M., Ng,H.-L., Rice,D.W., Yeates,T.O. and Eisenberg, D. (1999b) Detecting protein function and protein-protein interactions from genome sequences. Science, 285, 751-753
  13. Mellor, J.C, Yanai, I., Clodfelter, K.H., Mintseris, J. and DeLisi. C. (2002) Predictome: a database of putative functional links between proteins. Nucleic Acids Res., 30, 306-309.
  14. Morett,E., Korbel,J.O., Rajan,E., Saab-Rincon,G., Olvera,L., Olvera,M., Schmidt,S., Snel,B. and Bork,P. (2003) Systematic discovery of analogous enzymes in thiamin biosynthesis. Nat Biotechnol., 21, 790-795.
  15. Overbeek,R., Fonstein,M., D'Souza,M., Pusch,G.D. and Maltsev,N. (1999) The use of gene clusters to infer functional coupling. Proc Natl Acad Sci U S A. 96, 2896-2901.
  16. Pellegrini,M., Marcotte,E.M., Thompson,M.J., Eisenberg,D. and Yeates,T.O. (1999) Assigning protein functions by comparative analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. USA, 96, 4285-4288.
  17. Sali,A. (1999) Genomics: Functional links between proteins. Nature, 402, 23-26
  18. Salgado,H., Moreno-Hagelsieb,G., Smith,T.F. and Collado-Vides,J. (2000) Operons in Escherichia coli: genomic analyses and predictions. Proc. Natl. Acad. Sci. USA, 97, 6652-6657.
  19. Snel,B., Lehmann,G., Bork,P. and Huynen,M.A. (2000) STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res., 28, 3442-3444.
  20. Verjovsky Marcotte,C.J. and Marcotte,E.M. (2002). Predicting functional linkages from gene fusions with confidence. Applied Bioinformatics 1, 1-8.
Copyright © 2002 - 2005, Shailesh Date and Edward Marcotte. The protein link explorer data and server is the property of the University of Texas, and cannot be used for commercial purposes without written permission of Edward Marcotte and the University of Texas. It is forbidden to redistribute, derivatize, or encapsulate the protein link explorer data or server in another database without permission. Sale of information derived from it, whether directly or in revised form, is forbidden except by permission of the University of Texas and Edward Marcotte. All copies or mirrors of the protein link explorer must carry this notice.