The Atom of Evolution |
Bhak, Jonghwa
(Biomatics Lab, BioSystems, KAIST, NGIC, KRIBB, BiO Institute, OITEK Inc.)
Bolser, Dan (BiO Institute, MRC-DUNN) Park, Daeui (OITEK Inc.) Cho, Yoobok (OITEK Inc.) Yoo, Kiesuk (OITEK Inc.) Lee, Semin (Biomatics Lab, BioSystems, KAIST) Gong, SungSam (Biomatics Lab, BioSystems, KAIST) Jang, Insoo (NGIC, KRIBB) Park, Changbum (Biomatics Lab, BioSystems, KAIST) Huston, Maryana (BiO Institute) Choi, Hwanho (BiO Institute) |
1 | Bolser, D., Panos, D, Harrington, R., Park, J., and Schroeder, M., (2003). Visualisation and Graph- theoretic Analysis of a Large-scale Protein Structural Interactome., BMC Bioinformatics 445, 1471-2105 |
2 | Bray, D. (1995). Protein molecules as computational elements in living cells. Nature 376, 307-312 DOI PUBMED ScienceOn |
3 | Chia, J.M, and Kolatkar, P.R. (2004). Implications for domain fusn protein-protein interactions based on structuralio information. BMC Bioinformatics 26, 161 (Epub ahead of print) |
4 | Chothia, C. (1976). The nature of the accessible and buried surfaces in proteins. J.MoI.BioI. 105, 1-14 DOI |
5 | 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 DOI ScienceOn |
6 | 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, Y. Proc. Natl. Acad. Sci. USA 98, 4569-4574. Epub DOI ScienceOn |
7 | Ju, B.H., Park, B., Park J.H., and Han K. (2003). Visualization and analysis of protein interactions. Bioinformatics 19, 317-318 DOI ScienceOn |
8 | Gardiner, K., Davisson M.T., and Crnic, L.S. (2004). Building protein interaction maps for Down's syndrome. Brief Funct Genomic Proteomic 3, 142-156 DOI ScienceOn |
9 |
Lu, H., Zhu, X., Liu, H., Skoger |
10 | Kim, H., Park, J., and Han, K, (2003). Predicting Protein Interactions in Human by Homologous Interactions in Yeast. Lecture Notes in Computer Science 2637, 159-165 DOI ScienceOn |
11 | Marcotte, E.M., Pellegrini, M., Ng, H.L., Rice, D.W., Yeates, T.O., and Eisenberg, D. (1999). Detecting protein function and protein-protein interactions from genome sequences. Science 285, 751-753 DOI PUBMED ScienceOn |
12 | Moon, H.S., Bhak, J., Lee, K.H., and Lee, D. (2005). Architecture of Basic Building Blocks in Protein and Domain Structural Interaction Networks. Bioinformatics (in press) |
13 | Poupon, A. (2004). Voronoi and Voronoi-related tessellations in studies of protein structure and interaction. Curr. Opio. Stru. Biol. 14, 1-9 DOI ScienceOn |
14 | Jeong, H., Mason, S.P., Barabasi, A.L., and Oltvai, Z.N. (2001). Lethality and centrality in protein networks. Nature 411, 41-42 DOI ScienceOn |
15 | Raicu V., Jansma D.B., Miller R.J., and Friesen J.D. (2004). Protein interaction quantified in vivo by spectrally resolved fluorescence resonance energy transfer. Biochem J. Sep 7;Pt. (Epub ahead of print) |
16 | Richard, F.M. (1974). The interpretation of protein structures: total volume, group volume distributions and packing density. J. Mol. Biol. 82, 1-14 DOI PUBMED |
17 | Albert, R., Jeong, H., and Barabasi, A.L. (2000). Error and attack tolerance of complex networks. Nature 406, 378-382 DOI ScienceOn |
18 | Lawrence, M.C. and Colman, P.M. (1993). Shape complementarity at protein/protein interfaces. J. Mol. Biol. 234, 946-950 DOI ScienceOn |
19 | Schof, J.W. (1993). Microfossils of the EarIy Archean Apex Chert: New Evidence of the Antiquity of life. Science 260, 640-646 DOI PUBMED ScienceOn |
20 | Albert, R. and Othmer, H.G., (2003). The topology of the regulat- ory interactions predicts the expression pattern of the seg- ment polarity genes in Drosophila melanogaster. J.Theor. Biol. 223, 1-18 DOI ScienceOn |
21 | Chothia, C. and Janin, J. (1975). Principles of protein-protein recognition. Nature 256, 705-708 DOI ScienceOn |
22 | Richards, F.M. (1977). Area, volumes, Packing and protein structures, Ann. Rev. Biophys. Bioeng. 6, 151-176 DOI PUBMED ScienceOn |
23 | Ng, S.K. and Tan, S.H. (2004). Discovering protein-protein interactions. J. Bioinform Comput. Biol. 1, 711-741 DOI ScienceOn |
24 | Park, J., Lappe, M., and Teichmann, S.A. (2001). Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. J. Mol. Biol. 30, 307, 929-938 |
25 | Lappe, M., Park, J., Niggemann, 0., and Holm, L. (2001). Generating protein interaction maps from incomplete data: application to Fold assignment. Bioinformatics VoI.17 SuppI.1, S149-S156 DOI ScienceOn |
26 | Bolser, D.M. and Park, J. (2003). Biological Network Evolution Hypothesis Applied to Protein Structural Interactome. Genomics & Informatics 7-19 |
27 | Walhout, A.J., Boulton, S.J., and Vidal, M. (2000). Yeast two hybrid systems and protein interaction mapping projects for yeast and worm. Yeast 17, 88-94 DOI ScienceOn |
28 | Doolittle, R.F., Feng, D.F., Tsang, S., Cho, G., and Little, E., (1996). Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock. Science 27-1, 470-477 |
29 | Jones, S., Marin, A., and Thornton, J.M. (2000). Protein domain interfaces: characterization and comparison with oligomeric protein interfaces. Protein Engineering 13, 77-82 DOI PUBMED |
30 | Caffrey, D.R., Somaroo, S., Hughes, J.D., Mintseris, J., and Huang, E.S. (2004). Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Science 13, 190-202 DOI ScienceOn |
31 | Jones, S. and Thornton, J.M. (1997). Analysis of Protein-protein interaction sites using surface patches. J.MoI.Biol. 272, 121-132 DOI ScienceOn |
32 | Promislow, D.E. (2004). Protein networks, pleiotropy and the evolution of senescence. Proc. R. Soc. Lond. B. Biol. Sci. 271, 1225-1234 DOI ScienceOn |
33 | Miller, S., Janin, J., Lesk, A.M., and Chotia, C. (1987). Interior and surface of monomeric proteins. J. Mol. Biol. 196, 641-656 DOI PUBMED |
34 | Gagneur, J, Krause, R., Bouwmeester, T., and Casari, G. (2004). Modular decomposition of protein-protein interaction networks. Genome Biol. 5, R57. Epub DOI PUBMED |
35 | Lehner, B. and Fraser, F. (2004). A first-draft human protein-interaction map. Genome Biology 5:R63 doi:10.1186/ gb-2004-5-9-r63 DOI PUBMED |
36 | Albert, R. and Baraba'si, A.-L (2002). Statistical mechanics of complex networks. Rev. Mod. Phys. 74, 47-97 DOI ScienceOn |
37 | Jones, S. and Thornton, J.M. (1997). Principle of protein- protein interactions. Proc. Natl. Acad. Sci. USA 93, 13-20 DOI ScienceOn |
38 | Sanchez, C., Lachaize, C., Janody, F., Bellon, B., Roder, L, Euzenat, J., Rechenmann, F., and Jacq, B. (1999). Grasping at molecular interactions and genetic networksin Drosophila melanogaster using FlyNets, an Internet database. Nucleic Acids Res. 27, 89-94 DOI ScienceOn |
39 | Batagelj, V. and Mrvar, A. (2001). Pajek-analysis and visualization of large networks. LNCS 2265, 477-478 |
40 | Park, J., Dietmann, S., Heger, A., and Holm, L. (2000). Estimating the significance of sequence order in protein secondary structure prediction. Bioinformatics 16, 978-987 DOI ScienceOn |
41 | Varshney A., Brooks, F., and Richardson, D. (1995). Defining, Computing, and Visualizing Molecular Interfaces. Proceedings IEEE Visualization 95, 36-43 |
42 | Uetz, P., Giot, L, Cagney, G., Mansfield, T.A., Judson, RS., Knight, J.R., Lockshon, D., Narayan, V., Shnivasan, M., Pochart, P., Qureshi-Emili, A., Li, Y., Godwin, B., Conover, D., Kalbfleisch, T., Vijayadamodar, G., Yang, M., Johnston, M., Fields, S., and Rothberg, J.M. (2000). A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627 DOI ScienceOn |
43 | Kim, W., Bolser, D.M., and Park, J., (2004). Large scale co-evolution analysis of Protein Structural Interlogues using the global Protein Structural Interactome Map (PSIMAP). Bioinformatics 20, 1138-1150 DOI ScienceOn |
44 | Park, J. and Bolser, D., (2001). Conservation of protein interaction network in evolution. Genome Informatics 12, 135-140 |
45 | Searls, D.B. (1993). The Computational Linguistics of Biological Sequences, In Artificial Intelligence and Molecular Biology, L. Hunter, ed. (AAAI Press) PP.47-120 |
46 | Darwin, C. (1859). On the origins of species, London, http://pages.britishlibrary.net/charles.darwin/texts/origin1859/origin_fm.html |
47 | Iragne, F., Nikolski, M., Mathieu, B., Auber, D., and Sherman D. (2004). ProViz: Protein Interaction Visualization and Exploration. Bioinformatics (Epub ahead of print) |
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