The Community for Technology Leaders
RSS Icon
Subscribe
Issue No.02 - April-June (2010 vol.7)
pp: 354-364
Xiaowen Liu , City University of Hong Kong, Hong Kong
Jinyan Li , Nanyang Technological University, Singapore
Lusheng Wang , City University of Hong Kong, Hong Kong
ABSTRACT
HASH(0x2973610)
INDEX TERMS
Protein-protein interactions, interaction sites, quasi-bicliques.
CITATION
Xiaowen Liu, Jinyan Li, Lusheng Wang, "Modeling Protein Interacting Groups by Quasi-Bicliques: Complexity, Algorithm, and Application", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.7, no. 2, pp. 354-364, April-June 2010, doi:10.1109/TCBB.2008.61
REFERENCES
[1] M. Yannakakis, "Node Deletion Problems on Bipartite Graphs," SIAM J. Computing, vol. 10, pp. 310-327, 1981.
[2] A. Thomas, R. Cannings, N.A.M. Monk, and C. Cannings, "On the Structure of Protein-Protein Interaction Networks," Biochemical Soc. Trans., vol. 31, pp. 1491-1496, Dec. 2003.
[3] J.L. Morrison, R. Breitling, D.J. Higham, and D.R. Gilbert, "A Lock-and-Key Model for Protein-Protein Interactions," Bioinformatics, vol. 22, no. 16, pp. 2012-2019, Aug. 2006.
[4] B. Andreopoulos, A. An, X. Wang, M. Faloutsos, and M. Schroeder, "Clustering by Common Friends Finds Locally Significant Proteins Mediating Modules," Bioinformatics, vol. 23, no. 9, pp. 1124-1131, 2007.
[5] D. Bu, Y. Zhao, L. Cai, H. Xue, X. Zhu, H. Lu, J. Zhang, S. Sun, L. Ling, N. Zhang, G. Li, and R. Chen, "Topological Structure Analysis of the Protein-Protein Interaction Network in Budding Yeast," Nucleic Acids Research, vol. 31, no. 9, pp. 2443-2450, May 2003.
[6] H. Hishigaki, K. Nakai, T. Ono, A. Tanigami, and T. Takagi, "Assessment of Prediction Accuracy of Protein Function from Protein-Protein Interaction Data," Yeast, vol. 18, no. 6, pp. 523-531, Apr. 2001.
[7] H. Li, J. Li, and L. Wong, "Discovering Motif Pairs at Interaction Sites from Protein Sequences on a Proteome-Wide Scale," Bioinformatics, vol. 22, no. 8, pp. 989-996, 2006.
[8] M.R. Garey and D.S. Johnson, Computers and Intractability, A Guide to the Theory of NP-Completeness. W.H. Freeman, 1979.
[9] R. Peeters, "The Maximum Edge Biclique Problem Is NP-Complete," Discrete Applied Math., vol. 131, no. 3, pp. 651-654, 2003.
[10] R.M. Karp, "Reducibility among Combinatorial Problems," Complexity of Computer Computations, R.E. Miller and J.W. Thatcher, eds., pp. 85-103, 1972.
[11] D. Peleg, G. Schechtman, and A. Wool, "Approximating Bounded 0-1 Integer Linear Programs," Proc. Second Israel Symp. Theory of Computing and Systems (ISTCS), 1993.
[12] S. Pietrokovski, "Searching Databases of Conserved Sequence Regions by Aligning Protein Multiple-Alignments," Nucleic Acids Research, vol. 24, pp. 3836-3845, 1996.
[13] T.K. Attwood and M.E. Beck, "PRINTS—A Protein Motif Fingerprint Database," Protein Eng., Design and Selection, vol. 7, pp. 841-848, 1994.
[14] R.D. Finn, M. Marshall, and A. Bateman, "iPfam: Visualization of Protein-Protein Interactions in PDB at Domain and Amino Acid Resolutions," Bioinformatics, vol. 21, no. 3, pp. 410-412, Feb. 2005.
[15] G. Grahne and J. Zhu, "Efficiently Using Prefix-Trees in Mining Frequent Itemsets," Proc. Workshop Frequent Itemset Mining Implementations (FIMI), 2003.
[16] E.L. Sonnhammer, S.R. Eddy, and R. Durbin, "Pfam: A Comprehensive Database of Protein Domain Families Based on Seed Alignments," Proteins: Structure, Function and Genetics, vol. 28, pp. 405-420, 1997.
[17] R. Apweiler, T.K. Attwood, A. Bairoch, A. Bateman, E. Birney, M. Biswas, P. Bucher, L. Cerutti, F. Corpet, M.D. Croning, R. Durbin, L. Falquet, W. Fleischmann, J. Gouzy, H. Hermjakob, N. Hulo, I. Jonassen, D. Kahn, A. Kanapin, Y. Karavidopoulou, R. Lopez, B. Marx, N.J. Mulder, T.M. Oinn, M. Pagni, F. Servant, C.J. Sigrist, and E.M. Zdobnov, "The InterPro Database, an Integrated Documentation Resource for Protein Families, Domains and Functional Sites," Nucleic Acids Research, vol. 29, no. 1, pp. 37-40, Jan. 2001.
[18] V.I. Gordeliy, J. Labahn, R. Moukhametzianov, R. Efremov, J. Granzin, R. Schlesinger, G. Büldt, T. Savopol, A.J. Scheidig, J.P. Klare, and M. Engelhard, "Molecular Basis of Transmembrane Signalling by Sensory Rhodopsin II-Transducer Complex," Nature, vol. 419, no. 6906, pp. 484-487, Oct. 2002.
[19] V.B. Bergo, E.N. Spudich, K.J. Rothschild, and J.L. Spudich, "Photoactivation Perturbs the Membrane-Embedded Contacts between Sensory Rhodopsin II and Its Transducer," J. Biological Chemistry, vol. 280, no. 31, pp. 28365-28369, Aug. 2005.
[20] K. Inoue, J. Sasaki, J.L. Spudich, and M. Terazima, "Laser-Induced Transient Grating Analysis of Dynamics of Interaction between Sensory Rhodopsin II D75N and the HtrII Transducer," Biophysical J., vol. 92, no. 6, pp. 2028-2040, Mar. 2007.
[21] Y. Sudo, Y. Furutani, J.L. Spudich, and H. Kandori, "Early Photocycle Structural Changes in a Bacteriorhodopsin Mutant Engineered to Transmit Photosensory Signals," J. Biological Chemistry, vol. 282, no. 21, pp. 15550-15558, May 2007.
[22] E. Martz, "Protein Explorer: Easy yet Powerful Macromolecular Visualization," Trends in Biochemical Sciences, vol. 27, no. 3, pp. 107-109, 2002.
[23] J. Sivaraman, Y. Li, J. Banks, D.E. Cane, A. Matte, and M. Cygler, "Crystal Structure of Escherichia Coli PdxA, an Enzyme Involved in the Pyridoxal Phosphate Biosynthesis Pathway," J. Biological Chemistry, vol. 278, no. 44, pp. 43682-43690, Oct. 2003.
[24] A. Sakai, M. Kita, and Y. Tani, "Recent Progress of Vitamin B6 Biosynthesis," J. Nutritional Science and Vitaminology, vol. 50, no. 2, pp. 69-77, Apr. 2004.
[25] T.B. Fitzpatrick, N. Amrhein, B. Kappes, P. Macheroux, I. Tews, and T. Raschle, "Two Independent Routes of De Novo Vitamin B6 Biosynthesis: Not That Different After All," Biochemistry J., vol. 407, no. 1, pp. 1-13, Oct. 2007.
14 ms
(Ver 2.0)

Marketing Automation Platform Marketing Automation Tool