参考文献
[1]von Mering C,Krause R,Snel B,et al.Comparative Assessment of Large-scale Data Sets of Protein-protein Interactions[J].Nature,2002,417(6887):399-403.
[2]Fields S,Song O.A Novel Genetic System to Detect Protein-protein Interactions[J].Nature,1989,340(6230):245-246.
[3]Liang Zhi,Xu Meng,Teng Maikun,et al.Comparison of Protein Interaction Networks Reveals Species Conserva-tion and Divergence[J].BMC Bioinformatics,2006,7(1):457.
[4]Kolárˇ M,Lssig M,Berg J.From Protein Interactions to Functional Annotation:Graph Alignment in Herpes[J].BMC Systems Biology,2008,2(1):90.
[5]Sharan R,Suthram S,Kelley R M,et al.Conserved Patterns of Protein Interaction in Multiple Species[J].Proceedings of the National Academy of Sciences,2005,102(6):1974-1979.
[6]Singh R,Xu Jinbo,Berger B.Global Alignment of Multiple Protein Interaction Networks with Application to Functional Orthology Detection[J].Proceedings of the National Academy of Science,2008,105(35):12763-12768.
[7]郭杏莉,高琳,陈新.生物网络比对的模型与算法[J].软件学报,2010,21(9):2089-2106.
[8]Flannick J,Novak A,Srinivasan B S,et al.Graemlin:General and Robust Alignment of Multiple Large Interaction Networks[J].Genome Research,2006,16(9):1169-1181.
[9]Milenkovic' T,Ng W L,Hayes W,et al.Optimal Network Alignment with Graphlet Degree Vectors[J].Cancer Informatics,2010,9:121-137.
[10]Kuchaiev O,Milenkovic' T,Memievic' V,et al.Topological Network Alignment Uncovers Biological Function and Phylogeny[J].Journal of the Royal Society Interface,2010,7(50):1341-1354.
[11]Kuchaiev O,Prulj N.Integrative Network Alignment Reveals Large Regions of Global Network Similarity in Yeast and Human[J].Bioinformatics,2011,27(10):1390-1396.
[12]Memievic' V,Prulj N.C-GRAAL:Common-neighbors-based Global GRAph ALignment of Biological Net-works[J].Integrative Biology,2012,4(7):734-743.
(下转第220页)
(上接第214页)
[13]Aladagˇ A E,Erten C.SPINAL:Scalable Protein Interaction Network Alignment[J].Bioinformatics,2013,29(7):917-924.
[14]Klau G W.A New Graph-based Method for Pairwise Global Network Alignment[J].BMC Bioinformatics,2009,10(S1).
[15]Chindelevitch L,Liao C S,Berger B.Local Optimization for Global Alignment of Protein Interaction Net-works[M]//Altman R.Pacific Symposium on Biocom-puting 2010(BIOCOMPUTING 2010).[S.l.]:World Scientific Publishing
Company,2010:123-132.
[16]Uetz P,Giot L,Cagney G,et al.A Comprehensive Analysis of Protein-protein Interactions in Saccharomyces Cerevisiae[J].Nature,2000,403(6770):623-627.
[17]Rigaut G,Shevchenko A,Rutz B,et al.A Generic Protein Purification Method for Protein Complex Characterization and Proteome Exploration[J].Nature Biotechnology,1999,17(10):1030-1032.
[18]Ho Y,Gruhler A,Heilbut A,et al.Systematic Identification of Protein Complexes in Saccharomyces Cerevisiae by Mass Spectrometry[J].Nature,2002,415(6868):180-183.
[19]Zhu Heng,Bilgin M,Bangham R,et al.Global Analysis of Protein Activities Using Proteome Chips[J].Science,2001,293(5537):2101-2105.
[20]Yan Da,Cheng J,Lu Yi,et al.Blogel:A Block-centric Framework for Distributed Computation on Real-world Graphs[J].Proceedings of the VLDB Endowment,2014,7(14):1981-1992.
[21]任年海.一个有效的并行模型——BSP并行模型[J].计算机与现代化,2006,(3):34-36.
[22]李敏,陈建二,王建新.基于复杂网络理论的PPI 网络拓扑分析[J].计算机工程与应用,2008,44(8):20-22.
[23]Erwig M,Hagen F.The Graph Voronoi Diagram with Applications[J].Networks,2000,36(3):156-163.
[24]Karypis G,Kumar V.A Fast and High Quality Multilevel Scheme for Partitioning Irregular Graphs[J].SIAM Journal on Scientific Computing,1998,20(1):359-392.
[25]Park D,Singh R,Baym M,et al.IsoBase:A Database of Functionally Related Proteins Across PPI Networks[J].Nucleic Acids Research,2011,39(S1):295-300.
编辑金胡考 |