[1]
Zhang S, Jin G, Zhang XS, Chen L. Discovering functions and revealing mechanisms at molecular level from biological networks. Proteomics 2007; 7(16): 2856-69.
[2]
Zhang S, Tian D, Tran NH, Choi KP, Zhang L. Profiling the transcription factor regulatory networks of human cell types. Nucleic Acids Res 2014; 42(20): 12380-7.
[3]
Sharan R, Ideker T. Modeling cellular machinery through biological network comparison. Nat Biotechnol 2006; 24(4): 427-33.
[4]
Faisal FE, Meng L, Crawford J, Milenković T. The post-genomic era of biological network alignment. EURASIP J Bioinform Syst Biol 2015; 2015(1): 3.
[5]
Li Z, Zhang S, Wang Y, Zhang XS, Chen L. Alignment of molecular networks by integer quadratic programming. Bioinformatics 2007; 23(13): 1631-9.
[6]
Zhang S, Zhang XS, Chen L. Biomolecular network querying: a promising approach in systems biology. BMC Syst Biol 2008; 2(1): 5.
[7]
Pujol A, Mosca R, Farrés J, Aloy P. Unveiling the role of network and systems biology in drug discovery. Trends Pharmacol Sci 2010; 31(3): 115-23.
[8]
Faisal FE, Milenković T. Dynamic networks reveal key players in aging. Bioinformatics 2014; 30(12): 1721-9.
[9]
Faisal FE, Zhao H, Milenković T. Global network alignment in the context of agingIEEE/ACM Trans Comput Biol Bioinform 2015. 12(1): 40-52.
[10]
Sharan R, Suthram S, Kelley RM, et al. Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci USA 2005; 102(6): 275-86.
[11]
Flannick J, Novak A, Srinivasan BS, Mcadams HH, Batzoglou S. Graemlin: general and robust alignment of multiple large interaction networks. Genome Res 2006; 16(9): 1169-81.
[12]
Koyutürk M, Kim Y, Topkara U, Subramaniam S, Szpankowski W, Grama A. Pairwise alignment of protein interaction networks. J Bioinform Comput Biol 2006; 13(2): 182-99.
[13]
Berg J, Lässig M. Local graph alignment and motif search in biological networks. Proc Natl Acad Sci USA 2004; 101(41): 14689-94.
[14]
Liang Z, Xu M, Teng M, Niu L. NetAlign: a web-based tool for comparison of protein interaction networks. Bioinformatics 2006; 22(17): 2175-7.
[15]
Berg J, Lässig M. Cross-species analysis of biological networks by Bayesian alignment. Proc Natl Acad Sci USA 2006; 103(29): 10967-72.
[16]
Ciriello G, Mina M, Guzzi PH, Cannataro M, Guerra C. AlignNemo: a local network alignment method to integrate homology and topology. PLoS One 2012; 7(6): e38107.
[17]
Pache RA, Aloy P. A novel framework for the comparative analysis of biological networks. PLoS One 2012; 7(2): e31220.
[18]
Kelley BP, Yuan B, Lewitter F, Sharan R, Stockwell BR, Ideker T. PathBLAST: a tool for alignment of protein interaction networks. Nucleic Acids Res 2004; 32(Suppl. 2): W83-.
[19]
Clark C, Kalita J. A comparison of algorithms for the pairwise alignment of biological networks. Bioinformatics 2014; 30(16): 2351-9.
[20]
Liao CS, Lu K, Baym M, Singh R, Berger B. IsoRankN: spectral methods for global alignment of multiple protein networks. Bioinformatics 2009; 25(12): 253-8.
[21]
Kuchaiev O, Przulj N. Integrative network alignment reveals large regions of global network similarity in yeast and human. Bioinformatics 2011; 27(10): 1390-6.
[22]
Zaslavskiy M, Bach F, Vert JP. Global alignment of protein-protein interaction networks by graph matching methods. Bioinformatics 2009; 25(12): i259-67.
[23]
Phan HT, Sternberg MJ. PINALOG: a novel approach to align protein interaction networks--implications for complex detection and function prediction. Bioinformatics 2012; 28(9): 1239-45.
[24]
Neyshabur B, Khadem A, Hashemifar S, Arab SS. NETAL: a new graph-based method for global alignment of protein-protein interaction networks. Bioinformatics 2013; 29(13): 1654-62.
[25]
Saraph V, Milenković T. MAGNA: maximizing accuracy in global network alignment. Bioinformatics 2014; 30(20): 2931-40.
[26]
Sun Y, Crawford J, Tang J, Milenković T. Simultaneous Optimization of both Node and Edge Conservation in Network Alignment via Wave. Quant Biol 2015; 76(4): 439-56.
[27]
Sahraeian SM, Yoon BJ. SMETANA: accurate and scalable algorithm for probabilistic alignment of large-scale biological networks. PLoS One 2013; 8(7): e67995.
[28]
Hu J, Kehr B, Reinert K. NetCoffee: A fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks. Bioinformatics 2014; 30(4): 540-8.
[29]
Ali W, Rito T, Reinert G, Sun F, Deane CM. Alignment-free protein interaction network comparison. Bioinformatics 2014; 30(17): 430-7.
[30]
Vijayan V, Saraph V, Milenkovi T. MAGNA++: Maximizing Accuracy in Global Network Alignment via both node and edge conservation. Bioinformatics 2015; 31(14): 2409-11.
[31]
Hashemifar S, Ma J, Naveed H, Canzar S, Xu J. ModuleAlign: module-based global alignment of protein–protein interaction networks. Bioinformatics 2016; 32(17): i658-64.
[32]
Chindelevitch L, Ma CY, Liao CS, Berger B. Optimizing a global alignment of protein interaction networks. Bioinformatics 2013; 29(21): 2765-73.
[33]
Aladağ AE, Erten C. SPINAL: scalable protein interaction network alignment. Bioinformatics 2013; 29(7): 917-24.
[34]
Singh R, Xu J, Berger B. Global alignment of multiple protein interaction networks with application to functional orthology detection. Proc Natl Acad Sci USA 2008; 105(35): 12763-8.
[35]
Kuchaiev O, Milenković T, Memišević V, Hayes W, Pržulj N. Topological network alignment uncovers biological function and phylogeny. J R Soc Interface 2010; 7(50): 1341-54.
[36]
Przulj N. Biological network comparison using graphlet degree distribution. Bioinformatics 2007; 23(2): e177-83.
[37]
Patro R, Kingsford C. Global network alignment using multiscale spectral signatures. Bioinformatics 2012; 28(23): 3105-14.
[38]
Milenković T, Ng WL, Hayes W, Pržulj N. Optimal Network Alignment with Graphlet Degree Vectors. Cancer Inform 2010; 9(9): 121-37.
[39]
Collins SR, Kemmeren P, Zhao XC, et al. Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol Cell Proteomics 2007; 6(3): 439-50.
[40]
Radivojac P, Peng K, Clark WT, et al. An integrated approach to inferring gene-disease associations in humans. Proteins 2008; 72(3): 1030-7.
[41]
Park D, Singh R, Baym M, Liao CS, Berger B. IsoBase: a database of functionally related proteins across PPI networks. Nucleic Acids Res 2011; 39(Suppl. 1): D295-300.
[42]
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215(3): 403-10.
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