The post-genomic era of biological network alignment

被引：41
作者：
Faisal, Fazle E [1 ,2 ,3 ]
Meng, Lei [1 ]
Crawford, Joseph [1 ,2 ,3 ]
Milenković, Tijana [1 ,2 ,3 ]
机构：
[1] Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN
[2] Interdisciplinary Center for Network Science and Applications, University of Notre Dame, Notre Dame, IN
[3] ECK Institute for Global Health, University of Notre Dame, Notre Dame, IN
来源：
Eurasip Journal on Bioinformatics and Systems Biology | 2015年 / 2015卷 / 01期
基金：
美国国家科学基金会;
关键词：
Across-species knowledge transfer; Aging; Biological network research; Functional orthology; Network alignment; Protein-protein interactions;
D O I：
10.1186/s13637-015-0022-9
中图分类号：
学科分类号：
摘要：
Biological network alignment aims to find regions of topological and functional (dis)similarities between molecular networks of different species. Then, network alignment can guide the transfer of biological knowledge from well-studied model species to less well-studied species between conserved (aligned) network regions, thus complementing valuable insights that have already been provided by genomic sequence alignment. Here, we review computational challenges behind the network alignment problem, existing approaches for solving the problem, ways of evaluating their alignment quality, and the approaches’ biomedical applications. We discuss recent innovative efforts of improving the existing view of network alignment. We conclude with open research questions in comparative biological network research that could further our understanding of principles of life, evolution, disease, and therapeutics. © 2015, Faisal et al.
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页数：19
相关论文
共 117 条
[1]  
Altschul S.F., Gish W., Miller W., Lipman D.J., Basic local alignment search tool, J. Mol. Biol., 215, pp. 403-410, (1990)
[2]  
Biesecker L.G., Mullikin J.C., Facio F.M., Turner C., Cherukuri P.F., Blakesley R.W., Bouffard G.G., Chines P.S., Cruz P., Hansen N.F., Teer J.K., Maskeri B., Young A.C., Program N.C.S., Manolio T.A., Wilson A.F., Finkel T., Hwang P., Arai A., Remaley A.T., Sachdev V., Shamburek R., Cannon R.O., Green E.D., The ClinSeq project: piloting large-scale genome sequencing for research in genomic medicine, Genome Res., 19, pp. 1665-1674, (2009)
[3]  
Tsai S.Q., Iafrate A.J., Joung J.K., Genome editing: a tool for research and therapy: towards a functional understanding of variants for molecular diagnostics using genome editing, Nat. Med., 20, pp. 1103-1104, (2014)
[4]  
Alfoldi J., Lindblad-Toh K., Comparative genomics as a tool to understand evolution and disease, Genome Res., 23, pp. 1063-1068, (2013)
[5]  
Yu H., Braun P., Yildirim M.A., Lemmens I., Venkatesan K., Sahalie J., Hirozane-Kishikawa T., Gebreab F., Li N., Simonis N., Hao T., Rual J.F., Dricot A., Vazquez A., Murray R.R., Simon C., Tardivo L., Tam S., Svrzikapa N., Fan C., Smet de A.S., Motyl A., Hudson M.E., Park J., Xin X., Cusick M.E., Moore T., Boone C., Snyder M., Roth F.P., Et al., High-quality binary protein interaction map of the yeast interactome networks, Science, 322, pp. 104-110, (2008)
[6]  
Gstaiger M., Aebersold R., Applying mass spectrometry-based proteomics to genetics, genomics and network biology, Nat. Rev. Genet., 10, pp. 617-627, (2009)
[7]  
Breitkreutz B.J., Stark C., Reguly T., Boucher L., Breitkreutz A., Livstone M., Oughtred R., Lackner D.H., Bahler J., Wood V., Dolinski K., Tyers M., The BioGRID Interaction Database: 2008 update, Nucleic Acids Res., 36, pp. 637-640, (2008)
[8]  
Peri S., Navarro J.D., Kristiansen T.Z., Amanchy R., Surendranath V., Muthusamy B., Gandhi T.K., Chandrika K.N., Deshpande N., Suresh S., Et al., Human protein reference database as a discovery resource for proteomics, Nucleic Acids Res., 32, pp. 497-501, (2004)
[9]  
Cherry J.M., Adler C., Ball C., Chervitz S.A., Dwight S.S., Hester E.T., Jia Y., Juvik G., Roe T., Schroeder M., Weng S., Botstein D., SGD: saccharomyces genome database, Nucleic Acids Res., 26, 1, pp. 73-79, (1998)
[10]  
Xenarios I., Rice D.W., Salwinski L., Baron M.K., Marcotte E.M., Eisenberg D., DIP: the database of interacting proteins, Nucleic Acids Res., 28, 1, pp. 289-291, (2000)
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