[1]刘晓,陈璟,王子祥.用于成对PPI网络比对的分治与整合算法[J].智能系统学报,2022,17(5):960-968.[doi:10.11992/tis.202106001]
 LIU Xiao,CHEN Jing,WANG Zixiang.A divide-and-conquer and integration algorithm for pairwise alignment of PPI networks[J].CAAI Transactions on Intelligent Systems,2022,17(5):960-968.[doi:10.11992/tis.202106001]
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用于成对PPI网络比对的分治与整合算法

参考文献/References:
[1] HASHEMIFAR S, XU Jinbo. HubAlign: an accurate and efficient method for global alignment of protein-protein interaction networks[J]. Bioinformatics (Oxford, England), 2014, 30(17): i438–i444.
[2] MASKEY S, CHO Y R. LePrimAlign: local entropy-based alignment of PPI networks to predict conserved modules[J]. BMC genomics, 2019, 20(Suppl 9): 964.
[3] 苗孟君, 丁彦蕊. PPI网络比对用于植物乳杆菌的糖代谢研究[J]. 计算机工程与应用, 2018, 54(6): 49–54
MIAO mengjun, DING yanrui. PPI network alignment for study on carbohydrate metabolism of Lactobacillus Plantarum[J]. Computer engineering and applications, 2018, 54(6): 49–54
[4] GAO Jianliang, TIAN Ling, LYU Tengfei, et al. Protein2Vec: aligning multiple PPI networks with representation learning[J]. IEEE/ACM transactions on computational biology and bioinformatics, 2021, 18(1): 240–249.
[5] WOO H M, YOON B J. MONACO: accurate biological network alignment through optimal neighborhood matching between focal nodes[J]. Bioinformatics, 2020, 37(10): 1401–1410.
[6] MA Lijia, WANG Shiqiang, LIN Qiuzhen, et al. Multi-neighborhood learning for global alignment in biological networks[J]. IEEE/ACM transactions on computational biology and bioinformatics, 2021, 18(6): 2598–2611.
[7] KUCHAIEV O, MILENKOVIC T, MEMISEVIC V, et al. Topological network alignment uncovers biological function and phylogeny[J]. Journal of the royal society, interface, 2010, 7(50): 1341–1354.
[8] APARíCIO D, RIBEIRO P, MILENKOVI? T, et al. Temporal network alignment via GoT-WAVE[J]. Bioinformatics (Oxford, England), 2019, 35(18): 3527–3529.
[9] LLABRéS M, RIERA G, ROSSELLó F, et al. Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks[J]. BMC bioinformatics, 2020, 21(Suppl 6): 434.
[10] AYUB U, HAIDER I, NAVEED H. SAlign-a structure aware method for global PPI network alignment[J]. BMC bioinformatics, 2020, 21(1): 500.
[11] MAMANO N, HAYES W B. SANA: simulated annealing far outperforms many other search algorithms for biological network alignment[J]. Bioinformatics, 2017, 33(14): 2156–2164.
[12] WANG Shiqiang, MA Lijia, ZHANG Xiao. Adaptive artificial immune system for biological network alignment[M]//Intelligent Computing Theories and Application. Cham: Springer International Publishing, 2020: 560?570.
[13] VIJAYAN V, SARAPH V, MILENKOVI? T. MAGNA++: Maximizing Accuracy in Global Network Alignment via both node and edge conservation[J]. Bioinformatics, 2015, 31(14): 2409–2411.
[14] 陶斯涵, 丁彦蕊. 引入序列信息的残基相互作用网络比对算法[J]. 软件学报, 2019, 30(11): 3413–3426
DING yanrui, TAO sihan. Algorithm introduced sequence information for residue interaction network alignment[J]. Journal of software, 2019, 30(11): 3413–3426
[15] KAZEMI E, HASSANI H, GROSSGLAUSER M, et al. PROPER: global protein interaction network alignment through percolation matching[J]. BMC bioinformatics, 2016, 17(1): 1–16.
[16] HASHEMIFAR S, MA Jianzhu, NAVEED H, et al. ModuleAlign: module-based global alignment of protein-protein interaction networks[J]. Bioinformatics, 2016, 32(17): i658–i664.
[17] ZHU Lijuan, ZHANG Ju, ZHANG Yi, et al. NAIGO: an improved method to align PPI networks based on gene ontology and graphlets[J]. Frontiers in bioengineering and biotechnology, 2020, 8: 547.
[18] ALCALá A, ALBERICH R, LLABRéS M, et al. AligNet: alignment of protein-protein interaction networks[J]. BMC bioinformatics, 2020, 21(6): 1–22.
[19] GUZZI P H, MILENKOVIC T. Survey of local and global biological network alignment: the need to reconcile the two sides of the same coin[J]. Briefings in bioinformatics, 2018, 19(3): 472–481.
[20] ERTEN C. Global alignment of PPI networks[M]//Recent Advances in Biological Network Analysis. Cham: Springer International Publishing, 2020: 3-25.
[21] KALECKY K, CHO Y R. PrimAlign: PageRank-inspired Markovian alignment for large biological networks[J]. Bioinformatics (Oxford, England), 2018, 34(13): i537–i546.
[22] ASHBURNER M, BALL C A, BLAKE J A, et al. Gene ontology: tool for the unification of biology. The gene ontology consortium[J]. Nature genetics, 2000, 25(1): 25–29.
[23] KUHN H W. The Hungarian method for the assignment problem[J]. Naval research logistics quarterly, 1955, 2(1-2): 83–97.
[24] LEI Xiujuan, YANG Xiaoqin, FUJITA H. Random walk based method to identify essential proteins by integrating network topology and biological characteristics[J]. Knowledge-based systems, 2019, 167: 53–67.
[25] BORND?RFER R, HEISMANN O. The hypergraph assignment problem[J]. Discrete optimization, 2015, 15: 15–25.
[26] PARK D, SINGH R, BAYM M, et al. IsoBase: a database of functionally related proteins across PPI networks[J]. Nucleic acids research, 2011, 39: D295-D300.
[27] SAHRAEIAN S M E, YOON B J. A network synthesis model for generating protein interaction network families[J]. PLoS one, 2012, 7(8): e41474.
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备注/Memo

收稿日期:2021-06-01。
基金项目:江苏省青年科学基金项目(BK20150159);江苏省研究生科研创新计划(KYCX20_1939).
作者简介:刘晓,硕士研究生,主要研究方向为生物信息学;陈璟,副教授,博士,主要研究方向为复杂网络、室内定位。主持江苏省青年基金1项,参与国家自然科学基金3项,申请发明专利13项,授权发明专利4项,获得省部级奖4项,发表学术论文20余篇;王子祥,硕士研究生,主要研究方向为生物信息学
通讯作者:陈璟. E-mail: chenjing@jiangnan.edu.cn

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