在做毕设时收集了很多论文,过程繁琐,在这将收集到的论文和部分开源代码整理起来,并没有找全,部分代码链接失效,仅做参考。
一、PPI网络可视化软件下载链接:
Cytoscape: An Open Source Platform for Complex Network Analysis and Visualization
二、PPI网络文件网站:
- PANTHER:http://pantherdb.org/
- BIOGRID:BioGRID | Database of Protein, Chemical, and Genetic Interactions
三、论文资料:
【2004年】
1、NetworkBLAST: Conserved patterns of protein interactionin multiple species——局部+多网络+多对多【论文】【无】
2、PathBLAST: a tool for alignment of protein interaction networks——局部+多网络+多对多【论文】【代码】
3、MaWISH: Pairwise Alignment of Protein Interaction Networks——局部+多网络+多对多【论文】【无】
【2006年】
1、Græmlin: General and robust alignment of multiple large interaction networks——局部+多网络+多对多【论文】【无】
【2008年】
1、IsoRank: Global alignment of multiple protein interaction networks with application to functional orthology detection——全局+成对网络+一对一【论文】【网站】
2、IsoRankN: spectral methods for global alignment of multiple protein networks——全局+多网络+多对多【论文】【网站】
【2009年】
1、Domain-oriented edge-based alignment of protein interaction networks——局部+多网络+多对多【论文】【代码】
2、GNA: Global alignment of protein–protein interaction networks by graph matching methods——全局+成对网络+一对一【论文】【无】
3、NATALIE: A new graph-based method for pairwise global network alignment——全局+成对网络+一对一【论文】【无】
【2010年】
1、GRAAL: Topological network alignment uncovers biological function and phylogeny——全局+成对网络+一对一【论文】【代码】
2、MI-GRAAL: Integrative Network Alignment Reveals Large Regions of Global Network Similarity in Yeast and Human——全局+成对网络+一对一【论文】【软件】
3、H-GRAAL: Optimal network alignment with graphlet degree vectors——全局+成对网络+一对一【论文】【无】
【2012年】
1、C-GRAAL: Common-Neighbors-Based Global GRAph ALignment of Biological Networks——全局+成对网络+一对一【论文】【软件】
2、GHOST: Global network alignment using multiscale spectral signatures——全局+成对网络+一对一【论文】【代码】
3、AlignNemo: A Local Network Alignment Method to Integrate Homology and Topology——局部+成对网络+多对多【论文】【软件】
4、GraphAlignment: Bayesian pairwise alignment of biological networks——全局+成对网络+一对一【论文】【无】
【2013年】
1、NETAL: a new graph-based method for global alignment of protein–protein interaction networks——全局+成对网络+一对一【论文】【代码】
2、BEAMS: BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks——全局+多网络+多对多【论文】【代码】
3、NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks——全局+多网络+多对多【论文】【代码】
4、SPINAL: scalable protein interaction network alignment——全局+成对网络+一对一【论文】【代码】
5、PISwap: Optimizing a global alignment of protein interaction networks——全局+成对网络+一对一【论文】【代码】
【2014年】
1、Pin-Align: A New Dynamic Programming Approach to Align Protein-Protein Interaction Networks——局部+成对网络+一对一【论文】【无】
2、DualAligner: a dual alignment-based strategy to align protein interaction networks——局部+成对网络+一对一【论文】【代码】
3、HubAlign: an accurate and efficient method for global alignment of protein–protein interaction networks——全局+成对网络+一对一【论文】【代码】
4、MAGNA: Maximizing Accuracy in Global Network Alignment——全局+成对网络+一对一【论文】【代码】
【2015年】
1、L-GRAAL: Lagrangian graphlet-based network aligner——全局+成对网络+一对一【论文】【软件】
2、ACOGA: M Ộ T THU Ậ T TOÁN T Ố I Ư U Đ ÀN KI Ế N DÓNG HÀNG TOÀN C Ụ C M Ạ NG T ƯƠ NG TÁC PROTEIN——全局+成对网络+一对一【论文】【无】
3、CLMNA: Multi-Neighborhood Learning for Global Alignment in Biological Networks——全局+成对网络+一对一【论文】【无】
4、MAGNA++: Maximizing Accuracy in Global Network Alignment via both node and edge conservation——全局+成对网络+一对一【论文】【网站】
5、FASTAn: An efficient algorithm for global alignment of protein-protein interaction networks——全局+成对网络+一对一【论文】【无】
6、Fuse: multiple network alignment via data fusion——全局+多网络+一对一【论文】【软件】
7、LocalAli: an evolutionary-based local alignment approach to identify functionally conserved modules in multiple networks——局部+多网络+多对多【论文】【代码】
8、SiPAN: simultaneous prediction and alignment of protein–protein interaction networks——全局+成对网络+一对一【论文】【代码】
9、Optnetalign: multiobjective memetic algorithm for PPI network alignment——局部+成对网络+多对多【论文】【代码】
【2016年】
1、ConvexAlign: Joint Alignment of Multiple Protein-Protein Interaction Networks via Convex Optimization——全局+多网络+一对一【论文】【无】
2、SMAL: Global multiple protein-protein interaction network alignment by combining pairwise network alignments——全局+成对网络+一对一【论文】【无】
3、ModuleAlign: module-based global alignment of protein-protein interaction networks——全局+成对网络+一对一【论文】【代码】
4、ACOGNA: An efficient method for protein-protein interaction network alignment——全局+成对网络+一对一【论文】【无】
5、PROPER: global protein interaction network alignment through percolation matching——全局+成对网络+一对一【论文】【代码】
6、LNA-GNA: Local versus global biological network alignment——一种度量方法【论文】【代码】
7、MeAlign: Global Biological Network Alignment by Using Efficient Memetic Algorithm——局部【论文】【无】
【2017年】
1、BalanceAli: Multiple PPI Network Alignment With Balanced High Coverage and Consistency——全局+多网络+多对多【论文】【无】
2、DynaMAGNA++: Alignment of dynamic networks——动态【论文】【代码】
3、INDEX: Incremental depth extension approach for protein–protein interaction networks alignment——全局+成对网络+一对一【论文】【代码】
4、Ulign: Unified Alignment of Protein-Protein Interaction Networks——全局+成对网络+一对多【论文】【软件】
5、SANA: simulated annealing far outperforms many other search algorithms for biological network alignment——全局+成对网络+一对一【论文】【代码】
【2018年】
1、MAPPIN: A Novel Computational Approach for Global Alignment for Multiple Biological Networks——全局【论文】【无】
2、MultiMAGNA++: Multiple Network Alignment via MultiMAGNA++——全局+多网络【论文】【代码】
3、IBNAL: Index-Based Network Aligner of Protein-Protein Interaction Networks——全局+成对网络+一对一【论文】【无】
4、PrimAlign: PageRank-inspired Markovian alignment for large biological networks——全局+成对网络+一对一【论文】【代码】
5、GLAlign: A Novel Algorithm for Local Network Alignment——局部【论文】【代码】
6、ConnectedAlign: a PPI network alignment method for identifying conserved protein complexes across multiple species——全局+多网络+多对多【论文】【无】
7、DynaWAVE: Aligning dynamic networks with DynaWAVE——动态【论文】【代码】
【2019年】
1、LePrimAlign: local entropy-based alignment of PPI networks to predict conserved modules——局部+成对网络+多对多【论文】【无】
2、ACOGNA2: A novel algorithm for maximizing accuracy in global network alignment ——全局+成对网络+一对一【论文】【无】
3、NetCoffee2: A novel algorithm for alignment of multiple PPI networks based on simulated annealing——全局+成对、多网络+多对多【论文】【代码】
【2020年】
1、GPPIAL: A New Global PPI Network Aligner Based on Orthologs ——全局+成对网络+一对一【论文】【代码】
2、SAlign–a structure aware method for global PPI network alignment——全局+成对网络+一对一【论文】【代码】
3、AligNet: alignment of protein-protein interaction networks | BMC Bioinformatics——全局+成对网络+一对一【论文】【代码】
4、LNA: Using Network Embeddings for Improving Network Alignment——局部【论文】【无】
5、SL-GLAlign: improving local alignment of biological networks through simulated annealing——局部【论文】【代码】
6、ILALign: Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks——全局+成对网络+一对一【论文】【无】
7、ImAlign: Adaptive Artificial Immune System for Biological Network Alignment【论文】【无】
8、MPGM: Scalable and Accurate Multiple Network Alignment ——多网络【论文】【无】
【2021年】
1、MONACO: accurate biological network alignment through optimal neighborhood matching between focal nodes——局部+成对、多网络+一对一【论文】【代码】
2、BatAlign: Pairwise Biological Network Alignment Based on Discrete Bat Algorithm——全局+成对网络+一对一【论文】【无】
3、Protein2Vec: Aligning Multiple PPI Networks with Representation Learning——多网络【论文】【无】
4、RENA: The protein-protein interaction network alignment using recurrent neural network——全局+成对网络+一对一【论文】【无】
【2022年】
1、BioAlign: An Accurate Global PPI Network AlignmentAlgorithm——全局+成对网络+一对一【论文】【无】
【2023年】
1、AntNetAlign: Ant Colony Optimization for Network Alignment——全局+成对网络+一对一【论文】【代码】