Compact Integration of Multi-Network Topology for Functional Analysis of Genes
Tài liệu tham khảo
Ashburner, 2000, Gene ontology: Tool for the unification of biology, Nat. Genet., 25, 25, 10.1038/75556
Beauchamp, 1965, An improved index of centrality, Behav. Sci., 10, 161, 10.1002/bs.3830100205
Benjamini, 1995, Controlling the false discovery rate: A practical and powerful approach to multiple testing, J. R. Stat. Soc. B, 57, 289
Berger, 2013, Computational solutions for omics data, Nat. Rev. Genet., 14, 333, 10.1038/nrg3433
Bonacich, 1972, Factoring and weighting approaches to status scores and clique identification, J. Math. Sociol., 2, 113, 10.1080/0022250X.1972.9989806
Brandes, 2001, A faster algorithm for betweenness centrality, J. Math. Sociol., 25, 163, 10.1080/0022250X.2001.9990249
Brandes, 2005, Centrality measures based on current flow, 533
Cao, 2014, New directions for diffusion-based network prediction of protein function: Incorporating pathways with confidence, Bioinformatics, 30, i219, 10.1093/bioinformatics/btu263
Chan, 2011, Harnessing synthetic lethal interactions in anticancer drug discovery, Nat. Rev. Drug Discov., 10, 351, 10.1038/nrd3374
Chang, 2011, LIBSVM: A library for support vector machines, ACM Trans. Intell. Syst. Technol., 2, 27, 10.1145/1961189.1961199
Cheng, 2012, Prediction of drug-target interactions and drug repositioning via network-based inference, PLoS Comput. Biol., 8, e1002503, 10.1371/journal.pcbi.1002503
Clark, 2011, Analysis of protein function and its prediction from amino acid sequence, Proteins, 79, 2086, 10.1002/prot.23029
Costanzo, 2010, The genetic landscape of a cell, Science, 327, 425, 10.1126/science.1180823
Davis, 2006, The relationship between Precision-Recall and ROC curves, 233
Dutkowski, 2013, A gene ontology inferred from molecular networks, Nat. Biotechnol., 31, 38, 10.1038/nbt.2463
Enault, 2005, Phydbac “Gene Function Predictor”: A gene annotation tool based on genomic context analysis, BMC Bioinformatics, 6, 247, 10.1186/1471-2105-6-247
Franceschini, 2013, STRING v9.1: Protein-protein interaction networks, with increased coverage and integration, Nucleic Acids Res., 41, D808
Freeman, 1977, A set of measures of centrality based on betweenness, Sociometry, 40, 35, 10.2307/3033543
Garnett, 2012, Systematic identification of genomic markers of drug sensitivity in cancer cells, Nature, 483, 570, 10.1038/nature11005
Gaudet, 2011, Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium, Brief. Bioinform., 12, 449, 10.1093/bib/bbr042
Huttenhower, 2006, A scalable method for integration and functional analysis of multiple microarray datasets, Bioinformatics, 22, 2890, 10.1093/bioinformatics/btl492
Jerby-Arnon, 2014, Predicting cancer-specific vulnerability via data-driven detection of synthetic lethality, Cell, 158, 1199, 10.1016/j.cell.2014.07.027
Kim, 2013, YeastNet v3: A public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae, Nucleic Acids Res., 42, D731, 10.1093/nar/gkt981
Kramer, 2014, Inferring gene ontologies from pairwise similarity data, Bioinformatics, 30, i34, 10.1093/bioinformatics/btu282
Lee, 2011, Prioritizing candidate disease genes by network-based boosting of genome-wide association data, Genome Res., 21, 1109, 10.1101/gr.118992.110
Liao, 2009, IsoRankN: Spectral methods for global alignment of multiple protein networks, Bioinformatics, 25, i253, 10.1093/bioinformatics/btp203
Lin, 2007, A note on Platt’s probabilistic outputs for support vector machines, Mach. Learn., 68, 267, 10.1007/s10994-007-5018-6
Macropol, 2009, RRW: Repeated random walks on genome-scale protein networks for local cluster discovery, BMC Bioinformatics, 10, 283, 10.1186/1471-2105-10-283
Mikolov, T., Sutskever, I., and Chen, K. (2013). Distributed representations of words and phrases and their compositionality. Advances in Neural Information Processing Systems (NIPS). C.J.C. Burges, L. Bottou, M. Welling, Z. Ghahramani, K.Q. Weinberger, eds. Proceedings of the Neural Information Processing Systems, 3111–31119. Retrieved from http://papers.nips.cc/paper/5021-di.
Milenković, 2008, Uncovering biological network function via graphlet degree signatures, Cancer Inform., 6, 257, 10.4137/CIN.S680
Milenković, 2010, Optimal network alignment with graphlet degree vectors, Cancer Inform., 9, 121, 10.4137/CIN.S4744
Mostafavi, 2010, Fast integration of heterogeneous data sources for predicting gene function with limited annotation, Bioinformatics, 26, 1759, 10.1093/bioinformatics/btq262
Mostafavi, 2008, GeneMANIA: A real-time multiple association network integration algorithm for predicting gene function, Genome Biol., 9, S4, 10.1186/gb-2008-9-s1-s4
Mostafavi, 2012, Labeling nodes using three degrees of propagation, PLoS ONE, 7, e51947, 10.1371/journal.pone.0051947
Nepusz, 2012, Detecting overlapping protein complexes in protein-protein interaction networks, Nat. Methods, 9, 471, 10.1038/nmeth.1938
Page, L., Brin, S., Motwani, R., and Winograd, T. (1999). The PageRank citation ranking: Bringing order to the Web. Technical Report. Stanford Infolab. Retrieved from http://ilpubs.stanford.edu:8090/422.
Pal, 2005, Inference of protein function from protein structure, Structure, 13, 121, 10.1016/j.str.2004.10.015
Paladugu, 2008, Mining protein networks for synthetic genetic interactions, BMC Bioinformatics, 9, 426, 10.1186/1471-2105-9-426
Pandey, 2010, An integrative multi-network and multi-classifier approach to predict genetic interactions, PLoS Comput. Biol., 6, e1000928, 10.1371/journal.pcbi.1000928
Park, 2011, Resolving the structure of interactomes with hierarchical agglomerative clustering, BMC Bioinformatics, 12, S44, 10.1186/1471-2105-12-S1-S44
Pedregosa, 2011, Scikit-learn: Machine learning in Python, J. Mach. Learn. Res., 12, 2825
Platt, 1999, Probabilistic outputs for support vector machines and comparisons to regularized likelihood methods, Advances in Large Margin Classifiers, 10, 61
Plo, 2003, Association of XRCC1 and tyrosyl DNA phosphodiesterase (Tdp1) for the repair of topoisomerase I-mediated DNA lesions, DNA Repair (Amst.), 2, 1087, 10.1016/S1568-7864(03)00116-2
Radivojac, 2013, A large-scale evaluation of computational protein function prediction, Nat. Methods, 10, 221, 10.1038/nmeth.2340
Ruepp, 2004, The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes, Nucleic Acids Res., 32, 5539, 10.1093/nar/gkh894
Schwikowski, 2000, A network of protein-protein interactions in yeast, Nat. Biotechnol., 18, 1257, 10.1038/82360
Singh, 2008, Global alignment of multiple protein interaction networks with application to functional orthology detection, Proc. Natl. Acad. Sci. USA, 105, 12763, 10.1073/pnas.0806627105
Sneath, 1973
Stephenson, 1989, Rethinking centrality: Methods and examples, Soc. Networks, 11, 1, 10.1016/0378-8733(89)90016-6
Tong, 2006, Fast random walk with restart and its applications, 613
Wang, 2012, RIDDLE: Reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network, Genome Biol., 13, R125, 10.1186/gb-2012-13-12-r125
Wang, 2015, Exploiting ontology graph for predicting sparsely annotated gene function, Bioinformatics, 31, i357, 10.1093/bioinformatics/btv260
Watts, 1998, Collective dynamics of ‘small-world’ networks, Nature, 393, 440, 10.1038/30918
Wong, 2004, Combining biological networks to predict genetic interactions, Proc. Natl. Acad. Sci. USA, 101, 15682, 10.1073/pnas.0406614101
Wong, 2015, IMP 2.0: A multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks, Nucleic Acids Res., 43, W128, 10.1093/nar/gkv486
Xu, 2014, TXNL1-XRCC1 pathway regulates cisplatin-induced cell death and contributes to resistance in human gastric cancer, Cell Death Dis., 5, e1055, 10.1038/cddis.2014.27
Yu, 2013, Review of biological network data and its applications, Genomics Inform., 11, 200, 10.5808/GI.2013.11.4.200
Yu, 2016, Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems, Cell Syst., 2, 77, 10.1016/j.cels.2016.02.003
Zhang, A., Ramanathan, M., Hwang, W., and Cho, Y. (2010). Bridging centrality: A concept and formula to identify bridging nodes in scale-free networks. U.S. patent 7,808,921.
Zhu, 1997, Algorithm 778: L-BFGS-B: Fortran subroutines for large-scale bound-constrained optimization, ACM Trans. Math. Softw., 23, 550, 10.1145/279232.279236
Žitnik, 2015, Data fusion by matrix factorization, IEEE Trans. Pattern Anal. Mach. Intell., 37, 41, 10.1109/TPAMI.2014.2343973
Žitnik, 2015, Gene prioritization by compressive data fusion and chaining, PLoS Comput. Biol., 11, e1004552, 10.1371/journal.pcbi.1004552