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For: Teng Z, Guo M, Liu X, Dai Q, Wang C, Xuan P. Measuring gene functional similarity based on group-wise comparison of GO terms. Bioinformatics 2013;29:1424-32. [PMID: 23572412 DOI: 10.1093/bioinformatics/btt160] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
1
Mongardi S, Cascianelli S, Masseroli M. Biologically weighted LASSO: enhancing functional interpretability in gene expression data analysis. Bioinformatics 2024;40:btae605. [PMID: 39412436 PMCID: PMC11639179 DOI: 10.1093/bioinformatics/btae605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 09/12/2024] [Accepted: 10/14/2024] [Indexed: 11/01/2024]  Open
2
Jiang H, Wang Y, Yin C, Pan H, Chen L, Feng K, Chang Y, Sun H. SLIVER: Unveiling large scale gene regulatory networks of single-cell transcriptomic data through causal structure learning and modules aggregation. Comput Biol Med 2024;178:108690. [PMID: 38879931 DOI: 10.1016/j.compbiomed.2024.108690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/19/2024] [Accepted: 06/01/2024] [Indexed: 06/18/2024]
3
Pati SK, Gupta MK, Banerjee A, Mallik S, Zhao Z. PPIGCF: A Protein-Protein Interaction-Based Gene Correlation Filter for Optimal Gene Selection. Genes (Basel) 2023;14:genes14051063. [PMID: 37239423 DOI: 10.3390/genes14051063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/26/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023]  Open
4
Kartheeswaran KP, Rayan AXA, Varrieth GT. Enhanced disease-disease association with information enriched disease representation. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023;20:8892-8932. [PMID: 37161227 DOI: 10.3934/mbe.2023391] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
5
Tian Z, Fang H, Teng Z, Ye Y. GOGCN: Graph Convolutional Network on Gene Ontology for Functional Similarity Analysis of Genes. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:1053-1064. [PMID: 35687647 DOI: 10.1109/tcbb.2022.3181300] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
6
Ismail E, Gad W, Hashem M. HEC-ASD: a hybrid ensemble-based classification model for predicting autism spectrum disorder disease genes. BMC Bioinformatics 2022;23:554. [PMID: 36544099 PMCID: PMC9768984 DOI: 10.1186/s12859-022-05099-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022]  Open
7
Tian Z, Peng X, Fang H, Zhang W, Dai Q, Ye Y. MHADTI: predicting drug-target interactions via multiview heterogeneous information network embedding with hierarchical attention mechanisms. Brief Bioinform 2022;23:6761042. [PMID: 36242566 DOI: 10.1093/bib/bbac434] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/19/2022] [Accepted: 09/08/2022] [Indexed: 12/14/2022]  Open
8
Pati SK, Gupta MK, Shai R, Banerjee A, Ghosh A. Missing value estimation of microarray data using Sim-GAN. Knowl Inf Syst 2022. [DOI: 10.1007/s10115-022-01718-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
9
Tian Z, Fang H, Ye Y, Zhu Z. A novel gene functional similarity calculation model by utilizing the specificity of terms and relationships in gene ontology. BMC Bioinformatics 2022;23:47. [PMID: 35057740 PMCID: PMC8772239 DOI: 10.1186/s12859-022-04557-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/03/2022] [Indexed: 11/18/2022]  Open
10
Pesaranghader A, Matwin S, Sokolova M, Grenier JC, Beiko RG, Hussin J. OUP accepted manuscript. Bioinformatics 2022;38:3051-3061. [PMID: 35536192 PMCID: PMC9154256 DOI: 10.1093/bioinformatics/btac304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 02/12/2022] [Indexed: 11/24/2022]  Open
11
Paul M, Anand A. A New Family of Similarity Measures for Scoring Confidence of Protein Interactions Using Gene Ontology. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:19-30. [PMID: 34029194 DOI: 10.1109/tcbb.2021.3083150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
12
Nourani E. GoVec: Gene Ontology Representation Learning Using Weighted Heterogeneous Graph and Meta-Path. J Comput Biol 2021;28:1196-1207. [PMID: 34847734 DOI: 10.1089/cmb.2021.0069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
13
An Efficient Parallelized Ontology Network-Based Semantic Similarity Measure for Big Biomedical Document Clustering. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021;2021:7937573. [PMID: 34795792 PMCID: PMC8594978 DOI: 10.1155/2021/7937573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 10/11/2021] [Indexed: 01/03/2023]
14
Chen Q, Li Y, Tan K, Qiao Y, Pan S, Jiang T, Chen YPP. Network-based methods for gene function prediction. Brief Funct Genomics 2021;20:249-257. [PMID: 33686431 DOI: 10.1093/bfgp/elab006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/23/2022]  Open
15
Zhou G, Wang J, Zhang X, Guo M, Yu G. Predicting functions of maize proteins using graph convolutional network. BMC Bioinformatics 2020;21:420. [PMID: 33323113 PMCID: PMC7739465 DOI: 10.1186/s12859-020-03745-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]  Open
16
Zhong X, Rajapakse JC. Graph embeddings on gene ontology annotations for protein-protein interaction prediction. BMC Bioinformatics 2020;21:560. [PMID: 33323115 PMCID: PMC7739483 DOI: 10.1186/s12859-020-03816-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 10/13/2020] [Indexed: 01/15/2023]  Open
17
Parraga-Alava J, Inostroza-Ponta M. Influence of the go-based semantic similarity measures in multi-objective gene clustering algorithm performance. J Bioinform Comput Biol 2020;18:2050038. [PMID: 33148094 DOI: 10.1142/s0219720020500389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
18
Li JK, Li L, Li W, Wang Z, Gao F, Hu FY, Zhang S, Qu SF, Huang J, Wang LS, Wu JH, Chen F. Panel-based targeted exome sequencing reveals novel candidate susceptibility loci for age-related cataracts in Chinese Cohort. Mol Genet Genomic Med 2020;8:e1218. [PMID: 32337810 PMCID: PMC7336732 DOI: 10.1002/mgg3.1218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/05/2020] [Accepted: 02/25/2020] [Indexed: 01/19/2023]  Open
19
Zhao Y, Wang J, Chen J, Zhang X, Guo M, Yu G. A Literature Review of Gene Function Prediction by Modeling Gene Ontology. Front Genet 2020;11:400. [PMID: 32391061 PMCID: PMC7193026 DOI: 10.3389/fgene.2020.00400] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 03/30/2020] [Indexed: 12/14/2022]  Open
20
GO2Vec: transforming GO terms and proteins to vector representations via graph embeddings. BMC Genomics 2019;20:918. [PMID: 31874639 PMCID: PMC8424702 DOI: 10.1186/s12864-019-6272-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 11/12/2019] [Indexed: 12/13/2022]  Open
21
Cockroft NT, Cheng X, Fuchs JR. STarFish: A Stacked Ensemble Target Fishing Approach and its Application to Natural Products. J Chem Inf Model 2019;59:4906-4920. [PMID: 31589422 DOI: 10.1021/acs.jcim.9b00489] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
22
Yang Y, Fu X, Qu W, Xiao Y, Shen HB. MiRGOFS: a GO-based functional similarity measurement for miRNAs, with applications to the prediction of miRNA subcellular localization and miRNA-disease association. Bioinformatics 2019;34:3547-3556. [PMID: 29718114 DOI: 10.1093/bioinformatics/bty343] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 04/26/2018] [Indexed: 01/22/2023]  Open
23
Xue H, Peng J, Shang X. Predicting disease-related phenotypes using an integrated phenotype similarity measurement based on HPO. BMC SYSTEMS BIOLOGY 2019;13:34. [PMID: 30953559 PMCID: PMC6449884 DOI: 10.1186/s12918-019-0697-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
24
Rajakovich LJ, Pandelia ME, Mitchell AJ, Chang WC, Zhang B, Boal AK, Krebs C, Bollinger JM. A New Microbial Pathway for Organophosphonate Degradation Catalyzed by Two Previously Misannotated Non-Heme-Iron Oxygenases. Biochemistry 2019;58:1627-1647. [PMID: 30789718 PMCID: PMC6503667 DOI: 10.1021/acs.biochem.9b00044] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
25
Handling Big Data Scalability in Biological Domain Using Parallel and Distributed Processing: A Case of Three Biological Semantic Similarity Measures. BIOMED RESEARCH INTERNATIONAL 2019;2019:6750296. [PMID: 30809545 PMCID: PMC6369486 DOI: 10.1155/2019/6750296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/13/2019] [Indexed: 11/30/2022]
26
Acharya S, Saha S, Pradhan P. Novel symmetry-based gene-gene dissimilarity measures utilizing Gene Ontology: Application in gene clustering. Gene 2018;679:341-351. [PMID: 30184472 DOI: 10.1016/j.gene.2018.08.062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/21/2018] [Accepted: 08/21/2018] [Indexed: 11/25/2022]
27
Liu W, Liu J, Rajapakse JC. Gene Ontology Enrichment Improves Performances of Functional Similarity of Genes. Sci Rep 2018;8:12100. [PMID: 30108262 PMCID: PMC6092333 DOI: 10.1038/s41598-018-30455-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 07/25/2018] [Indexed: 12/23/2022]  Open
28
Peng J, Xue H, Hui W, Lu J, Chen B, Jiang Q, Shang X, Wang Y. An online tool for measuring and visualizing phenotype similarities using HPO. BMC Genomics 2018;19:571. [PMID: 30367579 PMCID: PMC6101067 DOI: 10.1186/s12864-018-4927-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]  Open
29
Liang X, Zhu L, Huang DS. Optimization of Gene Set Annotations Using Robust Trace-Norm Multitask Learning. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018;15:1016-1021. [PMID: 28391202 DOI: 10.1109/tcbb.2017.2690427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
30
Peng J, Zhang X, Hui W, Lu J, Li Q, Liu S, Shang X. Improving the measurement of semantic similarity by combining gene ontology and co-functional network: a random walk based approach. BMC SYSTEMS BIOLOGY 2018;12:18. [PMID: 29560823 PMCID: PMC5861498 DOI: 10.1186/s12918-018-0539-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
31
Peng J, Wang H, Lu J, Hui W, Wang Y, Shang X. Identifying term relations cross different gene ontology categories. BMC Bioinformatics 2017;18:573. [PMID: 29297309 PMCID: PMC5751813 DOI: 10.1186/s12859-017-1959-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]  Open
32
Tian Z, Guo M, Wang C, Liu X, Wang S. Refine gene functional similarity network based on interaction networks. BMC Bioinformatics 2017;18:550. [PMID: 29297381 PMCID: PMC5751769 DOI: 10.1186/s12859-017-1969-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]  Open
33
HashGO: hashing gene ontology for protein function prediction. Comput Biol Chem 2017;71:264-273. [DOI: 10.1016/j.compbiolchem.2017.09.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 09/25/2017] [Indexed: 10/18/2022]
34
Acharya S, Saha S, Nikhil N. Unsupervised gene selection using biological knowledge : application in sample clustering. BMC Bioinformatics 2017;18:513. [PMID: 29166852 PMCID: PMC5700545 DOI: 10.1186/s12859-017-1933-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/08/2017] [Indexed: 11/10/2022]  Open
35
Teng Z, Guo M, Liu X, Tian Z, Che K. Revealing protein functions based on relationships of interacting proteins and GO terms. J Biomed Semantics 2017;8:27. [PMID: 29297388 PMCID: PMC5763294 DOI: 10.1186/s13326-017-0139-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
36
Peng J, Li Q, Shang X. Investigations on factors influencing HPO-based semantic similarity calculation. J Biomed Semantics 2017;8:34. [PMID: 29297376 PMCID: PMC5763495 DOI: 10.1186/s13326-017-0144-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]  Open
37
Yu G, Lu C, Wang J. NoGOA: predicting noisy GO annotations using evidences and sparse representation. BMC Bioinformatics 2017;18:350. [PMID: 28732468 PMCID: PMC5521088 DOI: 10.1186/s12859-017-1764-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/14/2017] [Indexed: 01/11/2023]  Open
38
Exploring Approaches for Detecting Protein Functional Similarity within an Orthology-based Framework. Sci Rep 2017;7:381. [PMID: 28336965 PMCID: PMC5428484 DOI: 10.1038/s41598-017-00465-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 02/28/2017] [Indexed: 11/21/2022]  Open
39
Shui Y, Cho YR. Alignment of PPI Networks Using Semantic Similarity for Conserved Protein Complex Prediction. IEEE Trans Nanobioscience 2017;15:380-389. [PMID: 28113907 DOI: 10.1109/tnb.2016.2555802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
40
Pesquita C. Semantic Similarity in the Gene Ontology. Methods Mol Biol 2017;1446:161-173. [PMID: 27812942 DOI: 10.1007/978-1-4939-3743-1_12] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
41
Yu G, Luo W, Fu G, Wang J. Interspecies gene function prediction using semantic similarity. BMC SYSTEMS BIOLOGY 2016;10:121. [PMID: 28155711 PMCID: PMC5260010 DOI: 10.1186/s12918-016-0361-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
42
Tian Z, Wang C, Guo M, Liu X, Teng Z. An improved method for functional similarity analysis of genes based on Gene Ontology. BMC SYSTEMS BIOLOGY 2016;10:119. [PMID: 28155727 PMCID: PMC5259995 DOI: 10.1186/s12918-016-0359-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
43
Tian Z, Wang C, Guo M, Liu X, Teng Z. SGFSC: speeding the gene functional similarity calculation based on hash tables. BMC Bioinformatics 2016;17:445. [PMID: 27814675 PMCID: PMC5096311 DOI: 10.1186/s12859-016-1294-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 10/19/2016] [Indexed: 12/23/2022]  Open
44
Lu C, Wang J, Zhang Z, Yang P, Yu G. NoisyGOA: Noisy GO annotations prediction using taxonomic and semantic similarity. Comput Biol Chem 2016;65:203-211. [PMID: 27670689 DOI: 10.1016/j.compbiolchem.2016.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 09/07/2016] [Indexed: 10/21/2022]
45
A path-based measurement for human miRNA functional similarities using miRNA-disease associations. Sci Rep 2016;6:32533. [PMID: 27585796 PMCID: PMC5009308 DOI: 10.1038/srep32533] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/04/2016] [Indexed: 01/09/2023]  Open
46
Yu G, Fu G, Wang J, Zhu H. Predicting Protein Function via Semantic Integration of Multiple Networks. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2016;13:220-232. [PMID: 26800544 DOI: 10.1109/tcbb.2015.2459713] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
47
Pesaranghader A, Matwin S, Sokolova M, Beiko RG. simDEF: definition-based semantic similarity measure of gene ontology terms for functional similarity analysis of genes. Bioinformatics 2015;32:1380-7. [PMID: 26708333 DOI: 10.1093/bioinformatics/btv755] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/21/2015] [Indexed: 12/19/2022]  Open
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Cheng L, Li J, Hu Y, Jiang Y, Liu Y, Chu Y, Wang Z, Wang Y. Using Semantic Association to Extend and Infer Literature-Oriented Relativity Between Terms. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015;12:1219-1226. [PMID: 26684460 DOI: 10.1109/tcbb.2015.2430289] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
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Yu G, Zhu H, Domeniconi C, Liu J. Predicting protein function via downward random walks on a gene ontology. BMC Bioinformatics 2015;16:271. [PMID: 26310806 PMCID: PMC4551531 DOI: 10.1186/s12859-015-0713-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 08/20/2015] [Indexed: 12/24/2022]  Open
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Zhang SB, Lai JH. Semantic similarity measurement between gene ontology terms based on exclusively inherited shared information. Gene 2015;558:108-17. [DOI: 10.1016/j.gene.2014.12.062] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 12/15/2014] [Accepted: 12/24/2014] [Indexed: 11/25/2022]
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