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For: Fu G, Wang J, Yang B, Yu G. NegGOA: negative GO annotations selection using ontology structure. Bioinformatics 2016;32:2996-3004. [PMID: 27318205 DOI: 10.1093/bioinformatics/btw366] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/01/2016] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
1
Zou HT, Ji BY, Xie XL. A multi-source molecular network representation model for protein-protein interactions prediction. Sci Rep 2024;14:6184. [PMID: 38485942 PMCID: PMC10940665 DOI: 10.1038/s41598-024-56286-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/05/2024] [Indexed: 03/18/2024]  Open
2
Yu G, Huang Q, Zhang X, Guo M, Wang J. Tissue Specificity Based Isoform Function Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:3048-3059. [PMID: 34185647 DOI: 10.1109/tcbb.2021.3093167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
3
Yu G, Yang Y, Yan Y, Guo M, Zhang X, Wang J. DeepIDA: Predicting Isoform-Disease Associations by Data Fusion and Deep Neural Networks. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:2166-2176. [PMID: 33571094 DOI: 10.1109/tcbb.2021.3058801] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
4
Zhang Y, Duan L, Zheng H, Li-Ling J, Qin R, Chen Z, He C, Wang T. Mining Similar Aspects for Gene Similarity Explanation Based on Gene Information Network. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:1734-1746. [PMID: 33259307 DOI: 10.1109/tcbb.2020.3041559] [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]
5
Liu L, Zhu S. Computational Methods for Prediction of Human Protein-Phenotype Associations: A Review. PHENOMICS (CHAM, SWITZERLAND) 2021;1:171-185. [PMID: 36939789 PMCID: PMC9590544 DOI: 10.1007/s43657-021-00019-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/05/2021] [Accepted: 06/16/2021] [Indexed: 12/01/2022]
6
Zhao Y, Wang J, Guo M, Zhang X, Yu G. Cross-Species Protein Function Prediction with Asynchronous-Random Walk. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;18:1439-1450. [PMID: 31562099 DOI: 10.1109/tcbb.2019.2943342] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
7
Yu G, Zeng J, Wang J, Zhang H, Zhang X, Guo M. Imbalance deep multi‐instance learning for predicting isoform–isoform interactions. INT J INTELL SYST 2021. [DOI: 10.1002/int.22402] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
8
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
9
Makrodimitris S, van Ham RCHJ, Reinders MJT. Automatic Gene Function Prediction in the 2020's. Genes (Basel) 2020;11:E1264. [PMID: 33120976 PMCID: PMC7692357 DOI: 10.3390/genes11111264] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 02/06/2023]  Open
10
Yu G, Wang K, Domeniconi C, Guo M, Wang J. Isoform function prediction based on bi-random walks on a heterogeneous network. Bioinformatics 2020;36:303-310. [PMID: 31250882 DOI: 10.1093/bioinformatics/btz535] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 06/21/2019] [Accepted: 06/26/2019] [Indexed: 01/29/2023]  Open
11
Warwick Vesztrocy A, Dessimoz C. Benchmarking gene ontology function predictions using negative annotations. Bioinformatics 2020;36:i210-i218. [PMID: 32657372 PMCID: PMC7355306 DOI: 10.1093/bioinformatics/btaa466] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
12
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
13
Yu G, Wang K, Fu G, Guo M, Wang J. NMFGO: Gene Function Prediction via Nonnegative Matrix Factorization with Gene Ontology. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020;17:238-249. [PMID: 30059316 DOI: 10.1109/tcbb.2018.2861379] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
14
Mazurenko S, Prokop Z, Damborsky J. Machine Learning in Enzyme Engineering. ACS Catal 2019. [DOI: 10.1021/acscatal.9b04321] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
15
Plyusnin I, Holm L, Törönen P. Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences. PLoS Comput Biol 2019;15:e1007419. [PMID: 31682632 PMCID: PMC6855565 DOI: 10.1371/journal.pcbi.1007419] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/14/2019] [Accepted: 09/24/2019] [Indexed: 11/18/2022]  Open
16
Lou W, Pi R, Wang H, Ju Y. Low-cost similarity calculation on ontology fusion in knowledge bases. J Inf Sci 2019. [DOI: 10.1177/0165551519870456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
17
Zhang L, Yu G, Xia D, Wang J. Protein–protein interactions prediction based on ensemble deep neural networks. Neurocomputing 2019. [DOI: 10.1016/j.neucom.2018.02.097] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
18
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]
19
Rifaioglu AS, Doğan T, Saraç ÖS, Ersahin T, Saidi R, Atalay MV, Martin MJ, Cetin-Atalay R. Large-scale automated function prediction of protein sequences and an experimental case study validation on PTEN transcript variants. Proteins 2017;86:135-151. [PMID: 29098713 DOI: 10.1002/prot.25416] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 10/24/2017] [Accepted: 11/01/2017] [Indexed: 12/24/2022]
20
Notaro M, Schubach M, Robinson PN, Valentini G. Prediction of Human Phenotype Ontology terms by means of hierarchical ensemble methods. BMC Bioinformatics 2017;18:449. [PMID: 29025394 PMCID: PMC5639780 DOI: 10.1186/s12859-017-1854-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 10/02/2017] [Indexed: 03/12/2023]  Open
21
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
22
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
23
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]
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