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For: Kulmanov M, Khan MA, Hoehndorf R, Wren J. DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier. Bioinformatics 2018;34:660-668. [PMID: 29028931 PMCID: PMC5860606 DOI: 10.1093/bioinformatics/btx624] [Citation(s) in RCA: 254] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 09/27/2017] [Indexed: 12/29/2022]  Open
Number Cited by Other Article(s)
201
Poverennaya E, Kiseleva O, Romanova A, Pyatnitskiy M. Predicting Functions of Uncharacterized Human Proteins: From Canonical to Proteoforms. Genes (Basel) 2020;11:E677. [PMID: 32575886 PMCID: PMC7350264 DOI: 10.3390/genes11060677] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/09/2020] [Accepted: 06/19/2020] [Indexed: 01/22/2023]  Open
202
ElAbd H, Bromberg Y, Hoarfrost A, Lenz T, Franke A, Wendorff M. Amino acid encoding for deep learning applications. BMC Bioinformatics 2020;21:235. [PMID: 32517697 PMCID: PMC7285590 DOI: 10.1186/s12859-020-03546-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 05/12/2020] [Indexed: 12/25/2022]  Open
203
Mutwil M. Computational approaches to unravel the pathways and evolution of specialized metabolism. CURRENT OPINION IN PLANT BIOLOGY 2020;55:38-46. [PMID: 32200228 DOI: 10.1016/j.pbi.2020.01.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/19/2020] [Accepted: 01/31/2020] [Indexed: 05/13/2023]
204
Crawford J, Greene CS. Incorporating biological structure into machine learning models in biomedicine. Curr Opin Biotechnol 2020;63:126-134. [PMID: 31962244 PMCID: PMC7308204 DOI: 10.1016/j.copbio.2019.12.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 12/19/2022]
205
You R, Yao S, Xiong Y, Huang X, Sun F, Mamitsuka H, Zhu S. NetGO: improving large-scale protein function prediction with massive network information. Nucleic Acids Res 2020;47:W379-W387. [PMID: 31106361 PMCID: PMC6602452 DOI: 10.1093/nar/gkz388] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/24/2019] [Accepted: 05/01/2019] [Indexed: 01/19/2023]  Open
206
Jin S, Zeng X, Xia F, Huang W, Liu X. Application of deep learning methods in biological networks. Brief Bioinform 2020;22:1902-1917. [PMID: 32363401 DOI: 10.1093/bib/bbaa043] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 02/19/2020] [Accepted: 03/05/2020] [Indexed: 01/07/2023]  Open
207
Cai Y, Wang J, Deng L. SDN2GO: An Integrated Deep Learning Model for Protein Function Prediction. Front Bioeng Biotechnol 2020;8:391. [PMID: 32411695 PMCID: PMC7201018 DOI: 10.3389/fbioe.2020.00391] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 04/07/2020] [Indexed: 02/01/2023]  Open
208
Sangphukieo A, Laomettachit T, Ruengjitchatchawalya M. Photosynthetic protein classification using genome neighborhood-based machine learning feature. Sci Rep 2020;10:7108. [PMID: 32346070 PMCID: PMC7189237 DOI: 10.1038/s41598-020-64053-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 04/07/2020] [Indexed: 11/08/2022]  Open
209
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
210
Thapa N, Chaudhari M, McManus S, Roy K, Newman RH, Saigo H, Kc DB. DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction. BMC Bioinformatics 2020;21:63. [PMID: 32321437 PMCID: PMC7178942 DOI: 10.1186/s12859-020-3342-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 01/08/2020] [Indexed: 01/15/2023]  Open
211
Strodthoff N, Wagner P, Wenzel M, Samek W. UDSMProt: universal deep sequence models for protein classification. Bioinformatics 2020;36:2401-2409. [PMID: 31913448 PMCID: PMC7178389 DOI: 10.1093/bioinformatics/btaa003] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/13/2019] [Accepted: 01/02/2020] [Indexed: 01/03/2023]  Open
212
Peng J, Xue H, Wei Z, Tuncali I, Hao J, Shang X. Integrating multi-network topology for gene function prediction using deep neural networks. Brief Bioinform 2020;22:2096-2105. [PMID: 32249297 DOI: 10.1093/bib/bbaa036] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/09/2020] [Accepted: 02/25/2020] [Indexed: 01/18/2023]  Open
213
Fabris F, Palmer D, Salama KM, de Magalhães JP, Freitas AA. Using deep learning to associate human genes with age-related diseases. Bioinformatics 2020;36:2202-2208. [PMID: 31845988 PMCID: PMC7141856 DOI: 10.1093/bioinformatics/btz887] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/06/2019] [Accepted: 12/13/2019] [Indexed: 11/15/2022]  Open
214
The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization. Nat Ecol Evol 2020;4:841-852. [PMID: 32231327 PMCID: PMC7269910 DOI: 10.1038/s41559-020-1166-x] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 02/27/2020] [Indexed: 12/20/2022]
215
Liu C, Ma Y, Zhao J, Nussinov R, Zhang YC, Cheng F, Zhang ZK. Computational network biology: Data, models, and applications. PHYSICS REPORTS 2020;846:1-66. [DOI: 10.1016/j.physrep.2019.12.004] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
216
Makrodimitris S, van Ham RCHJ, Reinders MJT. Improving protein function prediction using protein sequence and GO-term similarities. Bioinformatics 2020;35:1116-1124. [PMID: 30169569 PMCID: PMC6449755 DOI: 10.1093/bioinformatics/bty751] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 07/04/2018] [Accepted: 08/28/2018] [Indexed: 12/26/2022]  Open
217
Yue X, Wang Z, Huang J, Parthasarathy S, Moosavinasab S, Huang Y, Lin SM, Zhang W, Zhang P, Sun H. Graph embedding on biomedical networks: methods, applications and evaluations. Bioinformatics 2020;36:1241-1251. [PMID: 31584634 PMCID: PMC7703771 DOI: 10.1093/bioinformatics/btz718] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 08/25/2019] [Accepted: 09/26/2019] [Indexed: 01/12/2023]  Open
218
de Jongh RP, van Dijk AD, Julsing MK, Schaap PJ, de Ridder D. Designing Eukaryotic Gene Expression Regulation Using Machine Learning. Trends Biotechnol 2020;38:191-201. [DOI: 10.1016/j.tibtech.2019.07.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/12/2019] [Accepted: 07/19/2019] [Indexed: 12/11/2022]
219
Mishra R, Mohapatra R, Mahanty B, Joshi RK. Analysis of microRNAs and their targets from onion (Allium cepa) using genome survey sequences (GSS) and expressed sequence tags (ESTs). Bioinformation 2019;15:907-917. [PMID: 32256010 PMCID: PMC7088424 DOI: 10.6026/97320630015907] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 12/30/2019] [Accepted: 12/31/2019] [Indexed: 01/31/2023]  Open
220
Shi Q, Chen W, Huang S, Wang Y, Xue Z. Deep learning for mining protein data. Brief Bioinform 2019;22:194-218. [PMID: 31867611 DOI: 10.1093/bib/bbz156] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/21/2019] [Accepted: 11/07/2019] [Indexed: 01/16/2023]  Open
221
Functional Gene Network of Prenyltransferases in Arabidopsis thaliana. Molecules 2019;24:molecules24244556. [PMID: 31842481 PMCID: PMC6943727 DOI: 10.3390/molecules24244556] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 12/17/2022]  Open
222
Wang J, Zhang J, Cai Y, Deng L. DeepMiR2GO: Inferring Functions of Human MicroRNAs Using a Deep Multi-Label Classification Model. Int J Mol Sci 2019;20:E6046. [PMID: 31801264 PMCID: PMC6928926 DOI: 10.3390/ijms20236046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 01/08/2023]  Open
223
Bonetta R, Valentino G. Machine learning techniques for protein function prediction. Proteins 2019;88:397-413. [PMID: 31603244 DOI: 10.1002/prot.25832] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/05/2019] [Accepted: 09/17/2019] [Indexed: 12/17/2022]
224
Mishra S, Rastogi YP, Jabin S, Kaur P, Amir M, Khatun S. A deep learning ensemble for function prediction of hypothetical proteins from pathogenic bacterial species. Comput Biol Chem 2019;83:107147. [PMID: 31698160 DOI: 10.1016/j.compbiolchem.2019.107147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/05/2019] [Accepted: 10/09/2019] [Indexed: 01/06/2023]
225
Mahapatra M, Mahanty B, Joshi RK. Genome wide identification and functional assignments of C2H2 Zinc-finger family transcription factors in Dichanthelium oligosanthes. Bioinformation 2019;15:689-696. [PMID: 31787818 PMCID: PMC6859702 DOI: 10.6026/97320630015689] [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] [Received: 04/15/2019] [Revised: 10/16/2019] [Accepted: 10/16/2019] [Indexed: 12/23/2022]  Open
226
Zitnik M, Nguyen F, Wang B, Leskovec J, Goldenberg A, Hoffman MM. Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities. AN INTERNATIONAL JOURNAL ON INFORMATION FUSION 2019;50:71-91. [PMID: 30467459 PMCID: PMC6242341 DOI: 10.1016/j.inffus.2018.09.012] [Citation(s) in RCA: 262] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
227
Investigation of machine learning techniques on proteomics: A comprehensive survey. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019;149:54-69. [PMID: 31568792 DOI: 10.1016/j.pbiomolbio.2019.09.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/16/2019] [Accepted: 09/23/2019] [Indexed: 11/21/2022]
228
Nakano FK, Lietaert M, Vens C. Machine learning for discovering missing or wrong protein function annotations : A comparison using updated benchmark datasets. BMC Bioinformatics 2019;20:485. [PMID: 31547800 PMCID: PMC6755698 DOI: 10.1186/s12859-019-3060-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/27/2019] [Indexed: 12/22/2022]  Open
229
Kulmanov M, Hoehndorf R. DeepGOPlus: improved protein function prediction from sequence. Bioinformatics 2019;36:422-429. [PMID: 31350877 PMCID: PMC9883727 DOI: 10.1093/bioinformatics/btz595] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/01/2019] [Accepted: 07/24/2019] [Indexed: 02/03/2023]  Open
230
Chen H, Shaw D, Zeng J, Bu D, Jiang T. DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning. Bioinformatics 2019;35:i284-i294. [PMID: 31510699 PMCID: PMC6612874 DOI: 10.1093/bioinformatics/btz367] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]  Open
231
Lv Z, Ao C, Zou Q. Protein Function Prediction: From Traditional Classifier to Deep Learning. Proteomics 2019;19:e1900119. [PMID: 31187588 DOI: 10.1002/pmic.201900119] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 05/20/2019] [Indexed: 11/12/2022]
232
Teso S, Masera L, Diligenti M, Passerini A. Combining learning and constraints for genome-wide protein annotation. BMC Bioinformatics 2019;20:338. [PMID: 31208327 PMCID: PMC6580517 DOI: 10.1186/s12859-019-2875-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 05/03/2019] [Indexed: 11/28/2022]  Open
233
Saha S, Chatterjee P, Basu S, Nasipuri M, Plewczynski D. FunPred 3.0: improved protein function prediction using protein interaction network. PeerJ 2019;7:e6830. [PMID: 31198622 PMCID: PMC6535044 DOI: 10.7717/peerj.6830] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 03/21/2019] [Indexed: 11/23/2022]  Open
234
Zhang F, Song H, Zeng M, Li Y, Kurgan L, Li M. DeepFunc: A Deep Learning Framework for Accurate Prediction of Protein Functions from Protein Sequences and Interactions. Proteomics 2019;19:e1900019. [PMID: 30941889 DOI: 10.1002/pmic.201900019] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/18/2019] [Indexed: 01/06/2023]
235
Zhu J, Zhao Q, Katsevich E, Sabatti C. Exploratory Gene Ontology Analysis with Interactive Visualization. Sci Rep 2019;9:7793. [PMID: 31127124 PMCID: PMC6534545 DOI: 10.1038/s41598-019-42178-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/14/2019] [Indexed: 12/17/2022]  Open
236
Stephenson N, Shane E, Chase J, Rowland J, Ries D, Justice N, Zhang J, Chan L, Cao R. Survey of Machine Learning Techniques in Drug Discovery. Curr Drug Metab 2019;20:185-193. [DOI: 10.2174/1389200219666180820112457] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 01/01/2018] [Accepted: 03/19/2018] [Indexed: 12/19/2022]
237
Sureyya Rifaioglu A, Doğan T, Jesus Martin M, Cetin-Atalay R, Atalay V. DEEPred: Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural Networks. Sci Rep 2019;9:7344. [PMID: 31089211 PMCID: PMC6517386 DOI: 10.1038/s41598-019-43708-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 04/27/2019] [Indexed: 01/22/2023]  Open
238
Leveraging implicit knowledge in neural networks for functional dissection and engineering of proteins. NAT MACH INTELL 2019. [DOI: 10.1038/s42256-019-0049-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
239
Nelson W, Zitnik M, Wang B, Leskovec J, Goldenberg A, Sharan R. To Embed or Not: Network Embedding as a Paradigm in Computational Biology. Front Genet 2019;10:381. [PMID: 31118945 PMCID: PMC6504708 DOI: 10.3389/fgene.2019.00381] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/09/2019] [Indexed: 12/20/2022]  Open
240
Deep learning in bioinformatics: Introduction, application, and perspective in the big data era. Methods 2019;166:4-21. [PMID: 31022451 DOI: 10.1016/j.ymeth.2019.04.008] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 03/23/2019] [Accepted: 04/15/2019] [Indexed: 12/13/2022]  Open
241
From Genotype to Phenotype: Augmenting Deep Learning with Networks and Systems Biology. ACTA ACUST UNITED AC 2019;15:68-73. [PMID: 31777764 DOI: 10.1016/j.coisb.2019.04.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
242
Nanda S, Hussain S. Genome-wide identification of the SPL gene family in Dichanthelium oligosanthes. Bioinformation 2019;15:165-171. [PMID: 31354191 PMCID: PMC6637398 DOI: 10.6026/97320630015165] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/12/2019] [Accepted: 01/12/2019] [Indexed: 11/23/2022]  Open
243
Wu J, Yin Q, Zhang C, Geng J, Wu H, Hu H, Ke X, Zhang Y. Function Prediction for G Protein-Coupled Receptors through Text Mining and Induction Matrix Completion. ACS OMEGA 2019;4:3045-3054. [PMID: 31459527 PMCID: PMC6649004 DOI: 10.1021/acsomega.8b02454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 01/11/2019] [Indexed: 06/10/2023]
244
Taha K, Iraqi Y, Al Aamri A. Predicting protein functions by applying predicate logic to biomedical literature. BMC Bioinformatics 2019;20:71. [PMID: 30736739 PMCID: PMC6368809 DOI: 10.1186/s12859-019-2594-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 01/03/2019] [Indexed: 12/02/2022]  Open
245
Kafkas Ş, Hoehndorf R. Ontology based text mining of gene-phenotype associations: application to candidate gene prediction. Database (Oxford) 2019;2019:baz019. [PMID: 30809638 PMCID: PMC6391585 DOI: 10.1093/database/baz019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/09/2019] [Accepted: 01/26/2019] [Indexed: 01/07/2023]
246
Su C, Tong J, Zhu Y, Cui P, Wang F. Network embedding in biomedical data science. Brief Bioinform 2018;21:182-197. [PMID: 30535359 DOI: 10.1093/bib/bby117] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/08/2018] [Accepted: 11/03/2018] [Indexed: 12/15/2022]  Open
247
Elbasir A, Moovarkumudalvan B, Kunji K, Kolatkar PR, Mall R, Bensmail H. DeepCrystal: a deep learning framework for sequence-based protein crystallization prediction. Bioinformatics 2018;35:2216-2225. [DOI: 10.1093/bioinformatics/bty953] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/31/2018] [Accepted: 11/17/2018] [Indexed: 12/11/2022]  Open
248
Smaili FZ, Gao X, Hoehndorf R. OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction. Bioinformatics 2018;35:2133-2140. [DOI: 10.1093/bioinformatics/bty933] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 11/02/2018] [Accepted: 11/07/2018] [Indexed: 12/11/2022]  Open
249
Saha S, Prasad A, Chatterjee P, Basu S, Nasipuri M. Protein function prediction from protein-protein interaction network using gene ontology based neighborhood analysis and physico-chemical features. J Bioinform Comput Biol 2018;16:1850025. [PMID: 30400756 DOI: 10.1142/s0219720018500257] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
250
Kulmanov M, Schofield PN, Gkoutos GV, Hoehndorf R. Ontology-based validation and identification of regulatory phenotypes. Bioinformatics 2018;34:i857-i865. [PMID: 30423068 PMCID: PMC6129279 DOI: 10.1093/bioinformatics/bty605] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]  Open
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