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For: Caniza H, Romero AE, Heron S, Yang H, Devoto A, Frasca M, Mesiti M, Valentini G, Paccanaro A. GOssTo: a stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology. Bioinformatics 2014;30:2235-6. [PMID: 24659104 PMCID: PMC4103586 DOI: 10.1093/bioinformatics/btu144] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
Number Cited by Other Article(s)
1
de Siqueira Santos S, Yang H, Galeano A, Paccanaro A. Host centric drug repurposing for viral diseases. PLoS Comput Biol 2025;21:e1012876. [PMID: 40173200 PMCID: PMC12052139 DOI: 10.1371/journal.pcbi.1012876] [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: 11/02/2024] [Revised: 05/05/2025] [Accepted: 02/14/2025] [Indexed: 04/04/2025]  Open
2
Gu Z. simona: a comprehensive R package for semantic similarity analysis on bio-ontologies. BMC Genomics 2024;25:869. [PMID: 39285315 PMCID: PMC11406866 DOI: 10.1186/s12864-024-10759-4] [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: 04/17/2024] [Accepted: 09/02/2024] [Indexed: 09/19/2024]  Open
3
Caniza H, Cáceres JJ, Torres M, Paccanaro A. LanDis: the disease landscape explorer. Eur J Hum Genet 2024;32:461-465. [PMID: 38200084 PMCID: PMC10999415 DOI: 10.1038/s41431-023-01511-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/01/2023] [Accepted: 11/23/2023] [Indexed: 01/12/2024]  Open
4
Hao DC, Chen H, Xiao PG, Jiang T. A Global Analysis of Alternative Splicing of Dichocarpum Medicinal Plants, Ranunculales. Curr Genomics 2022;23:207-216. [PMID: 36777007 PMCID: PMC9878827 DOI: 10.2174/1389202923666220527112929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/19/2022] [Accepted: 04/26/2022] [Indexed: 11/22/2022]  Open
5
Lastra-Díaz JJ, Lara-Clares A, Garcia-Serrano A. HESML: a real-time semantic measures library for the biomedical domain with a reproducible survey. BMC Bioinformatics 2022;23:23. [PMID: 34991460 PMCID: PMC8734250 DOI: 10.1186/s12859-021-04539-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/15/2021] [Indexed: 11/10/2022]  Open
6
Saxena R, Bishnoi R, Singla D. Gene Ontology: application and importance in functional annotation of the genomic data. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00015-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]  Open
7
Zheng F, Kelly MR, Ramms DJ, Heintschel ML, Tao K, Tutuncuoglu B, Lee JJ, Ono K, Foussard H, Chen M, Herrington KA, Silva E, Liu S, Chen J, Churas C, Wilson N, Kratz A, Pillich RT, Patel DN, Park J, Kuenzi B, Yu MK, Licon K, Pratt D, Kreisberg JF, Kim M, Swaney DL, Nan X, Fraley SI, Gutkind JS, Krogan NJ, Ideker T. Interpretation of cancer mutations using a multiscale map of protein systems. Science 2021;374:eabf3067. [PMID: 34591613 PMCID: PMC9126298 DOI: 10.1126/science.abf3067] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
8
Nguyen QH, Le DH. Similarity Calculation, Enrichment Analysis, and Ontology Visualization of Biomedical Ontologies using UFO. Curr Protoc 2021;1:e115. [PMID: 33900688 DOI: 10.1002/cpz1.115] [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: 01/27/2023]
9
Shaw D, Chen H, Xie M, Jiang T. DeepLPI: a multimodal deep learning method for predicting the interactions between lncRNAs and protein isoforms. BMC Bioinformatics 2021;22:24. [PMID: 33461501 PMCID: PMC7814738 DOI: 10.1186/s12859-020-03914-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/30/2020] [Indexed: 12/14/2022]  Open
10
Nepomuceno-Chamorro IA, Nepomuceno JA, Galván-Rojas JL, Vega-Márquez B, Rubio-Escudero C. Using prior knowledge in the inference of gene association networks. APPL INTELL 2020. [DOI: 10.1007/s10489-020-01705-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
11
SabziNezhad A, Jalili S. DPCT: A Dynamic Method for Detecting Protein Complexes From TAP-Aware Weighted PPI Network. Front Genet 2020;11:567. [PMID: 32676097 PMCID: PMC7333736 DOI: 10.3389/fgene.2020.00567] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/11/2020] [Indexed: 12/13/2022]  Open
12
Shaw D, Chen H, Jiang T. DeepIsoFun: a deep domain adaptation approach to predict isoform functions. Bioinformatics 2020;35:2535-2544. [PMID: 30535380 DOI: 10.1093/bioinformatics/bty1017] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/07/2018] [Accepted: 12/08/2018] [Indexed: 11/14/2022]  Open
13
Vascon S, Frasca M, Tripodi R, Valentini G, Pelillo M. Protein function prediction as a graph-transduction game. Pattern Recognit Lett 2020. [DOI: 10.1016/j.patrec.2018.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
14
Yassaee Meybodi F, Emdadi A, Rezvan A, Eslahchi C. CAMND: Comparative analysis of metabolic network decomposition based on previous and two new criteria, a web based application. Biosystems 2019;189:104081. [PMID: 31838143 DOI: 10.1016/j.biosystems.2019.104081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 10/06/2019] [Accepted: 11/26/2019] [Indexed: 11/29/2022]
15
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
16
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]
17
Wang D, Li J, Liu R, Wang Y. Optimizing gene set annotations combining GO structure and gene expression data. BMC SYSTEMS BIOLOGY 2018;12:133. [PMID: 30598093 PMCID: PMC6311910 DOI: 10.1186/s12918-018-0659-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
18
Duong D, Ahmad WU, Eskin E, Chang KW, Li JJ. Word and Sentence Embedding Tools to Measure Semantic Similarity of Gene Ontology Terms by Their Definitions. J Comput Biol 2018;26:38-52. [PMID: 30383443 DOI: 10.1089/cmb.2018.0093] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]  Open
19
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
20
Nikdelfaz O, Jalili S. Disease genes prediction by HMM based PU-learning using gene expression profiles. J Biomed Inform 2018;81:102-111. [PMID: 29571901 DOI: 10.1016/j.jbi.2018.03.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/22/2017] [Accepted: 03/12/2018] [Indexed: 12/24/2022]
21
Rezvan A, Eslahchi C. Comparison of different approaches for identifying subnetworks in metabolic networks. J Bioinform Comput Biol 2017;15:1750025. [DOI: 10.1142/s0219720017500251] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
22
Mazandu GK, Chimusa ER, Mulder NJ. Gene Ontology semantic similarity tools: survey on features and challenges for biological knowledge discovery. Brief Bioinform 2017;18:886-901. [PMID: 27473066 DOI: 10.1093/bib/bbw067] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Indexed: 01/02/2023]  Open
23
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
24
Nap JP, Sanchez-Perez GF, van Dijk ADJ. Similarities between plant traits based on their connection to underlying gene functions. PLoS One 2017;12:e0182097. [PMID: 28797052 PMCID: PMC5552327 DOI: 10.1371/journal.pone.0182097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 07/12/2017] [Indexed: 11/19/2022]  Open
25
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
26
A cytosolic Ezh1 isoform modulates a PRC2–Ezh1 epigenetic adaptive response in postmitotic cells. Nat Struct Mol Biol 2017;24:444-452. [DOI: 10.1038/nsmb.3392] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 02/24/2017] [Indexed: 12/13/2022]
27
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
28
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]
29
Peng J, Li H, Liu Y, Juan L, Jiang Q, Wang Y, Chen J. InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology. BMC Genomics 2016;17 Suppl 5:530. [PMID: 27586009 PMCID: PMC5009821 DOI: 10.1186/s12864-016-2828-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
30
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] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/01/2016] [Indexed: 11/14/2022]  Open
31
Gazestani VH, Nikpour N, Mehta V, Najafabadi HS, Moshiri H, Jardim A, Salavati R. A Protein Complex Map of Trypanosoma brucei. PLoS Negl Trop Dis 2016;10:e0004533. [PMID: 26991453 PMCID: PMC4798371 DOI: 10.1371/journal.pntd.0004533] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 02/20/2016] [Indexed: 12/27/2022]  Open
32
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]
33
Faisal FE, Meng L, Crawford J, Milenković T. The post-genomic era of biological network alignment. EURASIP JOURNAL ON BIOINFORMATICS & SYSTEMS BIOLOGY 2015;2015:3. [PMID: 28194172 PMCID: PMC5270500 DOI: 10.1186/s13637-015-0022-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 05/18/2015] [Indexed: 11/10/2022]
34
Mazandu GK, Chimusa ER, Mbiyavanga M, Mulder NJ. A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool. Bioinformatics 2015;32:477-9. [PMID: 26476781 DOI: 10.1093/bioinformatics/btv590] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 10/08/2015] [Indexed: 01/01/2023]  Open
35
Nepomuceno JA, Troncoso A, Nepomuceno-Chamorro IA, Aguilar-Ruiz JS. Integrating biological knowledge based on functional annotations for biclustering of gene expression data. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2015;119:163-80. [PMID: 25843807 DOI: 10.1016/j.cmpb.2015.02.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 02/17/2015] [Accepted: 02/27/2015] [Indexed: 05/06/2023]
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