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For: Liu H, Hu ZZ, Wu CH. DynGO: a tool for visualizing and mining of Gene Ontology and its associations. BMC Bioinformatics 2005;6:201. [PMID: 16091147 PMCID: PMC1199584 DOI: 10.1186/1471-2105-6-201] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2004] [Accepted: 08/09/2005] [Indexed: 11/16/2022]  Open
Number Cited by Other Article(s)
1
Liu Z, Zhao X. piRNAs as emerging biomarkers and physiological regulatory molecules in cardiovascular disease. Biochem Biophys Res Commun 2024;711:149906. [PMID: 38640879 DOI: 10.1016/j.bbrc.2024.149906] [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: 02/03/2024] [Revised: 04/01/2024] [Accepted: 04/05/2024] [Indexed: 04/21/2024]
2
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
3
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]
4
Le DH. UFO: A tool for unifying biomedical ontology-based semantic similarity calculation, enrichment analysis and visualization. PLoS One 2020;15:e0235670. [PMID: 32645039 PMCID: PMC7347127 DOI: 10.1371/journal.pone.0235670] [Citation(s) in RCA: 8] [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: 11/17/2019] [Accepted: 06/22/2020] [Indexed: 02/06/2023]  Open
5
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
6
Safaei A, Rezaei Tavirani M, Zamanian Azodi M, Lashay A, Mohammadi SF, Ghasemi Broumand M, Peyvandi AA, Okhovatian F, Peyvandi H, Rostami Nejad M. Diabetic Retinopathy and Laser Therapy in Rats: A Protein-Protein Interaction Network Analysis. J Lasers Med Sci 2017;8:S20-S21. [PMID: 29071030 DOI: 10.15171/jlms.2017.s4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
7
Shen F, Sohn S, Rastegar-Mojarad M, Liu S, Pankratz JJ, Hatton MA, Sowada N, Shrestha OK, Shurson SL, Liu H. Populating Physician Biographical Pages Based on EMR Data. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE PROCEEDINGS. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE 2017;2017:522-530. [PMID: 28815152 PMCID: PMC5543344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
8
Al-Dalky R, Taha K, Al Homouz D, Qasaimeh M. Applying Monte Carlo Simulation to Biomedical Literature to Approximate Genetic Network. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2016;13:494-504. [PMID: 26415184 DOI: 10.1109/tcbb.2015.2481399] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
9
Safaei A, Rezaei Tavirani M, Arefi Oskouei A, Zamanian Azodi M, Mohebbi SR, Nikzamir AR. Protein-protein interaction network analysis of cirrhosis liver disease. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2016;9:114-23. [PMID: 27099671 PMCID: PMC4833850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
10
Taha K, Homouz D, Al Muhairi H, Al Mahmoud Z. GRank: a middleware search engine for ranking genes by relevance to given genes. BMC Bioinformatics 2013;14:251. [PMID: 23957362 PMCID: PMC3765412 DOI: 10.1186/1471-2105-14-251] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Accepted: 08/13/2013] [Indexed: 11/24/2022]  Open
11
Khan M, Vaes E, Mombaerts P. Temporal patterns of odorant receptor gene expression in adult and aged mice. Mol Cell Neurosci 2013;57:120-9. [PMID: 23962816 DOI: 10.1016/j.mcn.2013.08.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 08/05/2013] [Accepted: 08/09/2013] [Indexed: 01/27/2023]  Open
12
Jupp S, Stevens R, Hoehndorf R. Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL. J Biomed Semantics 2012;3 Suppl 1:S3. [PMID: 22541594 PMCID: PMC3337258 DOI: 10.1186/2041-1480-3-s1-s3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]  Open
13
Mao KZ, Tang W. Recursive Mahalanobis separability measure for gene subset selection. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2011;8:266-272. [PMID: 20479500 DOI: 10.1109/tcbb.2010.43] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
14
Montecchi-Palazzi L, Kerrien S, Reisinger F, Aranda B, Jones AR, Martens L, Hermjakob H. The PSI semantic validator: a framework to check MIAPE compliance of proteomics data. Proteomics 2010;9:5112-9. [PMID: 19834897 DOI: 10.1002/pmic.200900189] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
15
Baker EJ, Jay JJ, Philip VM, Zhang Y, Li Z, Kirova R, Langston MA, Chesler EJ. Ontological Discovery Environment: a system for integrating gene-phenotype associations. Genomics 2009;94:377-87. [PMID: 19733230 DOI: 10.1016/j.ygeno.2009.08.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Revised: 08/19/2009] [Accepted: 08/27/2009] [Indexed: 10/20/2022]
16
Pesquita C, Faria D, Falcão AO, Lord P, Couto FM. Semantic similarity in biomedical ontologies. PLoS Comput Biol 2009;5:e1000443. [PMID: 19649320 PMCID: PMC2712090 DOI: 10.1371/journal.pcbi.1000443] [Citation(s) in RCA: 415] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]  Open
17
Ma'ayan A. Network integration and graph analysis in mammalian molecular systems biology. IET Syst Biol 2008;2:206-21. [PMID: 19045817 PMCID: PMC2745214 DOI: 10.1049/iet-syb:20070075] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
18
Topalis P, Tzavlaki C, Vestaki K, Dialynas E, Sonenshine DE, Butler R, Bruggner RV, Stinson EO, Collins FH, Louis C. Anatomical ontologies of mosquitoes and ticks, and their web browsers in VectorBase. INSECT MOLECULAR BIOLOGY 2008;17:87-89. [PMID: 18237287 DOI: 10.1111/j.1365-2583.2008.00781.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
19
Schlicker A, Albrecht M. FunSimMat: a comprehensive functional similarity database. Nucleic Acids Res 2007;36:D434-9. [PMID: 17932054 PMCID: PMC2238903 DOI: 10.1093/nar/gkm806] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
20
Huang DW, Sherman BT, Tan Q, Kir J, Liu D, Bryant D, Guo Y, Stephens R, Baseler MW, Lane HC, Lempicki RA. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res 2007;35:W169-75. [PMID: 17576678 PMCID: PMC1933169 DOI: 10.1093/nar/gkm415] [Citation(s) in RCA: 1667] [Impact Index Per Article: 92.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Revised: 04/14/2007] [Accepted: 05/06/2007] [Indexed: 12/20/2022]  Open
21
Othman RM, Deris S, Illias RM. A genetic similarity algorithm for searching the Gene Ontology terms and annotating anonymous protein sequences. J Biomed Inform 2007;41:65-81. [PMID: 17681495 DOI: 10.1016/j.jbi.2007.05.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2006] [Revised: 05/28/2007] [Accepted: 05/29/2007] [Indexed: 11/19/2022]
22
Schlicker A, Rahnenführer J, Albrecht M, Lengauer T, Domingues FS. GOTax: investigating biological processes and biochemical activities along the taxonomic tree. Genome Biol 2007;8:R33. [PMID: 17346342 PMCID: PMC1868936 DOI: 10.1186/gb-2007-8-3-r33] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2006] [Revised: 01/18/2007] [Accepted: 03/08/2007] [Indexed: 11/10/2022]  Open
23
Huang DW, Sherman BT, Tan Q, Collins JR, Alvord WG, Roayaei J, Stephens R, Baseler MW, Lane HC, Lempicki RA. The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol 2007;8:R183. [PMID: 17784955 PMCID: PMC2375021 DOI: 10.1186/gb-2007-8-9-r183] [Citation(s) in RCA: 1784] [Impact Index Per Article: 99.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Revised: 04/20/2007] [Accepted: 09/04/2007] [Indexed: 12/16/2022]  Open
24
Sealfon RSG, Hibbs MA, Huttenhower C, Myers CL, Troyanskaya OG. GOLEM: an interactive graph-based gene-ontology navigation and analysis tool. BMC Bioinformatics 2006;7:443. [PMID: 17032457 PMCID: PMC1618863 DOI: 10.1186/1471-2105-7-443] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2006] [Accepted: 10/10/2006] [Indexed: 11/28/2022]  Open
25
Sun H, Fang H, Chen T, Perkins R, Tong W. GOFFA: gene ontology for functional analysis--a FDA gene ontology tool for analysis of genomic and proteomic data. BMC Bioinformatics 2006;7 Suppl 2:S23. [PMID: 17118145 PMCID: PMC1683576 DOI: 10.1186/1471-2105-7-s2-s23] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]  Open
26
Zhang P, Zhang J, Sheng H, Russo JJ, Osborne B, Buetow K. Gene functional similarity search tool (GFSST). BMC Bioinformatics 2006;7:135. [PMID: 16536867 PMCID: PMC1421445 DOI: 10.1186/1471-2105-7-135] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2005] [Accepted: 03/14/2006] [Indexed: 11/21/2022]  Open
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