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For: Messina A, Fiannaca A, La Paglia L, La Rosa M, Urso A. BioGraph: a web application and a graph database for querying and analyzing bioinformatics resources. BMC Syst Biol 2018;12:98. [PMID: 30458802 PMCID: PMC6245492 DOI: 10.1186/s12918-018-0616-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Number Cited by Other Article(s)
1
Glen AK, Ma C, Mendoza L, Womack F, Wood EC, Sinha M, Acevedo L, Kvarfordt LG, Peene RC, Liu S, Hoffman AS, Roach JC, Deutsch EW, Ramsey SA, Koslicki D. ARAX: a graph-based modular reasoning tool for translational biomedicine. Bioinformatics 2023;39:7031241. [PMID: 36752514 PMCID: PMC10027432 DOI: 10.1093/bioinformatics/btad082] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/17/2022] [Accepted: 02/07/2023] [Indexed: 04/12/2023]  Open
2
Schäfer J, Tang M, Luu D, Bergmann AK, Wiese L. Graph4Med: a web application and a graph database for visualizing and analyzing medical databases. BMC Bioinformatics 2022;23:537. [PMID: 36503436 PMCID: PMC9743588 DOI: 10.1186/s12859-022-05092-0] [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: 03/24/2022] [Accepted: 12/01/2022] [Indexed: 12/14/2022]  Open
3
Toti D, Macari G, Barbierato E, Polticelli F. FGDB: a comprehensive graph database of ligand fragments from the Protein Data Bank. Database (Oxford) 2022;2022:6619197. [PMID: 35763362 PMCID: PMC9239314 DOI: 10.1093/database/baac044] [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: 02/14/2022] [Revised: 05/06/2022] [Accepted: 05/31/2022] [Indexed: 11/22/2022]
4
Ten simple rules for researchers who want to develop web apps. PLoS Comput Biol 2022;18:e1009663. [PMID: 34990469 PMCID: PMC8735566 DOI: 10.1371/journal.pcbi.1009663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
5
Doğan T, Atas H, Joshi V, Atakan A, Rifaioglu A, Nalbat E, Nightingale A, Saidi R, Volynkin V, Zellner H, Cetin-Atalay R, Martin M, Atalay V. CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations. Nucleic Acids Res 2021;49:e96. [PMID: 34181736 PMCID: PMC8450100 DOI: 10.1093/nar/gkab543] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 04/11/2021] [Accepted: 06/10/2021] [Indexed: 12/11/2022]  Open
6
Hassani‐Pak K, Singh A, Brandizi M, Hearnshaw J, Parsons JD, Amberkar S, Phillips AL, Doonan JH, Rawlings C. KnetMiner: a comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species. PLANT BIOTECHNOLOGY JOURNAL 2021;19:1670-1678. [PMID: 33750020 PMCID: PMC8384599 DOI: 10.1111/pbi.13583] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/17/2020] [Accepted: 03/16/2021] [Indexed: 05/03/2023]
7
Timón-Reina S, Rincón M, Martínez-Tomás R. An overview of graph databases and their applications in the biomedical domain. Database (Oxford) 2021;2021:baab026. [PMID: 34003247 PMCID: PMC8130509 DOI: 10.1093/database/baab026] [Citation(s) in RCA: 6] [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: 11/28/2020] [Revised: 03/24/2021] [Accepted: 04/30/2021] [Indexed: 01/18/2023]
8
D’Agostino D, Liò P, Aldinucci M, Merelli I. Advantages of using graph databases to explore chromatin conformation capture experiments. BMC Bioinformatics 2021;22:43. [PMID: 33902433 PMCID: PMC8073886 DOI: 10.1186/s12859-020-03937-0] [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: 12/09/2020] [Accepted: 12/15/2020] [Indexed: 11/10/2022]  Open
9
Queralt-Rosinach N, Stupp GS, Li TS, Mayers M, Hoatlin ME, Might M, Good BM, Su AI. Structured reviews for data and knowledge-driven research. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021;2020:5818923. [PMID: 32283553 PMCID: PMC7153956 DOI: 10.1093/database/baaa015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/21/2020] [Accepted: 02/07/2020] [Indexed: 12/25/2022]
10
Mei S, Huang X, Xie C, Mora A. GREG-studying transcriptional regulation using integrative graph databases. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020;2020:5735477. [PMID: 32055858 PMCID: PMC7018612 DOI: 10.1093/database/baz162] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/08/2019] [Accepted: 12/31/2019] [Indexed: 01/08/2023]
11
Mrozek D. A review of Cloud computing technologies for comprehensive microRNA analyses. Comput Biol Chem 2020;88:107365. [PMID: 32906056 DOI: 10.1016/j.compbiolchem.2020.107365] [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: 07/09/2020] [Revised: 08/05/2020] [Accepted: 08/18/2020] [Indexed: 01/08/2023]
12
Aguilera-Mendoza L, Marrero-Ponce Y, Beltran JA, Tellez Ibarra R, Guillen-Ramirez HA, Brizuela CA. Graph-based data integration from bioactive peptide databases of pharmaceutical interest: toward an organized collection enabling visual network analysis. Bioinformatics 2020;35:4739-4747. [PMID: 30994884 DOI: 10.1093/bioinformatics/btz260] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 03/30/2019] [Accepted: 04/10/2019] [Indexed: 11/13/2022]  Open
13
Struck A, Walsh B, Buchanan A, Lee JA, Spangler R, Stuart JM, Ellrott K. Exploring Integrative Analysis Using the BioMedical Evidence Graph. JCO Clin Cancer Inform 2020;4:147-159. [PMID: 32097025 PMCID: PMC7049249 DOI: 10.1200/cci.19.00110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2020] [Indexed: 12/22/2022]  Open
14
From a Conceptual Model to a Knowledge Graph for Genomic Datasets. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/978-3-030-33223-5_29] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
15
3D-PP: A Tool for Discovering Conserved Three-Dimensional Protein Patterns. Int J Mol Sci 2019;20:ijms20133174. [PMID: 31261733 PMCID: PMC6651053 DOI: 10.3390/ijms20133174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 01/25/2023]  Open
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