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For: Agapito G, Guzzi PH, Cannataro M. Visualization of protein interaction networks: problems and solutions. BMC Bioinformatics 2013;14 Suppl 1:S1. [PMID: 23368786 PMCID: PMC3548679 DOI: 10.1186/1471-2105-14-s1-s1] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
Number Cited by Other Article(s)
1
Dugied G, Laurent EM, Attia M, Gimeno JP, Bachiri K, Samavarchi-Tehrani P, Donati F, Rahou Y, Munier S, Amara F, Dos Santos M, Soler N, Volant S, Pietrosemoli N, Gingras AC, Pavlopoulos GA, van der Werf S, Falter-Braun P, Aloy P, Jacob Y, Komarova A, Sofianatos Y, Coyaud E, Demeret C. Multimodal SARS-CoV-2 interactome sketches the virus-host spatial organization. Commun Biol 2025;8:501. [PMID: 40140549 PMCID: PMC11947133 DOI: 10.1038/s42003-025-07933-z] [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: 09/18/2024] [Accepted: 03/12/2025] [Indexed: 03/28/2025]  Open
2
Bottino L, Settino M, Promenzio L, Cannataro M. Scoliosis Management through Apps and Software Tools. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023;20:ijerph20085520. [PMID: 37107802 PMCID: PMC10138677 DOI: 10.3390/ijerph20085520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/10/2023] [Accepted: 04/11/2023] [Indexed: 05/11/2023]
3
Robin V, Bodein A, Scott-Boyer MP, Leclercq M, Périn O, Droit A. Overview of methods for characterization and visualization of a protein-protein interaction network in a multi-omics integration context. Front Mol Biosci 2022;9:962799. [PMID: 36158572 PMCID: PMC9494275 DOI: 10.3389/fmolb.2022.962799] [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: 06/06/2022] [Accepted: 08/16/2022] [Indexed: 11/26/2022]  Open
4
Milano M, Agapito G, Cannataro M. Challenges and Limitations of Biological Network Analysis. BIOTECH 2022;11:24. [PMID: 35892929 PMCID: PMC9326688 DOI: 10.3390/biotech11030024] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 11/17/2022]  Open
5
Rout M, Kour B, Vuree S, Lulu SS, Medicherla KM, Suravajhala P. Diabetes mellitus susceptibility with varied diseased phenotypes and its comparison with phenome interactome networks. World J Clin Cases 2022;10:5957-5964. [PMID: 35949812 PMCID: PMC9254192 DOI: 10.12998/wjcc.v10.i18.5957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/02/2022] [Accepted: 04/22/2022] [Indexed: 02/06/2023]  Open
6
Analysis of Multifactor-Driven Myopia Disease Modules to Guide Personalized Treatment and Drug Development. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022;2022:5262259. [PMID: 35586671 PMCID: PMC9110184 DOI: 10.1155/2022/5262259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/22/2022] [Accepted: 04/02/2022] [Indexed: 11/17/2022]
7
Redhu N, Thakur Z. Network biology and applications. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00024-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]  Open
8
Kataria R, Kaundal R. Deciphering the Crosstalk Mechanisms of Wheat-Stem Rust Pathosystem: Genome-Scale Prediction Unravels Novel Host Targets. FRONTIERS IN PLANT SCIENCE 2022;13:895480. [PMID: 35800602 PMCID: PMC9253690 DOI: 10.3389/fpls.2022.895480] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 05/31/2022] [Indexed: 05/04/2023]
9
Identification of significant protein in protein-protein interaction of Alzheimer disease using top-k representative skyline query. JURNAL TEKNOLOGI DAN SISTEM KOMPUTER 2021. [DOI: 10.14710/jtsiskom.2021.13985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
10
Zhou W, Gao M, Liang C, Lin B, Wu Q, Chen R, Xiong X, Chen X, Wang S, Wu L, Wu Y, Li H, Fu X, Hong W. Systematic Understanding of the Mechanism of Baicalin against Gastric Cancer Using Transcriptome Analysis. BIOMED RESEARCH INTERNATIONAL 2021;2021:5521058. [PMID: 34337018 PMCID: PMC8315853 DOI: 10.1155/2021/5521058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/11/2021] [Indexed: 11/18/2022]
11
Kowalski A. A survey of human histone H1 subtypes interaction networks: Implications for histones H1 functioning. Proteins 2021;89:792-810. [PMID: 33550666 DOI: 10.1002/prot.26059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/23/2020] [Accepted: 01/31/2021] [Indexed: 11/08/2022]
12
Poverennaya EV, Kiseleva OI, Ivanov AS, Ponomarenko EA. Methods of Computational Interactomics for Investigating Interactions of Human Proteoforms. BIOCHEMISTRY (MOSCOW) 2020;85:68-79. [PMID: 32079518 DOI: 10.1134/s000629792001006x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
13
Struweg I. A Twitter Social Network Analysis: The South African Health Insurance Bill Case. LECTURE NOTES IN COMPUTER SCIENCE 2020. [PMCID: PMC7134296 DOI: 10.1007/978-3-030-45002-1_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
14
Tian Y, Yu M, Sun L, Liu L, Wang J, Hui K, Nan Q, Nie X, Ren Y, Ren X. Distinct Patterns of mRNA and lncRNA Expression Differences Between Lung Squamous Cell Carcinoma and Adenocarcinoma. J Comput Biol 2019;27:1067-1078. [PMID: 31750732 DOI: 10.1089/cmb.2019.0164] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
15
Kwon D, Lee D, Kim J, Lee J, Sim M, Kim J. Using INTERSPIA to Explore the Dynamics of Protein-Protein Interactions Among Multiple Species. ACTA ACUST UNITED AC 2019;68:e88. [PMID: 31751498 DOI: 10.1002/cpbi.88] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
16
Klymkowsky MW. Filaments and phenotypes: cellular roles and orphan effects associated with mutations in cytoplasmic intermediate filament proteins. F1000Res 2019;8. [PMID: 31602295 PMCID: PMC6774051 DOI: 10.12688/f1000research.19950.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/20/2019] [Indexed: 12/11/2022]  Open
17
Kwon D, Lee D, Kim J, Lee J, Sim M, Kim J. INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species. Nucleic Acids Res 2019;46:W89-W94. [PMID: 29746660 PMCID: PMC6031021 DOI: 10.1093/nar/gky378] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/27/2018] [Indexed: 02/06/2023]  Open
18
Liu D, Huo Y, Chen S, Xu D, Yang B, Xue C, Fu L, Bu L, Song S, Mei C. Identification of Key Genes and Candidated Pathways in Human Autosomal Dominant Polycystic Kidney Disease by Bioinformatics Analysis. Kidney Blood Press Res 2019;44:533-552. [DOI: 10.1159/000500458] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/04/2019] [Indexed: 11/19/2022]  Open
19
de Graaf SC, Klykov O, van den Toorn H, Scheltema RA. Cross-ID: Analysis and Visualization of Complex XL-MS-Driven Protein Interaction Networks. J Proteome Res 2019;18:642-651. [PMID: 30575379 PMCID: PMC6407916 DOI: 10.1021/acs.jproteome.8b00725] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
20
Cannataro M. Big Data Analysis in Bioinformatics. ENCYCLOPEDIA OF BIG DATA TECHNOLOGIES 2019:161-180. [DOI: 10.1007/978-3-319-77525-8_139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
21
Liu X, Chang C, Han M, Yin R, Zhan Y, Li C, Ge C, Yu M, Yang X. PPIExp: A Web-Based Platform for Integration and Visualization of Protein-Protein Interaction Data and Spatiotemporal Proteomics Data. J Proteome Res 2018;18:633-641. [PMID: 30565464 DOI: 10.1021/acs.jproteome.8b00713] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
22
Shao YC, Nie XC, Song GQ, Wei Y, Xia P, Xu XY. Prognostic value of DKK2 from the Dickkopf family in human breast cancer. Int J Oncol 2018;53:2555-2565. [PMID: 30320375 PMCID: PMC6203157 DOI: 10.3892/ijo.2018.4588] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 09/14/2018] [Indexed: 12/27/2022]  Open
23
Cannataro M. Big Data Analysis in Bioinformatics. ENCYCLOPEDIA OF BIG DATA TECHNOLOGIES 2018:1-19. [DOI: 10.1007/978-3-319-63962-8_139-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
24
Felgueiras J, Silva JV, Fardilha M. Adding biological meaning to human protein-protein interactions identified by yeast two-hybrid screenings: A guide through bioinformatics tools. J Proteomics 2018;171:127-140. [PMID: 28526529 DOI: 10.1016/j.jprot.2017.05.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 04/26/2017] [Accepted: 05/13/2017] [Indexed: 02/02/2023]
25
Glatigny A, Gambette P, Bourand-Plantefol A, Dujardin G, Mucchielli-Giorgi MH. Development of an in silico method for the identification of subcomplexes involved in the biogenesis of multiprotein complexes in Saccharomyces cerevisiae. BMC SYSTEMS BIOLOGY 2017;11:67. [PMID: 28693620 PMCID: PMC5504824 DOI: 10.1186/s12918-017-0442-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 06/28/2017] [Indexed: 11/23/2022]
26
Malhotra AG, Jha M, Singh S, Pandey KM. Construction of a Comprehensive Protein-Protein Interaction Map for Vitiligo Disease to Identify Key Regulatory Elements: A Systemic Approach. Interdiscip Sci 2017;10:500-514. [PMID: 28290051 DOI: 10.1007/s12539-017-0213-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 12/09/2016] [Accepted: 12/29/2016] [Indexed: 12/14/2022]
27
Discovery of functional module alignment. Neurocomputing 2016. [DOI: 10.1016/j.neucom.2016.04.055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
28
Roy S, Guzzi PH. Biological Network Inference from Microarray Data, Current Solutions, and Assessments. Methods Mol Biol 2016;1375:155-167. [PMID: 26507508 DOI: 10.1007/7651_2015_284] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
29
Giuseppe A, Milano M. Ontology-Based Analysis of Microarray Data. Methods Mol Biol 2016;1375:117-121. [PMID: 25971913 DOI: 10.1007/7651_2015_249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
30
Thébault P, Bourqui R, Benchimol W, Gaspin C, Sirand-Pugnet P, Uricaru R, Dutour I. Advantages of mixing bioinformatics and visualization approaches for analyzing sRNA-mediated regulatory bacterial networks. Brief Bioinform 2015;16:795-805. [PMID: 25477348 PMCID: PMC4570199 DOI: 10.1093/bib/bbu045] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 11/05/2014] [Indexed: 12/29/2022]  Open
31
Jeanquartier F, Jean-Quartier C, Holzinger A. Integrated web visualizations for protein-protein interaction databases. BMC Bioinformatics 2015;16:195. [PMID: 26077899 PMCID: PMC4466863 DOI: 10.1186/s12859-015-0615-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 05/15/2015] [Indexed: 12/27/2022]  Open
32
Talwar P, Silla Y, Grover S, Gupta M, Grewal GK, Kukreti R. Systems Pharmacology and Pharmacogenomics for Drug Discovery and Development. SYSTEMS AND SYNTHETIC BIOLOGY 2015. [DOI: 10.1007/978-94-017-9514-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
33
Hirst JD, Glowacki DR, Baaden M. Molecular simulations and visualization: introduction and overview. Faraday Discuss 2014;169:9-22. [DOI: 10.1039/c4fd90024c] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
34
Salazar GA, Meintjes A, Mazandu GK, Rapanoël HA, Akinola RO, Mulder NJ. A web-based protein interaction network visualizer. BMC Bioinformatics 2014;15:129. [PMID: 24885165 PMCID: PMC4029974 DOI: 10.1186/1471-2105-15-129] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 04/24/2014] [Indexed: 01/18/2023]  Open
35
Salazar GA, Meintjes A, Mulder N. PPI layouts: BioJS components for the display of Protein-Protein Interactions. F1000Res 2014;3:50. [PMID: 25075288 PMCID: PMC4103490 DOI: 10.12688/f1000research.3-50.v1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/03/2014] [Indexed: 01/17/2023]  Open
36
Li W, Kinch LN, Grishin NV. Pclust: protein network visualization highlighting experimental data. ACTA ACUST UNITED AC 2013;29:2647-8. [PMID: 23918248 DOI: 10.1093/bioinformatics/btt451] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
37
Rother M, Münzner U, Thieme S, Krantz M. Information content and scalability in signal transduction network reconstruction formats. MOLECULAR BIOSYSTEMS 2013;9:1993-2004. [PMID: 23636168 DOI: 10.1039/c3mb00005b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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