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For: Ostaszewski M, Gebel S, Kuperstein I, Mazein A, Zinovyev A, Dogrusoz U, Hasenauer J, Fleming RMT, Le Novère N, Gawron P, Ligon T, Niarakis A, Nickerson D, Weindl D, Balling R, Barillot E, Auffray C, Schneider R. Community-driven roadmap for integrated disease maps. Brief Bioinform 2019;20:659-70. [PMID: 29688273 DOI: 10.1093/bib/bby024] [Cited by in Crossref: 26] [Cited by in F6Publishing: 20] [Article Influence: 13.0] [Reference Citation Analysis]
Number Citing Articles
1 Vinhoven L, Voskamp M, Nietert MM. Mapping Compound Databases to Disease Maps-A MINERVA Plugin for CandActBase. J Pers Med 2021;11:1072. [PMID: 34834423 DOI: 10.3390/jpm11111072] [Reference Citation Analysis]
2 Aghamiri SS, Singh V, Naldi A, Helikar T, Soliman S, Niarakis A. Automated inference of Boolean models from molecular interaction maps using CaSQ. Bioinformatics 2020;36:4473-82. [PMID: 32403123 DOI: 10.1093/bioinformatics/btaa484] [Cited by in Crossref: 14] [Cited by in F6Publishing: 10] [Article Influence: 14.0] [Reference Citation Analysis]
3 Casaní-Galdón S, Pereira C, Conesa A. Padhoc: a computational pipeline for pathway reconstruction on the fly. Bioinformatics 2020;36:i795-803. [PMID: 33381819 DOI: 10.1093/bioinformatics/btaa811] [Reference Citation Analysis]
4 Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Daníelsdóttir AD, Krecke M, Merten D, Haraldsdóttir HS, Heinken A, Heirendt L, Magnúsdóttir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Žagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I. The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res 2019;47:D614-24. [PMID: 30371894 DOI: 10.1093/nar/gky992] [Cited by in Crossref: 104] [Cited by in F6Publishing: 89] [Article Influence: 52.0] [Reference Citation Analysis]
5 Hoch M, Smita S, Cesnulevicius K, Lescheid D, Schultz M, Wolkenhauer O, Gupta S. Network- and enrichment-based inference of phenotypes and targets from large-scale disease maps. NPJ Syst Biol Appl 2022;8:13. [PMID: 35473910 DOI: 10.1038/s41540-022-00222-z] [Reference Citation Analysis]
6 Mazein A, Ivanova O, Balaur I, Ostaszewski M, Berzhitskaya V, Serebriyskaya T, Ligon T, Hasenauer J, De Meulder B, Overall RW, Roy L, Knowles RG, Wheelock CE, Dahlen SE, Chung KF, Adcock IM, Roberts G, Djukanovic R, Pellet J, Gawron P, Balling R, Maitland-van der Zee AH, Schneider R, Sterk PJ, Auffray C; U-BIOPRED Study Group,., eTRIKS Consortium. AsthmaMap: An interactive knowledge repository for mechanisms of asthma. J Allergy Clin Immunol 2021;147:853-6. [PMID: 33309742 DOI: 10.1016/j.jaci.2020.11.032] [Reference Citation Analysis]
7 Rian K, Esteban-Medina M, Hidalgo MR, Çubuk C, Falco MM, Loucera C, Gunyel D, Ostaszewski M, Peña-Chilet M, Dopazo J. Mechanistic modeling of the SARS-CoV-2 disease map. BioData Min 2021;14:5. [PMID: 33478554 DOI: 10.1186/s13040-021-00234-1] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
8 Kuiper M, Bonello J, Fernández-Breis JT, Bucher P, Futschik ME, Gaudet P, Kulakovskiy IV, Licata L, Logie C, Lovering RC, Makeev VJ, Orchard S, Panni S, Perfetto L, Sant D, Schulz S, Zerbino DR, Lægreid A; GRECO Consortium. The Gene Regulation Knowledge Commons: The action area of GREEKC. Biochim Biophys Acta Gene Regul Mech 2021;:194768. [PMID: 34757206 DOI: 10.1016/j.bbagrm.2021.194768] [Reference Citation Analysis]
9 Glavaški M, Velicki L. Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms' representation. BioData Min 2021;14:45. [PMID: 34600580 DOI: 10.1186/s13040-021-00279-2] [Reference Citation Analysis]
10 Morgan AE, Mc Auley MT. Cholesterol Homeostasis: An In Silico Investigation into How Aging Disrupts Its Key Hepatic Regulatory Mechanisms. Biology (Basel) 2020;9:E314. [PMID: 33007859 DOI: 10.3390/biology9100314] [Cited by in Crossref: 4] [Cited by in F6Publishing: 2] [Article Influence: 2.0] [Reference Citation Analysis]
11 Miagoux Q, Singh V, de Mézquita D, Chaudru V, Elati M, Petit-Teixeira E, Niarakis A. Inference of an Integrative, Executable Network for Rheumatoid Arthritis Combining Data-Driven Machine Learning Approaches and a State-of-the-Art Mechanistic Disease Map. J Pers Med 2021;11:785. [PMID: 34442429 DOI: 10.3390/jpm11080785] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
12 Aarestrup FM, Albeyatti A, Armitage WJ, Auffray C, Augello L, Balling R, Benhabiles N, Bertolini G, Bjaalie JG, Black M, Blomberg N, Bogaert P, Bubak M, Claerhout B, Clarke L, De Meulder B, D'Errico G, Di Meglio A, Forgo N, Gans-Combe C, Gray AE, Gut I, Gyllenberg A, Hemmrich-Stanisak G, Hjorth L, Ioannidis Y, Jarmalaite S, Kel A, Kherif F, Korbel JO, Larue C, Laszlo M, Maas A, Magalhaes L, Manneh-Vangramberen I, Morley-Fletcher E, Ohmann C, Oksvold P, Oxtoby NP, Perseil I, Pezoulas V, Riess O, Riper H, Roca J, Rosenstiel P, Sabatier P, Sanz F, Tayeb M, Thomassen G, Van Bussel J, Van den Bulcke M, Van Oyen H. Towards a European health research and innovation cloud (HRIC). Genome Med 2020;12:18. [PMID: 32075696 DOI: 10.1186/s13073-020-0713-z] [Cited by in Crossref: 16] [Cited by in F6Publishing: 9] [Article Influence: 8.0] [Reference Citation Analysis]
13 Rian K, Hidalgo MR, Çubuk C, Falco MM, Loucera C, Esteban-Medina M, Alamo-Alvarez I, Peña-Chilet M, Dopazo J. Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data. Comput Struct Biotechnol J 2021;19:2968-78. [PMID: 34136096 DOI: 10.1016/j.csbj.2021.05.022] [Reference Citation Analysis]
14 Rougny A, Paulevé L, Teboul M, Delaunay F. A detailed map of coupled circadian clock and cell cycle with qualitative dynamics validation. BMC Bioinformatics 2021;22:240. [PMID: 33975535 DOI: 10.1186/s12859-021-04158-9] [Reference Citation Analysis]
15 Mazein A, Ostaszewski M, Kuperstein I, Watterson S, Le Novère N, Lefaudeux D, De Meulder B, Pellet J, Balaur I, Saqi M, Nogueira MM, He F, Parton A, Lemonnier N, Gawron P, Gebel S, Hainaut P, Ollert M, Dogrusoz U, Barillot E, Zinovyev A, Schneider R, Balling R, Auffray C. Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms. NPJ Syst Biol Appl 2018;4:21. [PMID: 29872544 DOI: 10.1038/s41540-018-0059-y] [Cited by in Crossref: 42] [Cited by in F6Publishing: 29] [Article Influence: 10.5] [Reference Citation Analysis]
16 Messina F, Montaldo C, Abbate I, Antonioli M, Bordoni V, Matusali G, Sacchi A, Giombini E, Fimia GM, Piacentini M, Capobianchi MR, Lauria FN, Ippolito G, On Behalf Of Covid-Scoping Review Working Group. Rationale and Criteria for a COVID-19 Model Framework. Viruses 2021;13:1309. [PMID: 34372515 DOI: 10.3390/v13071309] [Cited by in Crossref: 2] [Cited by in F6Publishing: 1] [Article Influence: 2.0] [Reference Citation Analysis]
17 Hassanzadeh P. The significance of bioengineered nanoplatforms against SARS-CoV-2: From detection to genome editing. Life Sci 2021;274:119289. [PMID: 33676931 DOI: 10.1016/j.lfs.2021.119289] [Cited by in Crossref: 4] [Cited by in F6Publishing: 4] [Article Influence: 4.0] [Reference Citation Analysis]
18 Humayun F, Domingo-Fernández D, Paul George AA, Hopp MT, Syllwasschy BF, Detzel MS, Hoyt CT, Hofmann-Apitius M, Imhof D. A Computational Approach for Mapping Heme Biology in the Context of Hemolytic Disorders. Front Bioeng Biotechnol 2020;8:74. [PMID: 32211383 DOI: 10.3389/fbioe.2020.00074] [Cited by in Crossref: 10] [Cited by in F6Publishing: 9] [Article Influence: 5.0] [Reference Citation Analysis]
19 Mazein A, Rougny A, Karr JR, Saez-Rodriguez J, Ostaszewski M, Schneider R. Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling. Brief Bioinform 2021:bbab103. [PMID: 33834185 DOI: 10.1093/bib/bbab103] [Reference Citation Analysis]
20 Kondratova M, Czerwinska U, Sompairac N, Amigorena SD, Soumelis V, Barillot E, Zinovyev A, Kuperstein I. A multiscale signalling network map of innate immune response in cancer reveals cell heterogeneity signatures. Nat Commun 2019;10:4808. [PMID: 31641119 DOI: 10.1038/s41467-019-12270-x] [Cited by in Crossref: 18] [Cited by in F6Publishing: 15] [Article Influence: 6.0] [Reference Citation Analysis]
21 Singh V, Kalliolias GD, Ostaszewski M, Veyssiere M, Pilalis E, Gawron P, Mazein A, Bonnet E, Petit-Teixeira E, Niarakis A. RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis. Database (Oxford) 2020;2020:baaa017. [PMID: 32311035 DOI: 10.1093/database/baaa017] [Cited by in Crossref: 9] [Cited by in F6Publishing: 8] [Article Influence: 4.5] [Reference Citation Analysis]
22 Hassanzadeh P. Nanotheranostics against COVID-19: From multivalent to immune-targeted materials. J Control Release 2020;328:112-26. [PMID: 32882269 DOI: 10.1016/j.jconrel.2020.08.060] [Cited by in Crossref: 11] [Cited by in F6Publishing: 10] [Article Influence: 5.5] [Reference Citation Analysis]
23 Todorov PV, Gyori BM, Bachman JA, Sorger PK. INDRA-IPM: interactive pathway modeling using natural language with automated assembly. Bioinformatics 2019;35:4501-3. [PMID: 31070726 DOI: 10.1093/bioinformatics/btz289] [Cited by in Crossref: 11] [Cited by in F6Publishing: 4] [Article Influence: 5.5] [Reference Citation Analysis]
24 Montaldo C, Messina F, Abbate I, Antonioli M, Bordoni V, Aiello A, Ciccosanti F, Colavita F, Farroni C, Najafi Fard S, Giombini E, Goletti D, Matusali G, Rozera G, Rueca M, Sacchi A, Piacentini M, Agrati C, Fimia GM, Capobianchi MR, Lauria FN, Ippolito G. Multi-omics approach to COVID-19: a domain-based literature review. J Transl Med 2021;19:501. [PMID: 34876157 DOI: 10.1186/s12967-021-03168-8] [Reference Citation Analysis]
25 Touré V, Flobak Å, Niarakis A, Vercruysse S, Kuiper M. The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling. Brief Bioinform 2021;22:bbaa390. [PMID: 33378765 DOI: 10.1093/bib/bbaa390] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 1.0] [Reference Citation Analysis]