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For: Hoksza D, Gawron P, Ostaszewski M, Hasenauer J, Schneider R. Closing the gap between formats for storing layout information in systems biology. Brief Bioinform 2020;21:1249-1260. [PMID: 31273380 PMCID: PMC7373180 DOI: 10.1093/bib/bbz067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/23/2019] [Accepted: 05/14/2019] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
1
Balaur I, Welter D, Rougny A, Inau ET, Mazein A, Ghosh S, Schneider R, Waltemath D, Ostaszewski M, Satagopam V. FAIR assessment of Disease Maps fosters open science and scientific crowdsourcing in systems biomedicine. Sci Data 2025;12:851. [PMID: 40410181 PMCID: PMC12102143 DOI: 10.1038/s41597-025-05147-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Accepted: 05/07/2025] [Indexed: 05/25/2025]  Open
2
Gottumukkala SB, Palanisamy A. Non-small cell lung cancer map and analysis: exploring interconnected oncogenic signal integrators. Mamm Genome 2025:10.1007/s00335-025-10110-6. [PMID: 39939487 DOI: 10.1007/s00335-025-10110-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2024] [Accepted: 01/29/2025] [Indexed: 02/14/2025]
3
Parchem K, Letsiou S, Petan T, Oskolkova O, Medina I, Kuda O, O'Donnell VB, Nicolaou A, Fedorova M, Bochkov V, Gladine C. Oxylipin profiling for clinical research: Current status and future perspectives. Prog Lipid Res 2024;95:101276. [PMID: 38697517 DOI: 10.1016/j.plipres.2024.101276] [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: 12/12/2023] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024]
4
Gottumukkala SB, Ganesan TS, Palanisamy A. Comprehensive molecular interaction map of TGFβ induced epithelial to mesenchymal transition in breast cancer. NPJ Syst Biol Appl 2024;10:53. [PMID: 38760412 PMCID: PMC11101644 DOI: 10.1038/s41540-024-00378-w] [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: 10/20/2023] [Accepted: 04/29/2024] [Indexed: 05/19/2024]  Open
5
Vega C, Ostaszewski M, Grouès V, Schneider R, Satagopam V. BioKC: a collaborative platform for curation and annotation of molecular interactions. Database (Oxford) 2024;2024:baae013. [PMID: 38537198 PMCID: PMC10972550 DOI: 10.1093/database/baae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 01/30/2024] [Accepted: 02/19/2024] [Indexed: 03/23/2025]
6
Gawron P, Hoksza D, Piñero J, Peña-Chilet M, Esteban-Medina M, Fernandez-Rueda JL, Colonna V, Smula E, Heirendt L, Ancien F, Groues V, Satagopam VP, Schneider R, Dopazo J, Furlong LI, Ostaszewski M. Visualization of automatically combined disease maps and pathway diagrams for rare diseases. FRONTIERS IN BIOINFORMATICS 2023;3:1101505. [PMID: 37502697 PMCID: PMC10369067 DOI: 10.3389/fbinf.2023.1101505] [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: 11/17/2022] [Accepted: 05/05/2023] [Indexed: 07/29/2023]  Open
7
Mazein A, Acencio ML, Balaur I, Rougny A, Welter D, Niarakis A, Ramirez Ardila D, Dogrusoz U, Gawron P, Satagopam V, Gu W, Kremer A, Schneider R, Ostaszewski M. A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance. FRONTIERS IN BIOINFORMATICS 2023;3:1197310. [PMID: 37426048 PMCID: PMC10325725 DOI: 10.3389/fbinf.2023.1197310] [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: 03/30/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023]  Open
8
Ladeira L, Gamba A, Lesage R, Ertvelde JV, Jiang J, Verhoeven A, Roodzant D, Teunis M, Jover R, Vanhaecke T, Vinken M, Geris L, Staumont B. P11-09 Physiology-based framework to study chemical-induced cholestasis. Toxicol Lett 2022. [DOI: 10.1016/j.toxlet.2022.07.459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
9
Staumont B, Ladeira L, Gamba A, Lesage R, Verhoeven A, Jiang J, Ertvelde JV, Barnes D, Janssen M, Kuchovska E, Berkhout J, Roodzant D, Teunis M, Bozada T, Luechtefeld T, Jover R, Vanhaecke T, Vinken M, Masereeuw R, Fritsche E, Piersma A, Heusinkveld H, Geris L. SOC-VI-08 Physiological maps: a benchmark tool for adverse outcome pathways and a cornerstone for the development of disease ontologies. Toxicol Lett 2022. [DOI: 10.1016/j.toxlet.2022.07.228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
10
Glavaški M, Velicki L. Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms' representation. BioData Min 2021;14:45. [PMID: 34600580 PMCID: PMC8487578 DOI: 10.1186/s13040-021-00279-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/14/2021] [Indexed: 11/25/2022]  Open
11
Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta‐Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic‐Milacic M, Senff Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel J, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, et alOstaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta‐Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic‐Milacic M, Senff Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel J, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban‐Medina M, Peña‐Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, De Meulder B, Ballereau S, Dugourd A, Naldi A, Noël V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Wilighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D'Eustachio P, Saez‐Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R, the COVID‐19 Disease Map Community. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Mol Syst Biol 2021;17:e10387. [PMID: 34664389 PMCID: PMC8524328 DOI: 10.15252/msb.202110387] [Show More Authors] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 12/13/2022]  Open
12
Hanspers K, Kutmon M, Coort SL, Digles D, Dupuis LJ, Ehrhart F, Hu F, Lopes EN, Martens M, Pham N, Shin W, Slenter DN, Waagmeester A, Willighagen EL, Winckers LA, Evelo CT, Pico AR. Ten simple rules for creating reusable pathway models for computational analysis and visualization. PLoS Comput Biol 2021;17:e1009226. [PMID: 34411100 PMCID: PMC8375987 DOI: 10.1371/journal.pcbi.1009226] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
13
Porubsky V, Smith L, Sauro HM. Publishing reproducible dynamic kinetic models. Brief Bioinform 2021;22:bbaa152. [PMID: 32793969 PMCID: PMC8138891 DOI: 10.1093/bib/bbaa152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/19/2020] [Accepted: 06/17/2020] [Indexed: 11/14/2022]  Open
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 PMCID: PMC8114686 DOI: 10.1186/s12859-021-04158-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 04/21/2021] [Indexed: 12/16/2022]  Open
15
Niarakis A, Kuiper M, Ostaszewski M, Malik Sheriff RS, Casals-Casas C, Thieffry D, Freeman TC, Thomas P, Touré V, Noël V, Stoll G, Saez-Rodriguez J, Naldi A, Oshurko E, Xenarios I, Soliman S, Chaouiya C, Helikar T, Calzone L. Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop. Brief Bioinform 2020;22:1848-1859. [PMID: 32313939 DOI: 10.1093/bib/bbaa046] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/20/2020] [Accepted: 03/08/2020] [Indexed: 12/14/2022]  Open
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