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For: Gawron P, Ostaszewski M, Satagopam V, Gebel S, Mazein A, Kuzma M, Zorzan S, McGee F, Otjacques B, Balling R, Schneider R. MINERVA-a platform for visualization and curation of molecular interaction networks. NPJ Syst Biol Appl 2016;2:16020. [PMID: 28725475 PMCID: PMC5516855 DOI: 10.1038/npjsba.2016.20] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 06/15/2016] [Accepted: 06/24/2016] [Indexed: 12/11/2022]  Open
Number Cited by Other Article(s)
1
Hemedan AA, Satagopam V, Schneider R, Ostaszewski M. Cohort-specific boolean models highlight different regulatory modules during Parkinson's disease progression. iScience 2024;27:110956. [PMID: 39429779 PMCID: PMC11489052 DOI: 10.1016/j.isci.2024.110956] [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: 03/28/2024] [Revised: 07/02/2024] [Accepted: 09/10/2024] [Indexed: 10/22/2024]  Open
2
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
3
Niarakis A, Ostaszewski M, Mazein A, Kuperstein I, Kutmon M, Gillespie ME, Funahashi A, Acencio ML, Hemedan A, Aichem M, Klein K, Czauderna T, Burtscher F, Yamada TG, Hiki Y, Hiroi NF, Hu F, Pham N, Ehrhart F, Willighagen EL, Valdeolivas A, Dugourd A, Messina F, Esteban-Medina M, Peña-Chilet M, Rian K, Soliman S, Aghamiri SS, Puniya BL, Naldi A, Helikar T, Singh V, Fernández MF, Bermudez V, Tsirvouli E, Montagud A, Noël V, Ponce-de-Leon M, Maier D, Bauch A, Gyori BM, Bachman JA, Luna A, Piñero J, Furlong LI, Balaur I, Rougny A, Jarosz Y, Overall RW, Phair R, Perfetto L, Matthews L, Rex DAB, Orlic-Milacic M, Gomez LCM, De Meulder B, Ravel JM, Jassal B, Satagopam V, Wu G, Golebiewski M, Gawron P, Calzone L, Beckmann JS, Evelo CT, D’Eustachio P, Schreiber F, Saez-Rodriguez J, Dopazo J, Kuiper M, Valencia A, Wolkenhauer O, Kitano H, Barillot E, Auffray C, Balling R, Schneider R. Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches. Front Immunol 2024;14:1282859. [PMID: 38414974 PMCID: PMC10897000 DOI: 10.3389/fimmu.2023.1282859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/22/2023] [Indexed: 02/29/2024]  Open
4
Veyssiere M, Sadat Aghamiri S, Hernandez Cervantes A, Henry T, Soumelis V. A mathematical model of Familial Mediterranean Fever predicts mechanisms controlling inflammation. Clin Immunol 2023;257:109839. [PMID: 37952562 DOI: 10.1016/j.clim.2023.109839] [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: 07/12/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/14/2023]
5
Acencio ML, Ostaszewski M, Mazein A, Rosenstiel P, Aden K, Mishra N, Andersen V, Sidiropoulos P, Banos A, Filia A, Rahmouni S, Finckh A, Gu W, Schneider R, Satagopam V. The SYSCID map: a graphical and computational resource of molecular mechanisms across rheumatoid arthritis, systemic lupus erythematosus and inflammatory bowel disease. Front Immunol 2023;14:1257321. [PMID: 38022524 PMCID: PMC10646502 DOI: 10.3389/fimmu.2023.1257321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]  Open
6
Xu J, Geng G, Nguyen ND, Perena-Cortes C, Samuels C, Sauro HM. SBcoyote: An extensible Python-based reaction editor and viewer. Biosystems 2023;232:105001. [PMID: 37595778 DOI: 10.1016/j.biosystems.2023.105001] [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: 02/16/2023] [Revised: 05/15/2023] [Accepted: 08/12/2023] [Indexed: 08/20/2023]
7
Aghakhani S, Silva-Saffar SE, Soliman S, Niarakis A. Hybrid computational modeling highlights reverse warburg effect in breast cancer-associated fibroblasts. Comput Struct Biotechnol J 2023;21:4196-4206. [PMID: 37705596 PMCID: PMC10495551 DOI: 10.1016/j.csbj.2023.08.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 08/18/2023] [Accepted: 08/18/2023] [Indexed: 09/15/2023]  Open
8
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
9
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
10
Hemedan AA, Schneider R, Ostaszewski M. Applications of Boolean modeling to study the dynamics of a complex disease and therapeutics responses. FRONTIERS IN BIOINFORMATICS 2023;3:1189723. [PMID: 37325771 PMCID: PMC10267406 DOI: 10.3389/fbinf.2023.1189723] [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: 03/19/2023] [Accepted: 05/18/2023] [Indexed: 06/17/2023]  Open
11
Gawron P, Smula E, Schneider R, Ostaszewski M. Exploration and comparison of molecular mechanisms across diseases using MINERVA Net. Protein Sci 2023;32:e4565. [PMID: 36648161 PMCID: PMC9885449 DOI: 10.1002/pro.4565] [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: 09/12/2022] [Revised: 12/16/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023]
12
Martins dos Santos V, Anton M, Szomolay B, Ostaszewski M, Arts I, Benfeitas R, Dominguez Del Angel V, Domínguez-Romero E, Ferk P, Fey D, Goble C, Golebiewski M, Gruden K, Heil KF, Hermjakob H, Kahlem P, Klapa MI, Koehorst J, Kolodkin A, Kutmon M, Leskošek B, Moretti S, Müller W, Pagni M, Rezen T, Rocha M, Rozman D, Šafránek D, T. Scott W, Sheriff RSM, Suarez Diez M, Van Steen K, Westerhoff HV, Wittig U, Wolstencroft K, Zupanic A, Evelo CT, Hancock JM. Systems Biology in ELIXIR: modelling in the spotlight. F1000Res 2022;11:ELIXIR-1265. [PMID: 36742342 PMCID: PMC9871403 DOI: 10.12688/f1000research.126734.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/24/2022] [Indexed: 11/09/2022]  Open
13
Martins dos Santos V, Anton M, Szomolay B, Ostaszewski M, Arts I, Benfeitas R, Dominguez Del Angel V, Domínguez-Romero E, Ferk P, Fey D, Goble C, Golebiewski M, Gruden K, Heil KF, Hermjakob H, Kahlem P, Klapa MI, Koehorst J, Kolodkin A, Kutmon M, Leskošek B, Moretti S, Müller W, Pagni M, Rezen T, Rocha M, Rozman D, Šafránek D, T. Scott W, Sheriff RSM, Suarez Diez M, Van Steen K, Westerhoff HV, Wittig U, Wolstencroft K, Zupanic A, Evelo CT, Hancock JM. Systems Biology in ELIXIR: modelling in the spotlight. F1000Res 2022;11:ELIXIR-1265. [PMID: 36742342 PMCID: PMC9871403 DOI: 10.12688/f1000research.126734.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/20/2024] [Indexed: 06/05/2024]  Open
14
Hoch M, Ehlers L, Bannert K, Stanke C, Brauer D, Caton V, Lamprecht G, Wolkenhauer O, Jaster R, Wolfien M. In silico investigation of molecular networks linking gastrointestinal diseases, malnutrition, and sarcopenia. Front Nutr 2022;9:989453. [DOI: 10.3389/fnut.2022.989453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022]  Open
15
Hemedan AA, Niarakis A, Schneider R, Ostaszewski M. Boolean modelling as a logic-based dynamic approach in systems medicine. Comput Struct Biotechnol J 2022;20:3161-3172. [PMID: 35782730 PMCID: PMC9234349 DOI: 10.1016/j.csbj.2022.06.035] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 11/17/2022]  Open
16
Network- and enrichment-based inference of phenotypes and targets from large-scale disease maps. NPJ Syst Biol Appl 2022;8:13. [PMID: 35473910 PMCID: PMC9042890 DOI: 10.1038/s41540-022-00222-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 03/22/2022] [Indexed: 01/09/2023]  Open
17
Garcia P, Jürgens‐Wemheuer W, Uriarte Huarte O, Michelucci A, Masuch A, Brioschi S, Weihofen A, Koncina E, Coowar D, Heurtaux T, Glaab E, Balling R, Sousa C, Kaoma T, Nicot N, Pfander T, Schulz‐Schaeffer W, Allouche A, Fischer N, Biber K, Kleine‐Borgmann F, Mittelbronn M, Ostaszewski M, Schmit KJ, Buttini M. Neurodegeneration and neuroinflammation are linked, but independent of alpha‐synuclein inclusions, in a seeding/spreading mouse model of Parkinson's disease. Glia 2022;70:935-960. [PMID: 35092321 PMCID: PMC9305192 DOI: 10.1002/glia.24149] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 12/16/2022]
18
Pereira C, Mazein A, Farinha CM, Gray MA, Kunzelmann K, Ostaszewski M, Balaur I, Amaral MD, Falcao AO. CyFi-MAP: an interactive pathway-based resource for cystic fibrosis. Sci Rep 2021;11:22223. [PMID: 34782688 PMCID: PMC8592983 DOI: 10.1038/s41598-021-01618-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/27/2021] [Indexed: 12/11/2022]  Open
19
Vinhoven L, Voskamp M, Nietert MM. Mapping Compound Databases to Disease Maps-A MINERVA Plugin for CandActBase. J Pers Med 2021;11:jpm11111072. [PMID: 34834423 PMCID: PMC8625161 DOI: 10.3390/jpm11111072] [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: 09/16/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022]  Open
20
Cabbia A, Hilbers PAJ, van Riel NAW. Simulating Metabolic Flexibility in Low Energy Expenditure Conditions Using Genome-Scale Metabolic Models. Metabolites 2021;11:metabo11100695. [PMID: 34677410 PMCID: PMC8537358 DOI: 10.3390/metabo11100695] [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: 05/21/2021] [Revised: 09/03/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022]  Open
21
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: 1.7] [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
22
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, 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. 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] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [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
23
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 PMCID: PMC8294520 DOI: 10.1093/bib/bbaa390] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/16/2022]  Open
24
Nielsen SS, Ostaszewski M, McGee F, Hoksza D, Zorzan S. Machine Learning to Support the Presentation of Complex Pathway Graphs. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;18:1130-1141. [PMID: 31484128 DOI: 10.1109/tcbb.2019.2938501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
25
MINERVA, A Platform for the Exploration of Disease Maps. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11685-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]  Open
26
Henry V, Moszer I, Dameron O, Vila Xicota L, Dubois B, Potier MC, Hofmann-Apitius M, Colliot O. Converting disease maps into heavyweight ontologies: general methodology and application to Alzheimer's disease. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021;2021:6137817. [PMID: 33590873 DOI: 10.1093/database/baab004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 01/17/2021] [Accepted: 01/27/2021] [Indexed: 11/12/2022]
27
Monraz Gomez LC, Kondratova M, Sompairac N, Lonjou C, Ravel JM, Barillot E, Zinovyev A, Kuperstein I. Atlas of Cancer Signaling Network: A Resource of Multi-Scale Biological Maps to Study Disease Mechanisms. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11683-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]  Open
28
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. AsthmaMap: An interactive knowledge repository for mechanisms of asthma. J Allergy Clin Immunol 2020;147:853-856. [PMID: 33309742 DOI: 10.1016/j.jaci.2020.11.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/17/2020] [Accepted: 11/10/2020] [Indexed: 10/22/2022]
29
Schultz A, Akbani R. SAMMI: a semi-automated tool for the visualization of metabolic networks. Bioinformatics 2020;36:2616-2617. [PMID: 31851289 DOI: 10.1093/bioinformatics/btz927] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/14/2019] [Accepted: 12/16/2019] [Indexed: 01/26/2023]  Open
30
Serhan CN, Gupta SK, Perretti M, Godson C, Brennan E, Li Y, Soehnlein O, Shimizu T, Werz O, Chiurchiù V, Azzi A, Dubourdeau M, Gupta SS, Schopohl P, Hoch M, Gjorgevikj D, Khan FM, Brauer D, Tripathi A, Cesnulevicius K, Lescheid D, Schultz M, Särndahl E, Repsilber D, Kruse R, Sala A, Haeggström JZ, Levy BD, Filep JG, Wolkenhauer O. The Atlas of Inflammation Resolution (AIR). Mol Aspects Med 2020;74:100894. [PMID: 32893032 PMCID: PMC7733955 DOI: 10.1016/j.mam.2020.100894] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
31
Serhan CN, Gupta SK, Perretti M, Godson C, Brennan E, Li Y, Soehnlein O, Shimizu T, Werz O, Chiurchiù V, Azzi A, Dubourdeau M, Gupta SS, Schopohl P, Hoch M, Gjorgevikj D, Khan FM, Brauer D, Tripathi A, Cesnulevicius K, Lescheid D, Schultz M, Särndahl E, Repsilber D, Kruse R, Sala A, Haeggström JZ, Levy BD, Filep JG, Wolkenhauer O. WITHDRAWN: The Atlas of Inflammation Resolution (AIR). Mol Aspects Med 2020:100893. [PMID: 32873427 DOI: 10.1016/j.mam.2020.100893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
32
Piereck B, Oliveira-Lima M, Benko-Iseppon AM, Diehl S, Schneider R, Brasileiro-Vidal AC, Barbosa-Silva A. LAITOR4HPC: A text mining pipeline based on HPC for building interaction networks. BMC Bioinformatics 2020;21:365. [PMID: 32838742 PMCID: PMC7447576 DOI: 10.1186/s12859-020-03620-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 06/19/2020] [Indexed: 11/11/2022]  Open
33
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: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [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
34
Hoksza D, Gawron P, Ostaszewski M, Smula E, Schneider R. MINERVA API and plugins: opening molecular network analysis and visualization to the community. Bioinformatics 2020;35:4496-4498. [PMID: 31074494 PMCID: PMC6821317 DOI: 10.1093/bioinformatics/btz286] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/29/2019] [Accepted: 04/16/2019] [Indexed: 11/14/2022]  Open
35
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 2020;47:D614-D624. [PMID: 30371894 PMCID: PMC6323901 DOI: 10.1093/nar/gky992] [Citation(s) in RCA: 215] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/09/2018] [Indexed: 12/31/2022]  Open
36
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: 3.3] [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
37
Ravel JM, Monraz Gomez LC, Sompairac N, Calzone L, Zhivotovsky B, Kroemer G, Barillot E, Zinovyev A, Kuperstein I. Comprehensive Map of the Regulated Cell Death Signaling Network: A Powerful Analytical Tool for Studying Diseases. Cancers (Basel) 2020;12:E990. [PMID: 32316560 PMCID: PMC7226067 DOI: 10.3390/cancers12040990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 03/10/2020] [Indexed: 12/25/2022]  Open
38
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 PMCID: PMC7170216 DOI: 10.1093/database/baaa017] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 01/21/2020] [Accepted: 02/13/2020] [Indexed: 02/07/2023]
39
Hoksza D, Gawron P, Ostaszewski M, Schneider R. MolArt: a molecular structure annotation and visualization tool. Bioinformatics 2019;34:4127-4128. [PMID: 29931246 PMCID: PMC6247942 DOI: 10.1093/bioinformatics/bty489] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 06/13/2018] [Indexed: 11/16/2022]  Open
40
Schymanski EL, Baker NC, Williams AJ, Singh RR, Trezzi JP, Wilmes P, Kolber PL, Kruger R, Paczia N, Linster CL, Balling R. Connecting environmental exposure and neurodegeneration using cheminformatics and high resolution mass spectrometry: potential and challenges. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2019;21:1426-1445. [PMID: 31305828 DOI: 10.1039/c9em00068b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
41
Sompairac N, Nazarov PV, Czerwinska U, Cantini L, Biton A, Molkenov A, Zhumadilov Z, Barillot E, Radvanyi F, Gorban A, Kairov U, Zinovyev A. Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets. Int J Mol Sci 2019;20:E4414. [PMID: 31500324 PMCID: PMC6771121 DOI: 10.3390/ijms20184414] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/02/2019] [Accepted: 09/04/2019] [Indexed: 12/13/2022]  Open
42
Duciel L, Monraz Gomez LC, Kondratova M, Kuperstein I, Saule S. The Phosphatase PRL-3 Is Involved in Key Steps of Cancer Metastasis. J Mol Biol 2019;431:3056-3067. [DOI: 10.1016/j.jmb.2019.06.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 05/24/2019] [Accepted: 06/06/2019] [Indexed: 12/17/2022]
43
Wu HY, Nöllenburg M, Sousa FL, Viola I. Metabopolis: scalable network layout for biological pathway diagrams in urban map style. BMC Bioinformatics 2019;20:187. [PMID: 30991966 PMCID: PMC6466808 DOI: 10.1186/s12859-019-2779-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 03/25/2019] [Indexed: 01/06/2023]  Open
44
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;20:659-670. [PMID: 29688273 PMCID: PMC6556900 DOI: 10.1093/bib/bby024] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/02/2018] [Indexed: 01/07/2023]  Open
45
Heirendt L, Arreckx S, Pfau T, Mendoza SN, Richelle A, Heinken A, Haraldsdóttir HS, Wachowiak J, Keating SM, Vlasov V, Magnusdóttir S, Ng CY, Preciat G, Žagare A, Chan SHJ, Aurich MK, Clancy CM, Modamio J, Sauls JT, Noronha A, Bordbar A, Cousins B, El Assal DC, Valcarcel LV, Apaolaza I, Ghaderi S, Ahookhosh M, Ben Guebila M, Kostromins A, Sompairac N, Le HM, Ma D, Sun Y, Wang L, Yurkovich JT, Oliveira MAP, Vuong PT, El Assal LP, Kuperstein I, Zinovyev A, Hinton HS, Bryant WA, Aragón Artacho FJ, Planes FJ, Stalidzans E, Maass A, Vempala S, Hucka M, Saunders MA, Maranas CD, Lewis NE, Sauter T, Palsson BØ, Thiele I, Fleming RMT. Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. Nat Protoc 2019;14:639-702. [PMID: 30787451 PMCID: PMC6635304 DOI: 10.1038/s41596-018-0098-2] [Citation(s) in RCA: 647] [Impact Index Per Article: 129.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
46
Fabregat A, Sidiropoulos K, Viteri G, Marin-Garcia P, Ping P, Stein L, D'Eustachio P, Hermjakob H. Reactome diagram viewer: data structures and strategies to boost performance. Bioinformatics 2018;34:1208-1214. [PMID: 29186351 PMCID: PMC6030826 DOI: 10.1093/bioinformatics/btx752] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 11/22/2017] [Indexed: 12/21/2022]  Open
47
Kondratova M, Sompairac N, Barillot E, Zinovyev A, Kuperstein I. Signalling maps in cancer research: construction and data analysis. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018;2018:4964960. [PMID: 29688383 PMCID: PMC5890450 DOI: 10.1093/database/bay036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 03/19/2018] [Indexed: 12/22/2022]
48
Ostaszewski M, Kieffer E, Danoy G, Schneider R, Bouvry P. Clustering approaches for visual knowledge exploration in molecular interaction networks. BMC Bioinformatics 2018;19:308. [PMID: 30157777 PMCID: PMC6116538 DOI: 10.1186/s12859-018-2314-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 08/14/2018] [Indexed: 12/02/2022]  Open
49
Fröhlich H, Balling R, Beerenwinkel N, Kohlbacher O, Kumar S, Lengauer T, Maathuis MH, Moreau Y, Murphy SA, Przytycka TM, Rebhan M, Röst H, Schuppert A, Schwab M, Spang R, Stekhoven D, Sun J, Weber A, Ziemek D, Zupan B. From hype to reality: data science enabling personalized medicine. BMC Med 2018;16:150. [PMID: 30145981 PMCID: PMC6109989 DOI: 10.1186/s12916-018-1122-7] [Citation(s) in RCA: 198] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/09/2018] [Indexed: 02/08/2023]  Open
50
Sidiropoulos K, Viteri G, Sevilla C, Jupe S, Webber M, Orlic-Milacic M, Jassal B, May B, Shamovsky V, Duenas C, Rothfels K, Matthews L, Song H, Stein L, Haw R, D'Eustachio P, Ping P, Hermjakob H, Fabregat A. Reactome enhanced pathway visualization. Bioinformatics 2018;33:3461-3467. [PMID: 29077811 PMCID: PMC5860170 DOI: 10.1093/bioinformatics/btx441] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/05/2017] [Indexed: 12/22/2022]  Open
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