Key community papers

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 Jun 2;4:21. doi: 10.1038/s41540-018-0059-y. eCollection 2018. PubMed PMID: 29872544.

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 Mar 25;20(2):659-670. doi: 10.1093/bib/bby024. PubMed PMID: 29688273.

Selected publications of the community members

Disease maps

Parton A, McGilligan V, Chemaly M, O’Kane M, Watterson S. New models of atherosclerosis and multi-drug therapeutic interventions. Bioinformatics. 2018 Dec 6. doi: 10.1093/bioinformatics/bty980. PubMed PMID: 30520978.

Mazein A, Knowles RG, Adcock I, Chung KF, Wheelock CE, Maitland-van der Zee AH, Sterk PJ, Auffray C; AsthmaMap Project Team. AsthmaMap: An expert-driven computational representation of disease mechanisms. Clin Exp Allergy. 2018 Aug;48(8):916-918. doi: 10.1111/cea.13211. PubMed PMID: 30133857.

Singh V, Ostaszewski M, Kalliolias GD, Chiocchia G, Olaso R, Petit-Teixeira E, Helikar T, Niarakis A. Computational Systems Biology Approach for the Study of Rheumatoid Arthritis: From a Molecular Map to a Dynamical Model. Genom Comput Biol. 2018;4(1). pii: e100050. doi: 10.18547/gcb.2018.vol4.iss1.e100050. Epub 2017 Dec 6. PubMed PMID: 29951575.

Kuperstein I, Bonnet E, Nguyen HA, Cohen D, Viara E, Grieco L, Fourquet S, Calzone L, Russo C, Kondratova M, Dutreix M, Barillot E, Zinovyev A. Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps. Oncogenesis. 2015 Jul 20;4:e160. doi: 10.1038/oncsis.2015.19. PubMed PMID: 26192618.

Fujita KA, Ostaszewski M, Matsuoka Y, Ghosh S, Glaab E, Trefois C, Crespo I, Perumal TM, Jurkowski W, Antony PM, Diederich N, Buttini M, Kodama A, Satagopam VP, Eifes S, Del Sol A, Schneider R, Kitano H, Balling R. Integrating pathways of Parkinson’s disease in a molecular interaction map. Mol Neurobiol. 2014 Feb;49(1):88-102. doi: 10.1007/s12035-013-8489-4. Epub 2013 Jul 7. Review. PubMed PMID: 23832570.

Map construction technology

Kondratova M, Sompairac N, Barillot E, Zinovyev A, Kuperstein I. Signalling maps in cancer research: construction and data analysis. Database (Oxford). 2018 Jan 1;2018. doi:10.1093/database/bay036. PubMed PMID: 29688383.

Applications of disease maps

Monraz Gomez LC, Kondratova M, Ravel JM, Barillot E, Zinovyev A, Kuperstein I. Application of Atlas of Cancer Signalling Network in preclinical studies. Brief Bioinform. 2018 May 3. doi: 10.1093/bib/bby031. PubMed PMID: 29726961.

Jdey W, Thierry S, Russo C, Devun F, Al Abo M, Noguiez-Hellin P, Sun JS, Barillot E, Zinovyev A, Kuperstein I, Pommier Y, Dutreix M. Drug-Driven Synthetic Lethality: Bypassing Tumor Cell Genetics with a Combination of AsiDNA and PARP Inhibitors. Clin Cancer Res. 2017 Feb 15;23(4):1001-1011. doi: 10.1158/1078-0432.CCR-16-1193. Epub 2016 Aug 24. PubMed PMID: 27559053.

Satagopam V, Gu W, Eifes S, Gawron P, Ostaszewski M, Gebel S, Barbosa-Silva A, Balling R, Schneider R. Integration and Visualization of Translational Medicine Data for Better Understanding of Human Diseases. Big Data. 2016 Jun;4(2):97-108. doi: 10.1089/big.2015.0057. PubMed PMID: 27441714.

Kuperstein I, Grieco L, Cohen DP, Thieffry D, Zinovyev A, Barillot E. The shortest path is not the one you know: application of biological network resources in precision oncology research. Mutagenesis. 2015 Mar;30(2):191-204. doi:10.1093/mutage/geu078. Review. PubMed PMID: 25688112.

Chanrion M, Kuperstein I, Barrière C, El Marjou F, Cohen D, Vignjevic D, Stimmer L, Paul-Gilloteaux P, Bièche I, Tavares Sdos R, Boccia GF, Cacheux W, Meseure D, Fre S, Martignetti L, Legoix-Né P, Girard E, Fetler L, Barillot E, Louvard D, Zinovyev A, Robine S. Concomitant Notch activation and p53 deletion trigger epithelial-to-mesenchymal transition and metastasis in mouse gut. Nat Commun. 2014 Oct 8;5:5005. doi:10.1038/ncomms6005. PubMed PMID: 25295490.


Hoksza D, Gawron P, Ostaszewski M, Smula E, Schneider R. MINERVA API and plugins: opening molecular network analysis and visualization to the community. Bioinformatics. 2019 Apr 25. pii: btz286. doi: 10.1093/bioinformatics/btz286. PubMed PMID: 31074494.

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 Sep 22;2:16020. doi: 10.1038/npjsba.2016.20. eCollection 2016. PubMed PMID: 28725475.

Bonnet E, Viara E, Kuperstein I, Calzone L, Cohen DP, Barillot E, Zinovyev A. NaviCell Web Service for network-based data visualization. Nucleic Acids Res. 2015 Jul 1;43(W1):W560-5. doi: 10.1093/nar/gkv450. Epub 2015 May 9. PubMed PMID: 25958393.

Kuperstein I, Cohen DP, Pook S, Viara E, Calzone L, Barillot E, Zinovyev A. NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. BMC Syst Biol. 2013 Oct 7;7:100. doi: 10.1186/1752-0509-7-100. PubMed PMID: 24099179.

Bonnet E, Calzone L, Rovera D, Stoll G, Barillot E, Zinovyev A. BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats. BMC Syst Biol. 2013 Mar 1;7:18. doi: 10.1186/1752-0509-7-18. PubMed PMID: 23453054.

Relevant projects

Disease maps

Matsuoka Y, Matsumae H, Katoh M, Eisfeld AJ, Neumann G, Hase T, Ghosh S, Shoemaker JE, Lopes TJ, Watanabe T, Watanabe S, Fukuyama S, Kitano H, Kawaoka Y. A comprehensive map of the influenza A virus replication cycle. BMC Syst Biol. 2013 Oct 2;7:97. doi:10.1186/1752-0509-7-97. PubMed PMID: 24088197.

Mizuno S, Iijima R, Ogishima S, Kikuchi M, Matsuoka Y, Ghosh S, Miyamoto T, Miyashita A, Kuwano R, Tanaka H. AlzPathway: a comprehensive map of signaling pathways of Alzheimer’s disease. BMC Syst Biol. 2012 May 30;6:52. doi:10.1186/1752-0509-6-52. PubMed PMID: 22647208.

Comprehensive pathway maps

Caron E, Ghosh S, Matsuoka Y, Ashton-Beaucage D, Therrien M, Lemieux S, Perreault C, Roux PP, Kitano H. A comprehensive map of the mTOR signaling network. Mol Syst Biol. 2010 Dec 21;6:453. doi: 10.1038/msb.2010.108. Review. PubMed PMID: 21179025.

Oda K, Kitano H. A comprehensive map of the toll-like receptor signaling network. Mol Syst Biol. 2006;2:2006.0015. Epub 2006 Apr 18. Review. PubMed PMID: 16738560.

Oda K, Matsuoka Y, Funahashi A, Kitano H. A comprehensive pathway map of epidermal growth factor receptor signaling. Mol Syst Biol. 2005;1:2005.0010. Epub 2005 May 25. PubMed PMID: 16729045.

Complementary approaches

Kodamullil AT, Younesi E, Naz M, Bagewadi S, Hofmann-Apitius M. Computable cause-and-effect models of healthy and Alzheimer’s disease states and their mechanistic differential analysis. Alzheimers Dement. 2015 Nov;11(11):1329-39. doi: 10.1016/j.jalz.2015.02.006. Epub 2015 Apr 4. PubMed PMID: 25849034.

Hoyt CT, Domingo-Fernández D, Aldisi R, Xu L, Kolpeja K, Spalek S, Wollert E, Bachman J, Gyori BM, Greene P, Hofmann-Apitius M. Re-curation and Rational Enrichment of Knowledge Graphs in Biological Expression Language. bioRxiv. Preprint 2019 Jan 31. doi: 10.1101/536409.