Diseasemap,eTRIKS,U-BIOPRED for

Alexander Mazein

Alexander Mazein

Senior Researcher

Senior Researcher in Computational Biology at the European Institute for Systems Biology and Medicine, Lyon, France. PhD in Bioinformatics, University of Edinburgh, UK, 2011. The leader of the Disease Maps community effort for comprehensive representation of disease mechanisms. Data integration and interpretation in connection to large-scale EU translational research projects including IMI eTRIKS (n°115446) and IMI U-BIOPRED (n°115010) projects. Systems Biology Graphical Notation (SBGN) editor for 2015 – 2018.

Research interests include knowledge formalisation, complexity management technologies, in-silico disease and health multiscale models, allergic diseases, autoimmune diseases, clinical applications for improved diagnostics and therapies via hypothesis generation and validation and the development of clinical decision support systems.

Keywords

Translational Research, Disease Mechanisms, Health and Wellness

EU Projects

  • eTRIKS – Role: Leader of the Disease Maps eTRIKS Lab
  • U-BIOPRED – Role: Leader of the AsthmaMap development

Community Projects

Tools

Experience

  • European Institute for Systems Biology and Medicine, France | Senior Researcher | 2014 – Present
  • Okinawa Institute of Science and Technology, Japan | Researcher | 2012 – 2013
  • University of Edinburgh, UK | Postdoctoral Research Associate | 2009 – 2011
  • University of Edinburgh, UK | PhD Student | 2006 – 2011
  • GeneGo, Inc. (now part of Thomson Reuters MetaCore) | Scientific Database Curator | 2005

Education

  • Ph.D., Bioinformatics
  • M.Sc., Biochemistry
  • M.Sc., Human and Animal Physiology

Selected publications

  • 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. PMID: 28725475.
  • Balaur I, Mazein A, Saqi M, Lysenko A, Rawlings CJ, Auffray C. Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks. Bioinformatics. 2016 Dec 19. pii: btw731. doi: 10.1093/bioinformatics/btw731. [Epub ahead of print] PubMed PMID: 27993779.
  • Touré V, Mazein A, Waltemath D, Balaur I, Saqi M, Henkel R, Pellet J, Auffray C. STON: exploring biological pathways using the SBGN standard and graph databases. BMC Bioinformatics. 2016 Dec 5;17(1):494. PubMed PMID: 27919219.
  • Mazein A, Watterson S, Griffiths WJ, Ghazal P (2013) A comprehensive machine-readable view of the mammalian cholesterol biosynthesis pathway. Biochem Pharmacol. 2013 Apr 10. doi:pii: S0006-2952(13)00221-9. 10.1016/j.bcp.2013.03.021. PubMed PMID: 23583456.
  • Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novère N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BO (2013) A community-driven global reconstruction of human metabolism. Nat Biotechnol. 2013 Mar 3. doi: 10.1038/nbt.2488. PubMed PMID: 23455439.
  • Junker A, Sorokin A, Czauderna T, Schreiber F, Mazein A (2012) Wiring diagrams in biology: towards the standardized representation of biological information. Trends in Biotechnology. 2012 Sep 11. pii: S0167-7799(12)00133-3. doi:10.1016/j.tibtech.2012.08.003. PubMed PMID: 22979995.
Alexander Mazein
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