Vassilis Aidinis Research Group

Mouse informatics resources: Creation, curation, coordination and interoperability

Much of the current effort in functional genomics, and our understanding of the biology of human disease, is underpinned by informatics infrastructures served by the scattered collection of relevant databases which exists in Europe. This infrastructure is essential for the support of a European Research Area in functional genomics and failure to integrate and sustain these databases will have deleterious effects on research competitiveness. In this context, we have created 1) The MUGEN mouse database (MMdb), a database of murine models of immune processes and immunological diseases aiming to share and publicize information on mouse strain characteristics and availability and 2) the Fleming mouse database, listing all locally available mouse strains. Moreover, in the context of a European commission co-ordination action grant, we are exploring database interoperability and sustainability, having organized a series of scientific meetings and produced a number of reports and scientific papers. Moreover we have created the Mouse Resource Browser (MRB), a database for searching and retrieving information about online mouse resources, as well as their interoperability mode (web services, dumps). Finally we have created CreZOO, a database of all European transgenic mouse lines expressing the Cre recombinase, an essential tool to exploit the increasing availability of targeted conditional alleles in the mouse. These four databases together with multiple links to other mouse-related electronic resources can be found at E-mouse. We are currently preparing a database application for the support of biobanking efforts.


Indicative selected publications

  • Aidinis V. Chandras C, Manoloukos M, Thanassopoulou A, Kranidioti K, Armaka M, Douni E, Kontoyiannis DL, Zouberakis M, Kollias G; the Mugen NoE consortium., 2008, "MUGEN mouse database; Animal models of human immunological diseases.", Nucleic Acids Res., 36 (Database issue) :D1048-54 [Pubmed]
  •  Schofield PN, Eppig J, Huala E, de Angelis MH, Harvey M, Davidson D, Weaver T, Brown S, Smedley D, Rosenthal N, Schughart K, Aidinis V, Tocchini-Valentini G, Hancock JM. 2010, "Research funding. Sustaining the data and bioresource commons.", Science. , 2010 Oct 29; 330(6004):592-3. [PubMed]. 
  •  Chandras C, Zouberakis M, Salimova E, Smedley D, Rosenthal N, Aidinis V. 2012, "CreZOO--the European virtual repository of Cre and other targeted conditional driver strains.", Database (Oxford), 2012 Jun 21; 2012:bas029. Print 2012. [PubMed].


Research and development of expression profiling through DNA microarrays

Expression profiling, the expression levels of thousand of genes, by DNA microarrays is a powerful tool for biologists, mathematicians and computer scientists in their attempt to decipher the complex organization of biological phenomena. The expression profile of any given cell, to any given status or response, constitutes a molecular fingerprint which could help to discriminate between malignant and benign, active or quiescent, resting or infected. Our laboratory has pioneered the establishment and development of this exciting technology in Greece, and is currently supervising the expression profiling unit of BSRC Fleming, offering services to academic and research centres, as well as the private sector, in the context of academic collaborations, participation in research networks, and/or contracted services.  


Indicative selected publications

  • Aidinis V., Carninci P., Armaka M., Witke W., Harokopos V., Pavelka N., Koczan D., Argyropoulos C., Thwin M., Möller S., Gopalakrishnakone P., Ricciardi-Castagnoli P., Thiesen H.J., Hayashizaki Y. and Kollias G., , 2005, "Twin expression profiling identifies cytoskeletal rearrangements in synovial fibroblasts as a novel pathophysiological determinant of modeled Rheumatoid Arthritis", PLoS Genetics, (Vol 1(4), e48 [PubMed].
  • The FANTOM consortium and RIKEN Genome Exploration Research group and Genome Science group., 2005, "The transcriptional landscape of the mammalian genome", Science., Sep 2., 309(5740):1559-63 [PubMed].
  • Tzouvelekis A, Harokopos V, Paparountas T, Oikonomou N, Chatziioannou A, Vilaras G, Tsiambas E, Karameris A, Bouros D and Aidinis V., 2007, "Comparative expression profiling in pulmonary fibrosis suggests a role of hypoxia-inducible factor-1alpha in disease pathogenesis", Am J Respir Crit Care Med, 176(11) :1108-19 [Pubmed]