Publications

DELIVERABLE AND PERIODIC REPORTS ARE AVAILABLE HERE

Peer-reviewed publications

   2014

• Faulconbridge, A., Burdett, T., Brandizi, M., Gostev, M., Pereira, R., Vasant, D., Sarkans, U., Brazma, A., Parkinson, H. Updates to BioSamples database at European Bioinformatics Institute. Nucleic acids research, Volume 42, Issue 1 (Open Access)
• Jupp, S., Malone, J., Bolleman, J., Brandizi, M., Davies, M., Garcia, L., Gaulton, A., Gehant, S., Laibe, C., Redaschi, N., Wimalaratne, S. M., Martin, M., Le Novère, N., Parkinson, H., Birney, E., Jenkinson, A. M. The EBI RDF Platform: Linked Open Data for the Life Sciences. Bioinformatics (ePub ahead of print)

• Valasatava Y, Rosato A, Cavallaro G, Andreini C. MetalS3, a database-mining tool for the identification of structurally similar metal sites. J Biol Inorg Chem [Epub ahead of print]

    2013

• Andreini, C., Cavallaro, G., Rosato, A., Valasatava, Y. MetalS2: a tool for the structural alignment of minimal functional sites in metal-binding proteins and nucleic acids. Journal of Chemical Information and Modeling, issue 53, Volume 11 (Open Access)
• Chambers, J., Davies, M., Gaulton, A., Hersey, A., Velankar, S., Petryszak, R., Hastings, J., Bellis, L., McGlinchey, S., Overington, J. P. UniChem: a unified chemical structure cross-referencing and identifier tracking system. Journal of Cheminformatics, Volume 5, Issue 3 (Open Access)
• Guyader, J. M., Bernardin, L., Douglas, N. H. M., Poot, D. H. J., Niessen, W. J., Klein, S. Influence of image registration on ADC images computed from free-breathing diffusion MRIs of the abdomen. SPIE Medical Imaging (In Press)
• Ison, J., Kalaš, M., Jonassen, I., Bolser, D., Uludag, M., McWilliam, H., Malone, J., Lopez, R., Pettifer, S., Rice, P. EDAM: An ontology of bioinformatics operations, types of data and identifiers, topics, and formats. Bioinformatics, Volume 29, Issue 10 (Open Access)
• Lagerstedt, I., Moore, W. J., Patwardhan, A., Sanz-García, E., Best, C., Swedlow, J. R., Kleywegt, G. J. Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB. Journal of Structural Biology, Volume 184, Issue 2 (Open Access)
• Pemovska T, Kontro M, Yadav B, Edgren H, Eldfors S, Szwajda A, Almusa H, Bespalov MM, Ellonen P, Elonen E, Gjertsen BT, Karjalainen R, Kulesskiy E, Lagström S, Lehto A, Lepistö M, Lundán T, Majumder MM, Marti JM, Mattila P, Murumägi A, Mustjoki S, Palva A, Parsons A, Pirttinen T, Rämet ME, Suvela M, Turunen L, Västrik I, Wolf M, Knowles J, Aittokallio T, Heckman CA, Porkka K, Kallioniemi O, Wennerberg K. Individualized systems medicine strategy to tailor treatments for patients with chemorefractory acute myeloid leukemia. Cancer Discovery, Volume 3, Issue 12 (Open Access)

    2012

• Bertini, I., Ferella, L., Luchinat, C., Parigi, G., Petoukhov, M. V., Ravera, E., Rosato, A., Svergun, D. I. MaxOcc: a web portal for maximum occurrence analysis. Journal of Biomolecular NMR, Volume 53, Issue 4. (MaxOcc will be integrated in WP9)

Other publications

    2014

• Principles of data management and sharing at European research infrastructures. Joint working paper byELIXIR and EU-OPENSCREEN with AnaEE,BBMRI, EATRIS, ECRIN,ERINHA, EMBRC, Euro-BioImaging,INFRAFRONTIER, INSTRUCT, ISBE,LifeWatch and MIRRI

    2013

• Field, L., Suhr, S., Ison, J., Wouter, L., Wittenburg, P., Broeder, D., Hardisty, A., Repo, S., Jenkinson, A. Realising the full potential of research data: common challenges in data management, sharing and integration across scientific disciplines. Joint working paper by the FP7 ESFRI cluster projects:BioMedBridges, CRISP, DASISH, ENVRI

Posters

   2013

• K. Joeri van der Velde et al: OmicsConnect: flexible multi-omics tools for high-throughput translational medicine. HandsOn Biobanks conference, The Hague
• Ingvar Lagerstedt, "Shape Matching service for Structural Biology", Gordon Research Conference on Three Dimensional Electron Microscopy, June 23-28, Colby-Sawyer College, New London, USA

   2012

• BioMedBridges project overview
• BioMedBridges tools and services registry
• Nathalie Conte et al.: PhenoBridge: Linking mouse model to human clinical data using Diabetes and Obesity as a framework (presented at Diabetes and Obesity conference 2012)
• Roland Krause et al: Towards a European legal framework for data protection–Implications for scientific research of the draft EU Data Protection Regulation (presented at the first EUDAT conference, October 2012)
• Narayanan Krishnan et al: PiMS - a BioMedBridges perspective (presented at NOBUGS conference 2012)

News articles

• Optimizing simulations for life — ScalaLife, includes interview with J. Ison on BioMedBridges Service Registry, isgtw, June 5, 2013

Presentations

   2012

• BioMedBridges project overview at 1st EUDAT conference, Barcelona, October 2012 (S. Suhr)
• Towards an intelligent framework to catalogue and search biobank (meta)data. HandsOn Biobanks, Uppsala, September 21, 2012 (M. Swertz et al)
• From big data to bedside? Bridging multi-disciplinary research to MD/Patients. NL eScience Symposium, Amsterdam, November 6, 2013  (M. Swertz et al)
• Introducing the BBMRI-NL biobank catalogue. Connecting biobanks, Utrecht, November 19, 2012 (M. Swertz et al)

   2013

• INFRAFRONTIER / BioMedBridges Webinar, Helmholtz Association, Germany, 16 and 24 July 2013, (P. Gormanns and M. Raess)
• BioMedBridges service registry - e-IRG workshop, Dublin, May 2013 (J. Ison)
• BioMedBridges - e-infrastructure: a hacker's perspective, e-IRG workshop, Dublin, May 2013 (J. Ison)
• OmicsConnect: flexible multi-omics data capture and integration tools for high-throughput biology. 14th Annual Bioinformatics Open Source Conference, Berlin, July 20^th, 2013 (K. Joeri van der Velde)
• BioMedBridges Standardization Activities. eTRIKS Consortium Teleconference, November 2013 (H. Parkinson)

   2014

• “Applying ChEMBL in target analysis." EMBL Advanced Course: Computational Aspects of High-Throughput Screening planning and analysis, Heidelberg ATC EMBL. October 2014 (J. Chambers)

• BioMedBridges Standardization Activities. Oxford E-science/BioDataSharing Teleconference, January 2014 (H. Parkinson)

Flyers

• BioMedBridges intro/"Why link up" flyer.

Videos

• Interview with Andrew Lyall - SIENA Channel, October 2011
• Interview with Stephanie Suhr - eScience talk, October 2012