publications

Publications

 

Peer-reviewed publications

2016

  • Malone J, Stevens R, Jupp S, Hancocks T, Parkinson H, Brooksbank C (2016) Ten Simple Rules for Selecting a Bio-ontology. PLoS Comput Biol 12(2): e1004743. doi:10.1371/journal.pcbi.1004743
  • Julie McMurry; Blomberg, Niklas; Burdett, Tony; Conte, Nathalie; et al. (resubmitted to PLoS Computational Biology) 10 Simple rules for design, provision, and reuse of identifiers for web-based life science data doi:10.5281/zenodo.31765

2015

  • Ison J, Rapacki K, Ménager H, Kalaš M et al. (2015) Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. 2016 Jan;44(D1) D38-47. doi:10.1093/nar/gkv1116. PMID: 26538599; PMCID: PMC4702812
  • Yates A, Akanni W, Amode MR, Barrell D et al. (2015) Ensembl 2016. Nucleic Acids Res. 2016 Jan;44(D1) D710-6. doi:10.1093/nar/gkv1157. PMID: 26687719; PMCID: PMC4702834
  • Pang C, Sollie A, Sijtsma A, Hendriksen D, Charbon B, de Haan M, de Boer T, Kelpin F, Jetten J, van der Velde JK, Smidt N, Sijmons R, Hillege H, Swertz MA (2015) SORTA: a system for ontology-based re-coding and technical annotation of biomedical phenotype data. Database (Oxford). 2015;2015. doi:10.1093/database/bav089. PMID: 26385205; PMCID: PMC4574036
  • Duarte AM, Psomopoulos FE, Blanchet C, Bonvin AM, Corpas M, Franc A, Jimenez RC, de Lucas JM, Nyrönen T, Sipos G, Suhr SB (2015) Future opportunities and trends for e-infrastructures and life sciences: going beyond the grid to enable life science data analysis. Front Genet. 2015;6 197. doi:10.3389/fgene.2015.00197. PMID: 26157454; PMCID: PMC4477178
  • Valasatava Y, Andreini C, Rosato A (2015) Hidden relationships between metalloproteins unveiled by structural comparison of their metal sites. Sci Rep. 2015;5 9486. doi:10.1038/srep09486. PMID: 25820752; PMCID: PMC4377587
  • Farabella I, Vasishtan D, Joseph AP, Pandurangan AP, Sahota H, Topf M (2015) TEMPy: a Python library for assessment of three-dimensional electron microscopy density fits. J Appl Crystallogr. 2015 Aug;48(Pt 4) 1314-1323. doi:10.1107/s1600576715010092. PMID: 26306092; PMCID: PMC4520291
  • Pang C, Hendriksen D, Dijkstra M, van der Velde KJ, Kuiper J, Hillege HL, Swertz MA (2015) BiobankConnect: software to rapidly connect data elements for pooled analysis across biobanks using ontological and lexical indexing. J Am Med Inform Assoc. 2015 Jan;22(1) 65-75. doi:10.1136/amiajnl-2013-002577. PMID: 25361575; PMCID: PMC4433361
  • Jensen AB, Ajslev TA, Brunak S, Sørensen TI (2015) Long-term risk of cardiovascular and cerebrovascular disease after removal of the colonic microbiota by colectomy: a cohort study based on the Danish National Patient Register from 1996 to 2014. BMJ Open. 2015;5(12) e008702. doi:10.1136/bmjopen-2015-008702. PMID: 26671951; PMCID: PMC4680005
  • Cunningham F, Moore B, Ruiz-Schultz N, Ritchie GR, Eilbeck K (2015) Improving the Sequence Ontology terminology for genomic variant annotation. J Biomed Semantics. 2015;6 32. doi:10.1186/s13326-015-0030-4. PMID: 26229585; PMCID: PMC4520272
  • Kuchinke W, Karakoyun T, Gengler S, Ohmann C (2015) First Clinical Research Informatics (CRI) Solutions Day: advanced IT support from EU projects for clinical trials. Journal of Clinical Bioinformatics. 2015;5(Suppl 1) A1-A1. PMCID: PMC4460745.
  • Braasch B, Karakoyun T. (2015) Clinical trials information mediator (CTIM). Journal of Clinical Bioinformatics. 2015;5(Suppl 1) S7-S7. PMCID: PMC4460620
  • Klein S, Vast E, van Soest J, Dekker A, Koek M, Niessen W (2015) XNAT imaging platform for BioMedBridges and CTMM TraIT. Journal of Clinical Bioinformatics. 2015;5(Suppl 1) S18-S18. PMCID: PMC4464222.
  • Sariyar Murat, Schluender Irene, Smee Carol, and Suhr Stephanie (2015) Sharing and Reuse of Sensitive Data and Samples: Supporting Researchers in Identifying Ethical and Legal Requirements. Biopreservation and Biobanking. August 2015, 13(4): 263-270. doi:10.1089/bio.2015.0014.

2014

  • Jon Chambers, Mark Davies, Anna Gaulton, George Papadatos, Anne Hersey and John P Overington (2015) 
    UniChem: extension of InChI-based compound mapping to salt, connectivity and stereochemistry layers. Journal of Cheminformatics 2014, 6:43, doi:10.1186/s13321-014-0043-5
  • Faulconbridge, A., Burdett, T., Brandizi, M., Gostev, M., Pereira, R., Vasant, D., Sarkans, U., Brazma, A., Parkinson, H. (2014) Updates to BioSamples database at European Bioinformatics Institute (2014) Nucleic Acids Research, 42 (D1) doi:10.1093/nar/gkt1081
  • 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. (2014) The EBI RDF Platform: Linked Open Data for the Life SciencesBioinformatics doi:10.1093/bioinformatics/btt765
  • Valasatava Y, Rosato A, Cavallaro G, Andreini C. (2014) MetalS3, a database-mining tool for the identification of structurally similar metal sites. J Biol Inorg Chem doi:10.1007/s00775-014-1128-3
  • Gutmanas A, Alhroub Y, Battle GM, Berrisford JM, Bochet E, Conroy MJ, Dana JM, Fernandez Montecelo MA, van Ginkel G, Gore SP, Haslam P, Hatherley R, Hendrickx PM, Hirshberg M, Lagerstedt I, Mir S, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Rinaldi L, Sahni G, Sanz-García E, Sen S, Slowley RA, Velankar S, Wainwright ME, Kleywegt GJ. (2014) PDBe: Protein Data Bank in Europe. Nucleic Acids Res. 2014 Jan;42(Database issue) D285-91. doi:10.1093/nar/gkt1180. PMID: 24288376; PMCID: PMC3965016.
  • Rinaldelli M, Ravera E, Calderone V, Parigi G, Murshudov GN, Luchinat C. (2014) Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences. Acta Crystallogr D Biol Crystallogr. 2014 Apr;70(Pt 4) 958-967. doi:10.1107/s1399004713034160. PMID: 24699641; PMCID: PMC4306559.
  • Cacciatore S, Luchinat C, Tenori L. (2014) Knowledge discovery by accuracy maximization. Proc Natl Acad Sci U S A. 2014 Apr;111(14) 5117-5122. doi:10.1073/pnas.1220873111. PMID: 24706821; PMCID: PMC3986136.

2013

  • Andreini, C., Cavallaro, G., Rosato, A., Valasatava, Y. (2013) MetalS2: a tool for the structural alignment of minimal functional sites in metal-binding proteins and nucleic acidsJournal of Chemical Information and Modeling, issue 53, Volume 11 (Open Access) doi:10.1021/ci400459w
  • Chambers, J., Davies, M., Gaulton, A., Hersey, A., Velankar, S., Petryszak, R., Hastings, J., Bellis, L., McGlinchey, S., Overington, J. P. (2013) UniChem: a unified chemical structure cross-referencing and identifier tracking system. Journal of Cheminformatics, Volume 5, Issue 3 (Open Access) doi:10.1186/1758-2946-5-3
  • Ison, J., Kalaš, M., Jonassen, I., Bolser, D., Uludag, M., McWilliam, H., Malone, J., Lopez, R., Pettifer, S., Rice, P. (2013) EDAM: An ontology of bioinformatics operations, types of data and identifiers, topics, and formatsBioinformatics, Volume 29, Issue 10 (Open Access) doi:10.1093/bioinformatics/btt113
  • Lagerstedt, I., Moore, W. J., Patwardhan, A., Sanz-García, E., Best, C., Swedlow, J. R., Kleywegt, G. J. (2013) Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB. Journal of Structural Biology, Volume 184, Issue 2 (Open Access) doi:10.1016/j.jsb.2013.09.021
  • 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. (2013) Individualized systems medicine strategy to tailor treatments for patients with chemorefractory acute myeloid leukemiaCancer Discovery, Volume 3, Issue 12 (Open Access) doi:10.1158/2159-8290.CD-13-0350
  • Gutmanas A, Oldfield TJ, Patwardhan A, Sen S, Velankar S, Kleywegt GJ. (2013) The role of structural bioinformatics resources in the era of integrative structural biology. Acta Crystallogr D Biol Crystallogr. 2013 May;69(Pt 5) 710-721. doi:10.1107/s0907444913001157. PMID: 23633580; PMCID: PMC3640467.

    2012

  • Bertini, I., Ferella, L., Luchinat, C., Parigi, G., Petoukhov, M. V., Ravera, E., Rosato, A., Svergun, D. I. (2012)  MaxOcc: a web portal for maximum occurrence analysisJournal of Biomolecular NMR, Volume 53, Issue 4. doi:10.1007/s10858-012-9638-1

Reports and other publications

    2015

  • Julie McMurry et al.. (2015). 10 Simple rules for design, provision, and reuse of identifiers for web-based life science data. Zenodo.doi:10.5281/zenodo.31765
  • Suhr, S, Jimenez, R, Brooksbank, C, Newhouse, S, Hancocks, T (2015) Data strategies for research infrastructures doi:10.5281/zenodo.16413  

    2014

  • Principles of data management and sharing at European research infrastructures Joint working paper by ELIXIR and EU-OPENSCREEN with AnaEE, BBMRI, EATRIS, ECRIN, ERINHA, EMBRC, Euro-BioImaging, INFRAFRONTIER, INSTRUCT, ISBE, LifeWatch and MIRRI doi:10.5281/zenodo.8304
  • Suhr, S, Cochrane, C, Stanford, N, Boiten, J-W, Swedlow, J, Morris, C, Jimenez, R, Neerincx, P (2015). REPORT: BioMedBridges workshop on e-Infrastructure support for the life sciences – Preparing for the data deluge. doi:10.5281/zenodo.13942

    2013

  • Field, L., Suhr, S., Ison, J., Wouter, L., Wittenburg, P., Broeder, D., Hardisty, A., Repo, S., Jenkinson, A. (2013) 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 doi:10.5281/zenodo.7636

Posters

   2015

  • Juty N, McMurry J, BioMedBridges consortium, Haendel M, Goble C, Parkinson H: 10 simple rules for making data web friendly. COMBINE, 12-16 October, Salt Lake City, Utah, U.S.A. doi:10.5281/zenodo.31906

   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

News articles

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 20th, 2013 (K. Joeri van der Velde)
  • BioMedBridges Standardization Activities. eTRIKS Consortium Teleconference, November 2013 (H. Parkinson)

   2014

Flyers

Videos