Francesca Diella

Summary

Affiliation: European Molecular Biology Laboratory
Country: Germany

Publications

  1. pmc Phospho.ELM: a database of phosphorylation sites--update 2011
    Holger Dinkel
    SCB Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 39:D261-7. 2011
  2. pmc Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins
    Francesca Diella
    Cellzome AG, Heidelberg, Germany
    BMC Bioinformatics 5:79. 2004
  3. pmc ELM--the database of eukaryotic linear motifs
    Holger Dinkel
    Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
    Nucleic Acids Res 40:D242-51. 2012
  4. pmc ELM: the status of the 2010 eukaryotic linear motif resource
    Cathryn M Gould
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 38:D167-80. 2010
  5. doi request reprint Attributes of short linear motifs
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Biosyst 8:268-81. 2012
  6. pmc Phospho.ELM: a database of phosphorylation sites--update 2008
    Francesca Diella
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Nucleic Acids Res 36:D240-4. 2008
  7. pmc The eukaryotic linear motif resource ELM: 10 years and counting
    Holger Dinkel
    Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, Department of Physiology, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA, Structural Studies Division, MRC, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK, Ruprecht Karls Universitat, 69117 Heidelberg, Germany, School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Co Dublin, Republic of Ireland, Laboratory of Bioinformatics and Biostatistics, Maria Sklodowska Curie Memorial Cancer Center and Institute of Oncology, WK Roentgena 5, 02 781 Warsaw, Poland, Protein Structure Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires Consejo Nacional de Investigaciones Científicas y Técnicas Avenida Patricias Argentinas 435 CP 1405 Buenos Aires, Argentina and Departamento de Química Biológica and IQUIBICEN CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Gúiraldes 2160 CP 1428, Argentina
    Nucleic Acids Res 42:D259-66. 2014
  8. pmc KEPE--a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors
    Francesca Diella
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Bioinformatics 25:1-5. 2009
  9. pmc Evidence for the concerted evolution between short linear protein motifs and their flanking regions
    Claudia Chica
    Structural and Computational Biology Unit, EMBL Heidelberg, Heidelberg, Germany
    PLoS ONE 4:e6052. 2009
  10. ncbi request reprint Protein disorder prediction: implications for structural proteomics
    Rune Linding
    EMBL, Biocomputing Unit, Meyerhofstr 1, D 69117 Heidelberg, Germany
    Structure 11:1453-9. 2003

Collaborators

Detail Information

Publications16

  1. pmc Phospho.ELM: a database of phosphorylation sites--update 2011
    Holger Dinkel
    SCB Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 39:D261-7. 2011
    ..Finally, special emphasis has been put on linking to external resources such as interaction networks and other databases...
  2. pmc Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins
    Francesca Diella
    Cellzome AG, Heidelberg, Germany
    BMC Bioinformatics 5:79. 2004
    ..The fast growing number of research reports on protein phosphorylation points to a general need for an accurate database dedicated to phosphorylation to provide easily retrievable information on phosphoproteins...
  3. pmc ELM--the database of eukaryotic linear motifs
    Holger Dinkel
    Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
    Nucleic Acids Res 40:D242-51. 2012
    ..The motif discovery portion of the ELM resource has added conservation, and structural attributes have been incorporated to aid users to discriminate biologically relevant motifs from stochastically occurring non-functional instances...
  4. pmc ELM: the status of the 2010 eukaryotic linear motif resource
    Cathryn M Gould
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 38:D167-80. 2010
    ..Using the links, researchers can explore the motifs, proteins, complex structures and associated literature to evaluate whether candidate motifs might be worth experimental investigation...
  5. doi request reprint Attributes of short linear motifs
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Biosyst 8:268-81. 2012
    ..Finally, the most interesting conclusions are examined in regard to their functional consequences...
  6. pmc Phospho.ELM: a database of phosphorylation sites--update 2008
    Francesca Diella
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Nucleic Acids Res 36:D240-4. 2008
    ..Phospho.ELM is available on line at: http://phospho.elm.eu.org...
  7. pmc The eukaryotic linear motif resource ELM: 10 years and counting
    Holger Dinkel
    Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, Department of Physiology, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA, Structural Studies Division, MRC, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK, Ruprecht Karls Universitat, 69117 Heidelberg, Germany, School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Co Dublin, Republic of Ireland, Laboratory of Bioinformatics and Biostatistics, Maria Sklodowska Curie Memorial Cancer Center and Institute of Oncology, WK Roentgena 5, 02 781 Warsaw, Poland, Protein Structure Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires Consejo Nacional de Investigaciones Científicas y Técnicas Avenida Patricias Argentinas 435 CP 1405 Buenos Aires, Argentina and Departamento de Química Biológica and IQUIBICEN CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Gúiraldes 2160 CP 1428, Argentina
    Nucleic Acids Res 42:D259-66. 2014
    ..Furthermore, detailed information about motif-mediated interactions has been annotated and made available in standard exchange formats. Where appropriate, links are provided to resources such as switches.elm.eu.org and KEGG pathways. ..
  8. pmc KEPE--a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors
    Francesca Diella
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Bioinformatics 25:1-5. 2009
    ..We noted that the sumoylation site in C/EBP homologues is conserved beyond the canonical consensus sequence for sumoylation. Therefore, we investigated whether this pattern might define a more general protein motif...
  9. pmc Evidence for the concerted evolution between short linear protein motifs and their flanking regions
    Claudia Chica
    Structural and Computational Biology Unit, EMBL Heidelberg, Heidelberg, Germany
    PLoS ONE 4:e6052. 2009
    ..Sometimes linear motifs appear as isolated islands of conservation in multiple sequence alignments. However, they also occur in larger blocks of sequence conservation, suggesting an active role for the neighbouring amino acids...
  10. ncbi request reprint Protein disorder prediction: implications for structural proteomics
    Rune Linding
    EMBL, Biocomputing Unit, Meyerhofstr 1, D 69117 Heidelberg, Germany
    Structure 11:1453-9. 2003
    ..The tool is freely available via a web interface (http://dis.embl.de) and can be downloaded for use in large-scale studies...
  11. ncbi request reprint Understanding eukaryotic linear motifs and their role in cell signaling and regulation
    Francesca Diella
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Front Biosci 13:6580-603. 2008
    ..The discrete deterministic properties implicit to these assemblies suggest that models for cell regulatory networks in systems biology should neither be overly dependent on stochastic nor on smooth deterministic approximations...
  12. pmc Deciphering a global network of functionally associated post-translational modifications
    Pablo Minguez
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Syst Biol 8:599. 2012
    ..The global network of co-evolving PTM types implies a complex and intertwined post-translational regulation landscape that is likely to regulate multiple functional states of many if not all eukaryotic proteins...
  13. doi request reprint Linear motif atlas for phosphorylation-dependent signaling
    Martin Lee Miller
    Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
    Sci Signal 1:ra2. 2008
    ..The atlas is available as a community resource (http://netphorest.info)...
  14. pmc Systematic discovery of in vivo phosphorylation networks
    Rune Linding
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
    Cell 129:1415-26. 2007
    ..Applying this approach to DNA damage signaling, we show that 53BP1 and Rad50 are phosphorylated by CDK1 and ATM, respectively. We describe a scalable strategy to evaluate predictions, which suggests that BCLAF1 is a GSK-3 substrate...
  15. ncbi request reprint A comparative study of the relationship between protein structure and beta-aggregation in globular and intrinsically disordered proteins
    Rune Linding
    European Molecular Biology Laboratory, Programme for Structural and Computational biology, Meyerhofstr 1, D 69117 Heidelberg, Germany
    J Mol Biol 342:345-53. 2004
    ..Finally, we discuss the fact that although IDPs have a much lower aggregation propensity than globular proteins, this does not necessarily mean that they have a lower potential for amyloidosis...
  16. pmc ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins
    Pål Puntervoll
    Department of Molecular Biology, University of Bergen, Norway
    Nucleic Acids Res 31:3625-30. 2003
    ..Current filters are for cell compartment, globular domain clash and taxonomic range. In favourable cases, the filters can reduce the number of retained matches by an order of magnitude or more...