Francesca D Ciccarelli

Summary

Affiliation: European Molecular Biology Laboratory
Country: Germany

Publications

  1. ncbi request reprint The WHy domain mediates the response to desiccation in plants and bacteria
    Francesca D Ciccarelli
    European Molecular Biology Laboratory, 69012 Heidelberg, Meyerhofstrasse 1, Germany
    Bioinformatics 21:1304-7. 2005
  2. pmc The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold
    Francesca D Ciccarelli
    European Molecular Biology Laboratory, Meyerhofstr, 1, 69012 Heidelberg, Germany
    BMC Bioinformatics 4:64. 2003
  3. ncbi request reprint The KIND module: a putative signalling domain evolved from the C lobe of the protein kinase fold
    Francesca D Ciccarelli
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69012 Heidelberg, Germany
    Trends Biochem Sci 28:349-52. 2003
  4. ncbi request reprint Toward automatic reconstruction of a highly resolved tree of life
    Francesca D Ciccarelli
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Science 311:1283-7. 2006
  5. pmc Complex genomic rearrangements lead to novel primate gene function
    Francesca D Ciccarelli
    European Molecular Biology Laboratory, 69012 Heidelberg, Germany
    Genome Res 15:343-51. 2005
  6. pmc Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways
    David Gatfield
    EMBL, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    EMBO J 22:3960-70. 2003
  7. pmc NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria
    Miguel A Andrade
    European Molecular Biology Laboratory, Meyerhofstr, 1, 69117 Heidelberg, Germany
    Genome Biol 3:RESEARCH0047. 2002
  8. ncbi request reprint A protocol for the update of references to scientific literature in biological databases
    Carolina Perez-Iratxeta
    European Molecular Biology Laboratory, Heidelberg, Germany
    Appl Bioinformatics 2:189-91. 2003
  9. pmc SMART 4.0: towards genomic data integration
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 32:D142-4. 2004
  10. ncbi request reprint The identification of a conserved domain in both spartin and spastin, mutated in hereditary spastic paraplegia
    Francesca D Ciccarelli
    European Molecular Biology Laboratory, Meyerhofstr 1, 69012 Heidelberg, Germany
    Genomics 81:437-41. 2003

Collaborators

Detail Information

Publications17

  1. ncbi request reprint The WHy domain mediates the response to desiccation in plants and bacteria
    Francesca D Ciccarelli
    European Molecular Biology Laboratory, 69012 Heidelberg, Meyerhofstrasse 1, Germany
    Bioinformatics 21:1304-7. 2005
    ..Although many resistance genes (R genes) associated to HR have been identified, very little is known about the molecular mechanisms activated after their expression...
  2. pmc The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold
    Francesca D Ciccarelli
    European Molecular Biology Laboratory, Meyerhofstr, 1, 69012 Heidelberg, Germany
    BMC Bioinformatics 4:64. 2003
    ..The characterization of their domain composition and organization provides useful information on the specific role of each region of their sequence...
  3. ncbi request reprint The KIND module: a putative signalling domain evolved from the C lobe of the protein kinase fold
    Francesca D Ciccarelli
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69012 Heidelberg, Germany
    Trends Biochem Sci 28:349-52. 2003
  4. ncbi request reprint Toward automatic reconstruction of a highly resolved tree of life
    Francesca D Ciccarelli
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Science 311:1283-7. 2006
    ..For example, we place the phylum Acidobacteria as a sister group of delta-Proteobacteria, support a Gram-positive origin of Bacteria, and suggest a thermophilic last universal common ancestor...
  5. pmc Complex genomic rearrangements lead to novel primate gene function
    Francesca D Ciccarelli
    European Molecular Biology Laboratory, 69012 Heidelberg, Germany
    Genome Res 15:343-51. 2005
    ..We have experimentally verified that at least one of the newly formed proteins has a cellular localization different from RanBP2's, and we show that positive selection did act on specific domains during evolution...
  6. pmc Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways
    David Gatfield
    EMBL, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    EMBO J 22:3960-70. 2003
    ..Our findings reveal that despite conservation of the NMD machinery, different mechanisms have evolved to discriminate premature from natural stop codons in metazoa...
  7. pmc NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria
    Miguel A Andrade
    European Molecular Biology Laboratory, Meyerhofstr, 1, 69117 Heidelberg, Germany
    Genome Biol 3:RESEARCH0047. 2002
    ..To find potential targets for drugs active against pathogenic bacteria, we have searched all completely sequenced genomes of pathogenic bacteria for genes relevant for iron transport...
  8. ncbi request reprint A protocol for the update of references to scientific literature in biological databases
    Carolina Perez-Iratxeta
    European Molecular Biology Laboratory, Heidelberg, Germany
    Appl Bioinformatics 2:189-91. 2003
    ..Human experts found the references that the algorithm scored highly were more relevant to the database entry than those scored lowly, suggesting that the algorithm was useful...
  9. pmc SMART 4.0: towards genomic data integration
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 32:D142-4. 2004
    ..Other improvements include the ability to query SMART by Gene Ontology terms, improved structure database searching and batch retrieval of multiple entries...
  10. ncbi request reprint The identification of a conserved domain in both spartin and spastin, mutated in hereditary spastic paraplegia
    Francesca D Ciccarelli
    European Molecular Biology Laboratory, Meyerhofstr 1, 69012 Heidelberg, Germany
    Genomics 81:437-41. 2003
    ....
  11. pmc Genome evolution reveals biochemical networks and functional modules
    Christian von Mering
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Proc Natl Acad Sci U S A 100:15428-33. 2003
    ..The results indicate that modularity in protein networks is intrinsically encoded in present-day genomes...
  12. pmc A complex prediction: three-dimensional model of the yeast exosome
    Patrick Aloy
    EMBL, Meyerhofstrasse, Heidelberg, Germany
    EMBO Rep 3:628-35. 2002
    ..The model suggests numerous experiments to probe exosome function, particularly with respect to subunits making direct atomic contacts and conserved, possibly functional residues within the predicted central pore of the complex...
  13. pmc Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates
    Irene Fumasoni
    Department of Experimental Oncology, European Institute of Oncology, IFOM IEO Campus, Via Adamello 16, 20139 Milan, Italy
    BMC Evol Biol 7:187. 2007
    ..However, mode and tempo of this divergence remain mostly unclear. Here we report the comparative analysis of PRDM genes, a family of putative transcriptional regulators involved in human tumorigenesis...
  14. ncbi request reprint Generation and annotation of the DNA sequences of human chromosomes 2 and 4
    Ladeana W Hillier
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 434:724-31. 2005
    ..Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions...
  15. ncbi request reprint CASH--a beta-helix domain widespread among carbohydrate-binding proteins
    Francesca D Ciccarelli
    Max Delbrueck Centrum, PO Box 740238, D 13092 Berlin, Germany
    Trends Biochem Sci 27:59-62. 2002
    ..The CASH domain is characterized by internal repetitions of glycines and hydrophobic residues that correspond to the repetitive units of a predicted or observed right-handed beta-helix structure of the pectate lyase superfamily...
  16. ncbi request reprint AMOP, a protein module alternatively spliced in cancer cells
    Francesca D Ciccarelli
    Trends Biochem Sci 27:113-5. 2002
    ..The presence of AMOP in cell adhesion molecules could be indicative of a role for this domain in adhesion...
  17. pmc Non-random retention of protein-coding overlapping genes in Metazoa
    Giulia Soldà
    1Department of Biology and Genetics for Medical Sciences, University of Milan, 20133 Milan, Italy
    BMC Genomics 9:174. 2008
    ..Here we report a comparative analysis of overlaps between genes coding for well-annotated proteins in five metazoan genomes (human, mouse, zebrafish, fruit fly and worm)...