Genomes and Genes
Francesca D Ciccarelli
Affiliation: European Molecular Biology Laboratory
- The WHy domain mediates the response to desiccation in plants and bacteriaFrancesca 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...
- The PAM domain, a multi-protein complex-associated module with an all-alpha-helix foldFrancesca 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...
- The KIND module: a putative signalling domain evolved from the C lobe of the protein kinase foldFrancesca D Ciccarelli
European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69012 Heidelberg, Germany
Trends Biochem Sci 28:349-52. 2003
- Toward automatic reconstruction of a highly resolved tree of lifeFrancesca 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...
- Complex genomic rearrangements lead to novel primate gene functionFrancesca 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...
- Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathwaysDavid 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...
- NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteriaMiguel 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...
- A protocol for the update of references to scientific literature in biological databasesCarolina 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...
- SMART 4.0: towards genomic data integrationIvica 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...
- The identification of a conserved domain in both spartin and spastin, mutated in hereditary spastic paraplegiaFrancesca D Ciccarelli
European Molecular Biology Laboratory, Meyerhofstr 1, 69012 Heidelberg, Germany
Genomics 81:437-41. 2003....
- Genome evolution reveals biochemical networks and functional modulesChristian 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...
- A complex prediction: three-dimensional model of the yeast exosomePatrick 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...
- Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebratesIrene 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...
- Generation and annotation of the DNA sequences of human chromosomes 2 and 4Ladeana 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...
- CASH--a beta-helix domain widespread among carbohydrate-binding proteinsFrancesca 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...
- AMOP, a protein module alternatively spliced in cancer cellsFrancesca 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...
- Non-random retention of protein-coding overlapping genes in MetazoaGiulia 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)...