Non-random retention of protein-coding overlapping genes in Metazoa (2008)
Soldà, Giulia, Suyama, Mikita, Pelucchi, Paride, Boi, Silvia, Guffanti, Alessandro, Rizzi, Ermanno, ...
Abstract Background Although the overlap of transcriptional units occurs frequently in eukaryotic genomes, its evolutionary and biological significance remains largely unclear. Here we report a...
Fumasoni, Irene, Meani, Natalia, Rambaldi, Davide, Scafetta, Gaia, Alcalay, Myriam, Ciccarelli, Francesca D
Abstract Background Progressive diversification of paralogs after gene expansion is essential to increase their functional specialization. However, mode and tempo of this divergence remain mostly...
SMART 4.0: towards genomic data integration (2004)
Letunic, Ivica, Copley, Richard R., Schmidt, Steffen, Ciccarelli, Francesca D., Doerks, Tobias, Schultz, Jörg, ...
SMART (Simple Modular Architecture Research Tool) is a web tool (http://smart.embl.de/) for the identification and annotation of protein domains, and provides a platform for the comparative study of...
The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold (2003)
Ciccarelli, Francesca D, Izaurralde, Elisa, Bork, Peer
Abstract Background Multimeric protein complexes have a role in many cellular pathways and are highly interconnected with various other proteins. The characterization of their domain composition and...
Andrade, Miguel A, Ciccarelli, Francesca D, Perez-Iratxeta, Carolina, Bork, Peer
Abstract Background Iron uptake from the host is essential for bacteria that infect animals. To find potential targets for drugs active against pathogenic bacteria, we have searched all completely...
Andrade, Miguel A, Ciccarelli, Francesca D, Perez-Iratxeta, Carolina, Bork, Peer
Iron uptake from the host is essential for bacteria that infect animals. A protein domain has been identified that appears in variable copy number in bacterial genes that are usually in the vicinity...
Nonsense-mediated mRNA decay in Drosophila:at the intersection of the yeast and mammalian pathways
Gatfield, David, Unterholzner, Leonie, Ciccarelli, Francesca D., Bork, Peer, Izaurralde, Elisa
The nonsense-mediated mRNA decay (NMD) pathway promotes the rapid degradation of mRNAs containing premature stop codons (PTCs). In Caenorhabditis elegans, seven genes (smg1–7) playing an essential...
Genome evolution reveals biochemical networks and functional modules
Von Mering, Christian, Zdobnov, Evgeny M., Tsoka, Sophia, Ciccarelli, Francesca D., Pereira-Leal, Jose B., Ouzounis, Christos A., ...
The analysis of completely sequenced genomes uncovers an astonishing variability between species in terms of gene content and order. During genome history, the genes are frequently rear-ranged,...
SMART 4.0: towards genomic data integration
Letunic, Ivica, Copley, Richard R., Schmidt, Steffen, Ciccarelli, Francesca D., Doerks, Tobias, Schultz, Jörg, ...
SMART (Simple Modular Architecture Research Tool) is a web tool (http://smart.embl.de/) for the identification and annotation of protein domains, and provides a platform for the comparative study of...
Forler, Daniel, Rabut, Gwénaël, Ciccarelli, Francesca D., Herold, Andrea, Köcher, Thomas, Niggeweg, Ricarda, ...
Metazoan NXF1-p15 heterodimers promote the nuclear export of bulk mRNA across nuclear pore complexes (NPCs). In vitro, NXF1-p15 forms a stable complex with the nucleoporin RanBP2/Nup358, a component...
A complex prediction: three-dimensional model of the yeast exosome
Aloy, Patrick, Ciccarelli, Francesca D., Leutwein, Christina, Gavin, Anne-Claude, Superti-Furga, Giulio, Bork, Peer, ...
We present a model of the yeast exosome based on the bacterial degradosome component polynucleotide phosphorylase (PNPase). Electron microscopy shows the exosome to resemble PNPase but with key...
Complex genomic rearrangements lead to novel primate gene function
Ciccarelli, Francesca D., Von Mering, Christian, Suyama, Mikita, Harrington, Eoghan D., Izaurralde, Elisa, Bork, Peer
Orthologous genes that maintain a single-copy status in a broad range of species may indicate a selection against gene duplication. If this is the case, then duplicates of such genes that do survive...
Andrade, Miguel A, Ciccarelli, Francesca D, Perez-Iratxeta, Carolina, Bork, Peer
Iron uptake from the host is essential for bacteria that infect animals. A protein domain has been identified that appears in variable copy number in bacterial genes that are usually in the vicinity...
Nonsense-mediated mRNA decay in Drosophila:at the intersection of the yeast and mammalian pathways
Gatfield, David, Unterholzner, Leonie, Ciccarelli, Francesca D., Bork, Peer, Izaurralde, Elisa
The nonsense-mediated mRNA decay (NMD) pathway promotes the rapid degradation of mRNAs containing premature stop codons (PTCs). In Caenorhabditis elegans, seven genes (smg1–7) playing an essential...
Genome evolution reveals biochemical networks and functional modules
Von Mering, Christian, Zdobnov, Evgeny M., Tsoka, Sophia, Ciccarelli, Francesca D., Pereira-Leal, Jose B., Ouzounis, Christos A., ...
The analysis of completely sequenced genomes uncovers an astonishing variability between species in terms of gene content and order. During genome history, the genes are frequently rear-ranged,...
SMART 4.0: towards genomic data integration
Letunic, Ivica, Copley, Richard R., Schmidt, Steffen, Ciccarelli, Francesca D., Doerks, Tobias, Schultz, Jörg, ...
SMART (Simple Modular Architecture Research Tool) is a web tool (http://smart.embl.de/) for the identification and annotation of protein domains, and provides a platform for the comparative study of...
Forler, Daniel, Rabut, Gwénaël, Ciccarelli, Francesca D., Herold, Andrea, Köcher, Thomas, Niggeweg, Ricarda, ...
Metazoan NXF1-p15 heterodimers promote the nuclear export of bulk mRNA across nuclear pore complexes (NPCs). In vitro, NXF1-p15 forms a stable complex with the nucleoporin RanBP2/Nup358, a component...
Complex genomic rearrangements lead to novel primate gene function
Ciccarelli, Francesca D., Von Mering, Christian, Suyama, Mikita, Harrington, Eoghan D., Izaurralde, Elisa, Bork, Peer
Orthologous genes that maintain a single-copy status in a broad range of species may indicate a selection against gene duplication. If this is the case, then duplicates of such genes that do survive...
A complex prediction: three-dimensional model of the yeast exosome
Aloy, Patrick, Ciccarelli, Francesca D., Leutwein, Christina, Gavin, Anne-Claude, Superti-Furga, Giulio, Bork, Peer, ...
We present a model of the yeast exosome based on the bacterial degradosome component polynucleotide phosphorylase (PNPase). Electron microscopy shows the exosome to resemble PNPase but with key...