Rè, Matteo, Pesole, Graziano, Horner, David S
Abstract Background The conservation of sequences between related genomes has long been recognised as an indication of functional significance and recognition of sequence homology is one of the...
Creanza, Teresa M, Horner, David S, D'Addabbo, Annarita, Maglietta, Rosalia, Mignone, Flavio, Ancona, Nicola, ...
Abstract Background The identification of protein coding elements in sets of mammalian conserved elements is one of the major challenges in the current molecular biology research. Many features have...
Picardi, Ernesto, Mignone, Flavio, Pesole, Graziano
Abstract Background ESTs and full-length cDNAs represent an invaluable source of evidence for inferring reliable gene structures and discovering potential alternative splicing events. In newly...
A transcriptional sketch of a primary human breast cancer by 454 deep sequencing (2009)
Guffanti, Alessandro, Iacono, Michele, Pelucchi, Paride, Kim, Namshin, Soldà, Giulia, Croft, Larry J, ...
Abstract Background The cancer transcriptome is difficult to explore due to the heterogeneity of quantitative and qualitative changes in gene expression linked to the disease status. An increasing...
A transcriptional sketch of a primary human breast cancer by 454 deep sequencing (2009)
PESOLE, GRAZIANO, MIGNONE, FLAVIO
A transcriptional sketch of a primary human breast cancer by 454 deep sequencing / A. Guffanti, M. Iacono, P. Pelucchi, N. Kim, G. Soldà, L.J. Croft, R.J. Taft, E. Rizzi, M. Askarian-Amiri, R.J....
Mitochondrial DNA sequence variations in some Italian wild boar populations (2009)
GISSI, CARMELA, PESOLE, GRAZIANO, LATTUADA, LAURA, QUAGLIA, FEDERICA, BACCHETTA, RENATO, MANTECCA, PARIDE, ...
Mitochondrial DNA sequence variations in some Italian wild boar populations / L. Lattuada, F. Quaglia, F. Iannelli, C. Gissi, P. Mantecca, R. Bacchetta, M. Polli. - In: Journal of animal breeding and...
Mitochondrial DNA sequence variations in some Italian wild boar populations (2009)
GISSI, CARMELA, PESOLE, GRAZIANO, LATTUADA, LAURA, QUAGLIA, FEDERICA, BACCHETTA, RENATO, MANTECCA, PARIDE, ...
Mitochondrial DNA sequence variations in some Italian wild boar populations / L. Lattuada, F. Quaglia, F. Iannelli, C. Gissi, P. Mantecca, R. Bacchetta, M. Polli. - In: Journal of animal breeding and...
Zambelli, Federico, Pesole, Graziano, Pavesi, Giulio
The first step in gene expression, transcription, is modulated by the interaction of transcription factors with their corresponding binding sites on the DNA sequence. Pscan is a software tool that...
Mangiulli, Marina, Valletti, Alessio, Caratozzolo, Mariano Francesco, Tullo, Apollonia, Sbisà, Elisabetta, Pesole, Graziano, ...
p63 belongs to a family of transcription factors, which, while demonstrating striking conservation of functional domains, regulate distinct biological functions. Its principal role is in the...
Weeder Web: a Web-Based Tool for the Discovery of Transcription Factor Binding Sites (2008)
Giulio Pavesi, Giancarlo Mauri, Graziano Pesole
Understanding the complex mechanisms governing basic biological processes requires the characterization of regulatory motifs modulating gene expression at transcriptional and post-transcriptional...
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society (2008)
Bmc Bioinformatics, Manuela Helmer-citterich, Rita Casadio, Ro Guffanti, Giancarlo Mauri, Luciano Milanesi, ...
Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita (2008)
Abad, Pierre, Gouzy, Jerome, Aury, Jean-Marc, Castagnone-Sereno, Philippe, Danchin, Etienne G. J., Deleury, Emeline, ...
© 2008 Nature Publishing Group. This article is distributed under the terms of the Creative Commons Attribution-Noncommercial-Share Alike license. The definitive version was published in Nature...
IANNELLI, FABIO, GISSI, CARMELA, PESOLE, GRAZIANO
One ring to divide them all: mitochondrial genomics unveils two cryptic species in Ciona intestinalis / F. Iannelli, G. Pesole, P. Sordino, C. Gissi. - In: Invertebrate Survival Journal. - ISSN...
Mignone, Flavio, Anselmo, Anna, Donvito, Giacinto, Maggi, Giorgio P, Grillo, Giorgio, Pesole, Graziano
Abstract Background The accurate detection of genes and the identification of functional regions is still an open issue in the annotation of genomic sequences. This problem affects new genomes but...
ANSELMO, ANNA, MIGNONE, FLAVIO, PESOLE, GRAZIANO
Genome-wide identification of coding and non-coding conserved sequence tags in human and mouse genomes / F. Mignone, A. Anselmo, G. Donvito, G.P. Maggi, G. Grillo, G. Pesole. - In: BMC Genomics...
Giulio Pavesi is assistant professor of Computer Science at the (2008)
Giancarlo Mauri, Graziano Pesole
research interests are mainly focused on bioinformatics in general, and regulatory motif discovery in particular. He also works on discrete models of complex systems.
ASPIC: a Novel Method to Predict Alternative Splicing (2008)
Paola Bonizzoni, Riccardo Dondi, Raffaella Rizzi, Graziano Pesole
In this paper a new method for detecting splicing sites is proposed. It is based on a combined analysis of all available transcript data in order to produce all transcript alignments to the genomic...
Vaccarelli, Giovanna, Miccoli, Maria C, Antonacci, Rachele, Pesole, Graziano, Ciccarese, Salvatrice
Abstract Background In humans and mice ("γδ low species") less than 5% of the peripheral blood T lymphocytes are gamma/delta T cells, whereas in chicken and artiodactyls ("γδ high species")...
CATTANEO, ELENA, TARTARI, MARZIA, LO SARDO, VALENTINA, PESOLE, GRAZIANO, ZUCCATO, CHIARA
Phylogenetic comparison of huntingtin homologues reveals the appearance of a primitive polyQ in sea urchin / M. Tartari, C. Gissi, V. Lo Sardo, C. Zuccato, E. Picardi, G. Pesole G, E. Cattaneo. - In:...
Exalign: a new method for comparative analysis of exon-intron gene structures (2008)
PAVESI, GIULIO, ZAMBELLI, FEDERICO, PESOLE, GRAZIANO
Exalign: a new method for comparative analysis of exon-intron gene structures / G. Pavesi, F. Zambelli, C. Caggese, G. Pesole. - In: Nucleic Acids Research. - ISSN 0305-1048. - 36:8(2008). - p....
ASPicDB: A database resource for alternative splicing analysis (2008)
PAVESI, GIULIO, MIGNONE, FLAVIO, PESOLE, GRAZIANO, ANSELMO, ANNA
ASPicDB: A database resource for alternative splicing analysis / T. Castrignanò, M. D'Antonio, A. Anselmo, D. Carrabino, A. D'Onorio, A.M. D'Erchia, F. Licciulli, M. Mangiulli, F. Mignone, G....
Correlated substitution analysis and the prediction of amino acid structural contacts (2008)
HORNER, DAVID STEPHEN, PESOLE, GRAZIANO
Correlated substitution analysis and the prediction of amino acid structural contacts / D.S. Horner, W. Pirovano, G. Pesole. - In: Briefings in Bioinformatics. - ISSN 1467-5463. - 9:1(2008). - p....
GISSI, CARMELA, PESOLE, GRAZIANO, IANNELLI, FABIO
Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species / C. Gissi, F. Iannelli, G. Pesole. - In: Heredity. - ISSN 0018-067X. - 101:4(2008). - p. 301-320.
GISSI, CARMELA, PESOLE, GRAZIANO, CATTANEO, ELENA, TARTARI, MARZIA, ZUCCATO, CHIARA, LO SARDO, VALENTINA, ...
Phylogenetic comparison of huntingtin homologues reveals the appearance of a primitive polyQ in sea urchin / M. Tartari, C. Gissi, V. Lo Sardo, C. Zuccato, E. Picardi, G. Pesole, E. Cattaneo. - In:...
GRIGGIO, FRANCESCA, IANNELLI, FABIO, GISSI, CARMELA, PESOLE, GRAZIANO
The fast evolutionary dynamics of ascidian mitochondrial genome: an exception to the general deuterostome evolutionary trend / C. Gissi, F. Iannelli, F. Griggio, G. Pesole. - In: Invertebrate...
GISSI, CARMELA, PESOLE, GRAZIANO, CATTANEO, ELENA, TARTARI, MARZIA, ZUCCATO, CHIARA, LO SARDO, VALENTINA, ...
Phylogenetic comparison of huntingtin homologues reveals the appearance of a primitive polyQ in sea urchin / M. Tartari, C. Gissi, V. Lo Sardo, C. Zuccato, E. Picardi, G. Pesole, E. Cattaneo. - In:...
Genomic analysis of conserved micro RNAs genes in Grapevine (2008)
PICCOLO, VIVIANA, HORNER, DAVID STEPHEN, PESOLE, GRAZIANO, MICA, ERICA
Genomic analysis of conserved micro RNAs genes in Grapevine / E. Mica, V. Piccolo, A. Ferrarini, C. Casati, M. Delledonne, M. Morgante, M. Pezzotti, G. Pesole, M.E. Pè, D. Horner. - 2008....
PICCOLO, VIVIANA, HORNER, DAVID STEPHEN, PESOLE, GRAZIANO, MICA, ERICA, PE', MARIO ENRICO
Characterization and analysis of the expression pattern of microRNAs in the grapevine Vitis vinifera / V. Piccolo, E. Mica, E. Pè, G. Pesole, D. Horner. - In: EMBnet.news. - ISSN 1023-4144. -...
PICCOLO, VIVIANA, MICA, ERICA, PE', MARIO ENRICO, HORNER, DAVID STEPHEN, PESOLE, GRAZIANO, ...
Characterization and analysis of the expression pattern of microRNAs in the grapevine Vitis vinifera / V. Piccolo, E. Mica, E. Pè, G. Pesole, D. Horner. - 2008. ((Intervento presentato al 10. FISV...
Exalign: a new method for comparative analysis of exon–intron gene structures (2008)
ZAMBELLI, FEDERICO, PAVESI, GIULIO, PESOLE, GRAZIANO
Exalign: a new method for comparative analysis of exon–intron gene structures / F. Zambelli, G. Pavesi, G. Pesole. - 2008. ((Intervento presentato al 10. FISV Annual Congress, Riva del Garda (TN),...
Tartari, Marzia, Gissi, Carmela, Lo Sardo, Valentina, Zuccato, Chiara, Picardi, Ernesto, Pesole, Graziano, ...
Huntingtin is a completely soluble 3,144 amino acid (aa) protein characterized by the presence of an amino-terminal polymorphic polyglutamine (polyQ) tract, whose aberrant expansion causes the...
Exalign: a new method for comparative analysis of exon-intron gene structures (2008)
Pavesi, Giulio, Zambelli, Federico, Caggese, Corrado, Pesole, Graziano
The evolution of genes is usually studied and reconstructed at the sequence level, that is, by comparing and aligning their genomic, transcript or protein sequences. However, including the...
Correlated substitution analysis and the prediction of amino acid structural contacts (2008)
Horner, David S., Pirovano, Walter, Pesole, Graziano
It has long been suspected that analysis of correlated amino acid substitutions should uncover pairs or clusters of sites that are spatially proximal in mature protein structures. Accordingly,...
GRIGGIO, FRANCESCA, IANNELLI, FABIO, GISSI, CARMELA, PESOLE, GRAZIANO
The fast evolutionary dynamics of ascidian mitochondrial genome: an exception to the general deuterostome evolutionary trend / C. Gissi, F. Iannelli, F. Griggio, G. Pesole. - In: Invertebrate...
Porcelli, Damiano, Barsanti, Paolo, Pesole, Graziano, Caggese, Corrado
Abstract Background When orthologous sequences from species distributed throughout an optimal range of divergence times are available, comparative genomics is a powerful tool to address problems such...
Mitogenomics reveals two cryptic species in Ciona intestinalis (2007)
IANNELLI, FABIO, GISSI, CARMELA, PESOLE, GRAZIANO
Mitogenomics reveals two cryptic species in Ciona intestinalis / F. Iannelli, G. Pesole, P. Sordino, C. Gissi. - In: Trends in Genetics. - ISSN 0168-9525. - 23:9(2007 Sep). - p. 419-422.
Iannelli, Fabio, Griggio, Francesca, Pesole, Graziano, Gissi, Carmela
Abstract Background Within Chordata, the subphyla Vertebrata and Cephalochordata (lancelets) are characterized by a remarkable stability of the mitochondrial (mt) genome, with constancy of gene...
Sbisà, Elisabetta, Catalano, Domenico, Grillo, Giorgio, Licciulli, Flavio, Turi, Antonio, Liuni, Sabino, ...
Abstract Background The p53 gene family consists of the three genes p53, p63 and p73, which have polyhedral non-overlapping functions in pivotal cellular processes such as DNA synthesis and repair,...
Horner, David S, Lefkimmiatis, Konstantinos, Reyes, Aurelio, Gissi, Carmela, Saccone, Cecilia, Pesole, Graziano
Abstract Background Phylogenetic relationships between Lagomorpha, Rodentia and Primates and their allies (Euarchontoglires) have long been debated. While it is now generally agreed that Rodentia...
HORNER, DAVID STEPHEN, PESOLE, GRAZIANO, GISSI, CARMELA
Phylogenetic analyses of complete mitochondrial genome sequences suggest a basal divergence of the enigmatic rodent Anomalurus / D.S. Horner, K. Lefkimmiatis, A. Reyes, C. Gissi, C. Saccone, G....
Pavesi, Giulio, Zambelli, Federico, Pesole, Graziano
Abstract Background This work addresses the problem of detecting conserved transcription factor binding sites and in general regulatory regions through the analysis of sequences from homologous...
PAVESI, GIULIO, ZAMBELLI, FEDERICO, PESOLE, GRAZIANO
WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences / Giulio Pavesi, Federico Zambelli, Graziano Pesole. - In: BMC Bioinformatics [risorsa elettronica]....
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla (2007)
HORNER, DAVID STEPHEN, PE', MARIO ENRICO, MICA, ERICA, PESOLE, GRAZIANO
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla / O. Jaillon, J.M. Aury, B. Noel, A. Policriti, C. Clepet, A. Casagrande, N. Choisne, S. Aubourg, N....
MIGNONE, FLAVIO, RE', MATTEO, PESOLE, GRAZIANO
A high performance grid-web service framework for the identification of 'conserved sequence tags' / P. D’Onorio De Meo, D. Carrabino, N. Sanna, T. Castrignano, G. Grillo, F. Licciulli, S. Liuni, M....
GISSI, CARMELA, GRIGGIO, FRANCESCA, PESOLE, GRAZIANO, IANNELLI, FABIO
The mitochondrial genome of Phallusia mammillata and Phallusia fumigata (Tunicata, Ascidiacea): high genome plasticity at intra-genus level / F. Iannelli, F. Griggio, G. Pesole, C. Gissi. - In: BMC...
Mitogenomics reveals two cryptic species in Ciona intestinalis (2007)
GISSI, CARMELA, IANNELLI, FABIO, PESOLE, GRAZIANO
Mitogenomics reveals two cryptic species in Ciona intestinalis / F. Iannelli, G. Pesole, P. Sordino, C. Gissi. - In: Trends in Genetics. - ISSN 0168-9525. - 23:9(2007). - p. 419-422.
BMC Evolutionary Biology 2007, 7:215 doi:10.1186/1471-2148-7-215 (2007)
Damiano Porcelli, Paolo Barsanti, Graziano Pesole, Damiano Porcelli, Paolo Barsanti, Graziano Pesole, ...
PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. The nuclear OXPHOS genes in insecta: a common...
GISSI, CARMELA, GRIGGIO, FRANCESCA, PESOLE, GRAZIANO, IANNELLI, FABIO
The mitochondrial genome of Phallusia mammillata and Phallusia fumigata (Tunicata, Ascidiacea): high genome plasticity at intra-genus level / F. Iannelli, F. Griggio, G. Pesole, C. Gissi. - In: BMC...
miRNA DISCOVERY IN GRAPEVINE BY IN SILICO APPROACHES (2007)
PICCOLO, VIVIANA, HORNER, DAVID STEPHEN, MICA, ERICA, PESOLE, GRAZIANO
miRNA DISCOVERY IN GRAPEVINE BY IN SILICO APPROACHES / E. Mica, V. Piccolo, M.E. Pè, G. Pesole, D. Horner. - In: Proceedings of the 51st Italian Society of Agricultural Genetics Annual Congress. -...
PICCOLO, VIVIANA, PESOLE, GRAZIANO, HORNER, DAVID STEPHEN
A Support Vector Machine for the Discrimination of MicroRNA Precursors from Other Genomic Hairpin Structures / V. Piccolo, G. Pesole, D. Horner. - 2007. Annual Meeting Bioinformatics Italian Society...
MiRNA discovery in grapevine by in silico approaches (2007)
PICCOLO, VIVIANA, MICA, ERICA, HORNER, DAVID STEPHEN, PESOLE, GRAZIANO
MiRNA discovery in grapevine by in silico approaches / E. Mica, V. Piccolo, M.E. Pè, G. Pesole, D. Horner. - 2007. ((Intervento presentato al 51. Italian Society of Agricultural Genetics Annual...
ZAMBELLI, FEDERICO, PAVESI, GIULIO, PESOLE, GRAZIANO
Finding transcription factors with over-represented binding sites in sequences from co-regulated or co-expressed genes / F. Zambelli, W. Breviario, G. Pesole, G. Pavesi. - 2007. ((Intervento...
PICCOLO, VIVIANA, HORNER, DAVID STEPHEN, PESOLE, GRAZIANO, RE', MATTEO
Towards an integrated pipeline for the in-silico prediction of plant microRNAs and their precursors / V. Piccolo, M. Rè, G. Pesole, D. Horner. - 2007. ((Intervento presentato al 9. Congresso annuale...
Huntingtin gene evolution in Chordata and its peculiar features in the ascidian Cionagenus (2006)
Gissi, Carmela, Pesole, Graziano, Cattaneo, Elena, Tartari, Marzia
Abstract Background To gain insight into the evolutionary features of the huntingtin (htt) gene in Chordata, we have sequenced and characterized the full-length htt mRNA in the ascidian Ciona...
Huntingtin gene evolution in Chordata and its peculiar features in the ascidian Ciona genus (2006)
GISSI, CARMELA, CATTANEO, ELENA, PESOLE, GRAZIANO, TARTARI, MARZIA
Huntingtin gene evolution in Chordata and its peculiar features in the ascidian Ciona genus / Carmela Gissi, Graziano Pesole, Elena Cattaneo, Marzia Tartari. - In: BMC Genomics (2006) 7:288 [risorsa...
Huntingtin gene evolution in Chordata and its peculiar features in the ascidian Ciona genus (2006)
GISSI, CARMELA, CATTANEO, ELENA, PESOLE, GRAZIANO, TARTARI, MARZIA
Huntingtin gene evolution in Chordata and its peculiar features in the ascidian Ciona genus / Carmela Gissi, Graziano Pesole, Elena Cattaneo, Marzia Tartari. - In: BMC Genomics (2006) 7:288 [risorsa...
Discrimination of Non-Protein-Coding Transcripts from Protein-Coding mRNA (2006)
MIGNONE, FLAVIO, PESOLE, GRAZIANO
Discrimination of Non-Protein-Coding Transcripts from Protein-Coding mRNA / Martin C. Frith, Timothy L. Bailey, Takeya Kasukawa, Flavio Mignone, Sarah K. Kummerfeld, Martin Madera, Sirisha Sunkara,...
GISSI, CARMELA, PESOLE, GRAZIANO
Mitochondrial phylogeny of Anura (Amphibia): a case study of congruent phylogenetic reconstruction using amino acid and nucleotide characters / Carmela Gissi, Diego San Mauro, Graziano Pesole, Rafael...
PAVESI, GIULIO, ZAMBELLI, FEDERICO, PESOLE, GRAZIANO
MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes / Giulio Pavesi, Paolo Mereghetti, Federico Zambelli, Marco Stefani, Giancarlo Mauri, Graziano...
MIGNONE, FLAVIO, PESOLE, GRAZIANO, IACONO, MICHELE, RE', MATTEO
A new strategy to identify novel genes and gene isoforms: Analysis of human chromosomes 15, 21 and 22 / Matteo Rè, Flavio Mignone, Michele Iacono, Giorgio Grillo, Sabino Liuni, Graziano Pesole. -...
GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags (2006)
MIGNONE, FLAVIO, PESOLE, GRAZIANO
GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags / Tiziana Castrignanò, Paolo D'Onorio De Meo, Giorgio Grillo, Sabino Liuni, Flavio Mignone, Ivano Giuseppe...
ANSELMO, ANNA, PESOLE, GRAZIANO, RIZZI, RAFFAELLA, BONIZZONI, PAOLA
ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization / T. Castrignanò, R. Rizzi, I.G. Talamo, P.D. De Meo, A. Anselmo, P. Bonizzoni, G. Pesole. - In:...
Paola Bonizzoni, Raffaella Rizzi, Graziano Pesole
The fact that a large majority of mammalian genes are subject to alternative splicing indicates that this phenomenon represents a major mechanism for increasing proteome complexity. Here, we provide...
GISSI, CARMELA, PESOLE, GRAZIANO
Mitochondrial phylogeny of Anura (Amphibia): a case study of congruent phylogenetic reconstruction using amino acid and nucleotide characters / Carmela Gissi, Diego San Mauro, Graziano Pesole, Rafael...
PAVESI, GIULIO, ZAMBELLI, FEDERICO, PESOLE, GRAZIANO
MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes / Giulio Pavesi, Paolo Mereghetti, Federico Zambelli, Marco Stefani, Giancarlo Mauri, Graziano...
MIGNONE, FLAVIO, PESOLE, GRAZIANO, IACONO, MICHELE, RE', MATTEO
A new strategy to identify novel genes and gene isoforms: Analysis of human chromosomes 15, 21 and 22 / Matteo Rè, Flavio Mignone, Michele Iacono, Giorgio Grillo, Sabino Liuni, Graziano Pesole. -...
GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags (2006)
MIGNONE, FLAVIO, PESOLE, GRAZIANO
GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags / Tiziana Castrignanò, Paolo D'Onorio De Meo, Giorgio Grillo, Sabino Liuni, Flavio Mignone, Ivano Giuseppe...
ZAMBELLI, FEDERICO, PAVESI, GIULIO, PESOLE, GRAZIANO
Computational Tools for the Discovery of Regulatory Elements in Nucleotide Sequences from Co-Regulated or Homologous Genes / G. Pavesi, F. Zambelli, G. Mauri, G. Pesole. - 2006. ((Intervento...
Analisi di Geni e Genomi (2006)
MUZI FALCONI, MARCO, PLEVANI, PAOLO, GINELLI, ENRICO, PESOLE, GRAZIANO, R.J. Reece
Analisi di Geni e Genomi / R.J. Reece. - Napoli : EdiSES, 2006. ((Trad. di Marco Muzi Falconi, Paolo Plevani, Enrico Ginelli, Graziano Pesole. - ISBN 88-7959-346-3.
Castrignanò, Tiziana, Rizzi, Raffaella, Talamo, Ivano Giuseppe, De Meo, Paolo D'Onorio, Anselmo, Anna, Bonizzoni, Paola, ...
Alternative splicing (AS) is now emerging as a major mechanism contributing to the expansion of the transcriptome and proteome complexity of multicellular organisms. The fact that a single gene locus...
Pavesi, Giulio, Mereghetti, Paolo, Zambelli, Federico, Stefani, Marco, Mauri, Giancarlo, Pesole, Graziano
Understanding the complex mechanisms regulating gene expression at the transcriptional and post-transcriptional levels is one of the greatest challenges of the post-genomic era. The MoD (MOtif...
Computational methods for alternative splicing prediction (2006)
Bonizzoni, Paola, Rizzi, Raffaella, Pesole, Graziano
The fact that a large majority of mammalian genes are subject to alternative splicing indicates that this phenomenon represents a major mechanism for increasing proteome complexity. Here, we provide...
Bonizzoni, Paola, Rizzi, Raffaella, Pesole, Graziano
The fact that a large majority of mammalian genes are subject to alternative splicing indicates that this phenomenon represents a major mechanism for increasing proteome complexity. Here, we provide...
Bmc Genomics, Carmela Gissi, Graziano Pesole, Elena Cattaneo, Marzia Tartari, Open Access, ...
Research article Huntingtin gene evolution in Chordata and its peculiar features in the ascidian Ciona genus
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society (2005)
Helmer-Citterich, Manuela, Casadio, Rita, Guffanti, Alessandro, Mauri, Giancarlo, Milanesi, Luciano, Pesole, Graziano, ...
Abstract The BITS2005 Conference brought together about 200 Italian scientists working in the field of Bioinformatics, students in Biology, Computer Science and Bioinformatics on March 17–19 2005,...
Regularized Least Squares Cancer Classifiers from DNA microarray data (2005)
Ancona, Nicola, Maglietta, Rosalia, D'Addabbo, Annarita, Liuni, Sabino, Pesole, Graziano
Abstract Background The advent of the technology of DNA microarrays constitutes an epochal change in the classification and discovery of different types of cancer because the information provided by...
Bonizzoni, Paola, Rizzi, Raffaella, Pesole, Graziano
Abstract Background: Currently available methods to predict splice sites are mainly based on the independent and progressive alignment of transcript data (mostly ESTs) to the genomic sequence. Apart...
Compositional biases and the mitochondrial phylogeny of arthropods (2005)
GISSI, CARMELA, PESOLE, GRAZIANO, HORNER, DAVID STEPHEN
Compositional biases and the mitochondrial phylogeny of arthropods / O Rota Stabelli, D Horner , C Gissi, P Foster, G Pesole. - In: BITS Conference/ [a cura di] BITS. - [s.l.] : BITS, 2005.
Delving into ascidiaceans mtDNA : preliminary data from three newly completed genomes (2005)
GISSI, CARMELA, PESOLE, GRAZIANO, IANNELLI, FABIO, GRIGGIO, FRANCESCA, Bill Smith, Billie Swalla
Delving into ascidiaceans mtDNA : preliminary data from three newly completed genomes / C. Gissi, F. Iannelli, F. Griggio, G. Pesole. - In: 3. International Tunicate Conference / [a cura di] Bill...
Delving into ascidiaceans mtDNA : preliminary data from three newly completed genomes (2005)
GISSI, CARMELA, GRIGGIO, FRANCESCA, IANNELLI, FABIO, PESOLE, GRAZIANO, Pierre Pontarotti
Delving into ascidiaceans mtDNA : preliminary data from three newly completed genomes / F. Iannelli, C. Gissi, F. Griggio, G. Pesole. - In: 9. Evolutionary Biology Meeting at Marseilles / [a cura di]...
Tiziana Castrignanò, De Meo, Giorgio Grillo, Sabino Liuni, Graziano Pesole
a tool for genome-wide search of coding and non-coding
Bmc Bioinformatics, Paola Bonizzoni, Raffaella Rizzi, Graziano Pesole
Software ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences
Regularized least squares cancer classifiers from dna microarray data (2005)
Nicola Ancona, Rosalia Maglietta, Sabino Liuni, Graziano Pesole
microarray data
Compositional biases and the mitochondrial phylogeny of arthropods (2005)
GISSI, CARMELA, PESOLE, GRAZIANO, HORNER, DAVID STEPHEN
Compositional biases and the mitochondrial phylogeny of arthropods / O Rota Stabelli, D Horner , C Gissi, P Foster, G Pesole. - In: BITS Conference/ [a cura di] BITS. - [s.l.] : BITS, 2005.
Delving into ascidiaceans mtDNA : preliminary data from three newly completed genomes (2005)
GISSI, CARMELA, PESOLE, GRAZIANO, IANNELLI, FABIO, GRIGGIO, FRANCESCA, Bill Smith, Billie Swalla
Delving into ascidiaceans mtDNA : preliminary data from three newly completed genomes / C. Gissi, F. Iannelli, F. Griggio, G. Pesole. - In: 3. International Tunicate Conference / [a cura di] Bill...
Delving into ascidiaceans mtDNA : preliminary data from three newly completed genomes (2005)
GISSI, CARMELA, GRIGGIO, FRANCESCA, IANNELLI, FABIO, PESOLE, GRAZIANO, Pierre Pontarotti
Delving into ascidiaceans mtDNA : preliminary data from three newly completed genomes / F. Iannelli, C. Gissi, F. Griggio, G. Pesole. - In: 9. Evolutionary Biology Meeting at Marseilles / [a cura di]...
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society (2005)
Helmer-Citterich, Manuela, Casadio, Rita, Guffanti, Alessandro, Mauri, Giancarlo, Milanesi, Luciano, Pesole, Graziano, ...
The BITS2005 Conference brought together about 200 Italian scientists working in the field of Bioinformatics, students in Biology, Computer Science and Bioinformatics on March 17–19 2005, in Milan....
Mignone, Flavio, Grillo, Giorgio, Licciulli, Flavio, Iacono, Michele, Liuni, Sabino, Kersey, Paul J., ...
The 5′ and 3′ untranslated regions of eukaryotic mRNAs play crucial roles in the post-transcriptional regulation of gene expression through the modulation of nucleo-cytoplasmic mRNA transport,...
Boccia, Angelo, Petrillo, Mauro, Di Bernardo, Diego, Guffanti, Alessandro, Mignone, Flavio, Confalonieri, Stefano, ...
The identification and study of evolutionarily conserved genomic sequences that surround disease-related genes is a valuable tool to gain insight into the functional role of these genes and to better...
GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags (2005)
Castrignanò, Tiziana, De Meo, Paolo D'Onorio, Grillo, Giorgio, Liuni, Sabino, Mignone, Flavio, Talamo, Ivano Giuseppe, ...
Summary: GenoMiner is a software tool that searches for regions of similarity between user submitted genome or transcript sequences and user specified whole genome assemblies. The program then...
IANNELLI, FABIO, GISSI, CARMELA, PESOLE, GRAZIANO
Complete mtDNA of Ciona intestinalis reveals extensive gene rearrangement and the presence of an atp8 and an extra trnM gene in ascidians / C. Gissi, F. Iannelli, G. Pesole. - In: Journal of...
HORNER, DAVID STEPHEN, PESOLE, GRAZIANO, MIGNONE, FLAVIO
WebVar: a resource for the rapid estimation of relative site variability from multiple sequence alignments / F. Mignone, D.S. Horner, G. Pesole. - In: Bioinformatics. - ISSN 1367-4803. - 20:8(2004)....
Phylogenetic analyses: a brief introduction to methods and their applications (2004)
HORNER, DAVID STEPHEN, PESOLE, GRAZIANO, D.S. Horner, G. Pesole
Phylogenetic analyses: a brief introduction to methods and their applications / D.S. Horner, G. Pesole. - In: Expert Reviews in Molecular Diagnostics. - ISSN 1473-7159. - 4:3(2004). - p. 339-350.
Summary: DNAfan (DNA Feature ANalyzer) is a tool (2004)
Andreas Gisel, Maria Panetta, Giorgio Grillo, Vito Flavio Licciulli, Sabino Liuni, Cecilia Saccone, ...
Giulio Pavesi, Paolo Mereghetti, Giancarlo Mauri, Graziano Pesole
One of the greatest challenges that modern molecular biology is facing is the understanding of the complex mechanisms regulating gene expression. A fundamental step in this process requires the...
HORNER, DAVID STEPHEN, PESOLE, GRAZIANO, MIGNONE, FLAVIO
WebVar: a resource for the rapid estimation of relative site variability from multiple sequence alignments / F. Mignone, D.S. Horner, G. Pesole. - In: Bioinformatics. - ISSN 1367-4803. - 20:8(2004)....
Phylogenetic analyses: a brief introduction to methods and their applications (2004)
HORNER, DAVID STEPHEN, PESOLE, GRAZIANO, D.S. Horner, G. Pesole
Phylogenetic analyses: a brief introduction to methods and their applications / D.S. Horner, G. Pesole. - In: Expert Reviews in Molecular Diagnostics. - ISSN 1473-7159. - 4:3(2004). - p. 339-350.
BERTONI, GIOVANNI, PESOLE, GRAZIANO
Mode of binding of the Fur protein to target DNA : negative regulation of iron-controlled gene expression / V. De Lorenzo, J. Perez-Martin, L. Escolar, G. Pesole, G. Bertoni. - [s.l.] : American...
Gisel, Andreas, Panetta, Maria, Grillo, Giorgio, Licciulli, Vito Flavio, Liuni, Sabino, Saccone, Cecilia, ...
Summary: DNAfan (DNA Feature ANalyzer) is a tool combining sequence-filtering and pattern searching. DNAfan automatically extracts user-defined sets of sequence fragments from large sequence sets....
Congruent Mammalian Trees from Mitochondrial and Nuclear Genes Using Bayesian Methods (2004)
Reyes, Aurelio, Gissi, Carmela, Catzeflis, Francois, Nevo, Eviatar, Pesole, Graziano, Saccone, Cecilia
Analyses of mitochondrial and nuclear gene sequences have often produced different mammalian tree topologies, undermining confidence in the merit of molecular approaches with respect to...
Mignone, Flavio, Horner, David S., Pesole, Graziano
Summary: WebVar is an online resource that provides estimates of relative site-variability from multiple alignments of homologous protein or nucleic acid sequences. WebVar provides a variety of...
Gisel, Andreas, Panetta, Maria, Grillo, Giorgio, Licciulli, Vito Flavio, Liuni, Sabino, Saccone, Cecilia, ...
Summary: DNAfan (DNA Feature ANalyzer) is tool combining sequence-filtering and pattern searching. DNAfan automatically extracts user-defined sets of sequence fragments from large sequence sets....
Pavesi, Giulio, Mauri, Giancarlo, Stefani, Marco, Pesole, Graziano
The recent interest sparked due to the discovery of a variety of functions for non-coding RNA molecules has highlighted the need for suitable tools for the analysis and the comparison of RNA...
Pavesi, Giulio, Mereghetti, Paolo, Mauri, Giancarlo, Pesole, Graziano
One of the greatest challenges that modern molecular biology is facing is the understanding of the complex mechanisms regulating gene expression. A fundamental step in this process requires the...
Castrignanò, Tiziana, Canali, Alessandro, Grillo, Giorgio, Liuni, Sabino, Mignone, Flavio, Pesole, Graziano
The identification and characterization of genome tracts that are highly conserved across species during evolution may contribute significantly to the functional annotation of whole-genome sequences....
In silico representation and discovery of transcription factor binding sites (2004)
Pavesi, Giulio, Mauri, Giancarlo, Pesole, Graziano
Understanding the complex mechanisms governing basic biological processes requires the characterisation of regulatory motifs modulating gene expression at transcriptional and posttranscriptional...
Mignone, Flavio, Horner, David S., Pesole, Graziano
Summary: WebVar is an online resource that provides estimates of relative site variability from multiple alignments of homologous protein or nucleic acid sequences. WebVar provides a variety of...
Mignone, Flavio, Horner, David S., Pesole, Graziano
Summary: WebVar is an online resource that provides estimates of relative site-variability from multiple alignments of homologous protein or nucleic acid sequences. WebVar provides a variety of...
Gisel, Andreas, Panetta, Maria, Grillo, Giorgio, Licciulli, Vito Flavio, Liuni, Sabino, Saccone, Cecilia, ...
Summary: DNAfan (DNA Feature ANalyzer) is tool combining sequence-filtering and pattern searching. DNAfan automatically extracts user-defined sets of sequence fragments from large sequence sets....
Changes in Escherichia coli transcriptome during acclimatization at low temperature (2003)
BRIANI, FEDERICA, DEHO', GIOVANNI, PESOLE, GRAZIANO
Changes in Escherichia coli transcriptome during acclimatization at low temperature / A. Polissi, W. De Laurentis, S. Zangrossi, F. Briani, V. Longhi, G. Pesole, G. Dehò. - In: Research in...
The estimation of relative site variability among aligned homologous protein sequences (2003)
HORNER, DAVID STEPHEN, PESOLE, GRAZIANO, D. Horner, G. Pesole
The estimation of relative site variability among aligned homologous protein sequences / D. Horner, G. Pesole. - In: Bioinformatics. - ISSN 1367-4803. - 19:5(2003). - p. 600-606.
Changes in Escherichia coli transcriptome during acclimatization at low temperature (2003)
BRIANI, FEDERICA, DEHO', GIOVANNI, PESOLE, GRAZIANO
Changes in Escherichia coli transcriptome during acclimatization at low temperature / A. Polissi, W. De Laurentis, S. Zangrossi, F. Briani, V. Longhi, G. Pesole, G. Dehò. - In: Research in...
The estimation of relative site variability among aligned homologous protein sequences (2003)
HORNER, DAVID STEPHEN, PESOLE, GRAZIANO, D. Horner, G. Pesole
The estimation of relative site variability among aligned homologous protein sequences / D. Horner, G. Pesole. - In: Bioinformatics. - ISSN 1367-4803. - 19:5(2003). - p. 600-606.
Congruent Mammalian Trees from Mitochondrial and Nuclear Genes Using Bayesian Methods (2003)
Reyes, Aurelio, Gissi, Carmela, Catzeflis, Francois, Nevo, Eviatar, Pesole, Graziano, Saccone, Cecilia
Analyses of mitochondrial and nuclear gene sequences have often produced different mammalian tree topologies, undermining confidence in the merit of molecular approaches with respect to "traditional"...
Grillo, Giorgio, Licciulli, Flavio, Liuni, Sabino, Sbisà, Elisabetta, Pesole, Graziano
Regulation of gene expression at transcriptional and post-transcriptional level involves the interaction between short DNA or RNA tracts and the corresponding trans-acting protein factors. Detection...
Translational control of Scamper expression via a cell-specific internal ribosome entry site (2003)
De Pietri Tonelli, Davide, Mihailovich, Marija, Schnurbus, Raphaela, Pesole, Graziano, Grohovaz, Fabio, Zacchetti, Daniele
The mRNA of Scamper, a putative intracellular calcium channel activated by sphingosylphosphocholine, contains a long 5′ transcript leader with several upstream AUGs. In this work we have...
Transcript Mapping and Genome Annotation of Ascidian mtDNA Using EST Data (2003)
Gissi, Carmela, Pesole, Graziano
Mitochondrial transcripts of two ascidian species were reconstructed through sequence assembly of publicly available ESTs resembling mitochondrial DNA sequences (mt-ESTs). This strategy allowed us to...
Transcript Mapping and Genome Annotation of Ascidian mtDNA Using EST Data (2003)
Gissi, Carmela, Pesole, Graziano
Mitochondrial transcripts of two ascidian species were reconstructed through sequence assembly of publicly available ESTs resembling mitochondrial DNA sequences (mt-ESTs). This strategy allowed us to...
Mignone, Flavio, Grillo, Giorgio, Liuni, Sabino, Pesole, Graziano
The identification of conserved sequence tags (CSTs) through comparative genome analysis may reveal important regulatory elements involved in shaping the spatio‐temporal expression of genetic...
Congruent Mammalian Trees from Mitochondrial and Nuclear Genes Using Bayesian Methods (2003)
Reyes, Aurelio, Gissi, Carmela, Catzeflis, Francois, Nevo, Eviatar, Pesole, Graziano, Saccone, Cecilia
Analyses of mitochondrial and nuclear gene sequences have often produced different mammalian tree topologies, undermining confidence in the merit of molecular approaches with respect to "traditional"...
Untranslated regions of mRNAs (2002)
Mignone, Flavio, Gissi, Carmela, Liuni, Sabino, Pesole, Graziano
Abstract Gene expression is finely regulated at the post-transcriptional level. Features of the untranslated regions of mRNAs that control their translation, degradation and localization include...
MitoNuc: a database of nuclear genes coding for mitochondrial proteins. Update 2002 (2002)
Attimonelli, Marcella, Catalano, Domenico, Gissi, Carmela, Grillo, Giorgio, Licciulli, Flavio, Liuni, Sabino, ...
Mitochondria, besides their central role in energy metabolism, have recently been found to be involved in a number of basic processes of cell life and to contribute to the pathogenesis of many...
Pesole, Graziano, Liuni, Sabino, Grillo, Giorgio, Licciulli, Flavio, Mignone, Flavio, Gissi, Carmela, ...
The 5′- and 3′-untranslated regions (5′- and 3′-UTRs) of eukaryotic mRNAs are known to play a crucial role in post-transcriptional regulation of gene expression modulating nucleo-cytoplasmic...
An algorithm for finding signals of unknown length in DNA sequences (2001)
PAVESI, GIULIO, PESOLE, GRAZIANO
An algorithm for finding signals of unknown length in DNA sequences / Giulio Pavesi, Giancarlo Mauri, Graziano Pesole. - In: Bioinformatics. - ISSN 1460-2059. - 17:Suppl. 1(2001). - p. S207-S214.
An algorithm for finding signals of unknown length in DNA sequences (2001)
Pavesi, Giulio, Mauri, Giancarlo, Pesole, Graziano
Pattern discovery in unaligned DNA sequences is a challenging problem in both computer science and molecular biology. Several different methods and techniques have been proposed so far, but in most...
MitoNuc and MitoAln: two related databases of nuclear genes coding for mitochondrial proteins (2000)
Pesole, Graziano, Gissi, Carmela, Catalano, Domenico, Grillo, Giorgio, Licciulli, Flavio, Liuni, Sabino, ...
Mitochondria, besides their central role in energy metabolism, have recently been found to be involved in a number of basic processes of cell life and to contribute to the pathogenesis of many...
Pesole, Graziano, Liuni, Sabino, Grillo, Giorgio, Licciulli, Flavio, Larizza, Alessandra, Makalowski, Wojciech, ...
The 5′ and 3′ untranslated regions of eukaryotic mRNAs may play a crucial role in the regulation of gene expression controlling mRNA localization, stability and translational efficiency. For this...
Pesole, Graziano, Grillo, Giorgio, Larizza, Alessandra, Liuni, Sabino
The crucial role of the non-coding portion of genomes is now widely acknowledged. In particular, mRNA untranslated regions are involved in many post-transcriptional regulatory pathways that control...
Where Do Rodents Fit? Evidence from the Complete Mitochondrial Genome of Sciurus vulgaris (2000)
Reyes, Aurelio, Gissi, Carmela, Pesole, Graziano, Catzeflis, François M., Saccone, Cecilia
Lineage-Specific Evolutionary Rate in Mammalian mtDNA (2000)
Gissi, Carmela, Reyes, Aurelio, Pesole, Graziano, Saccone, Cecilia
The existence of a lineage-specific nucleotide substitution rate in mammalian mtDNA has been investigated by analyzing the mtDNA of all available species, that is, 35 complete mitochondrial genomes...
Pesole, Graziano, Liuni, Sabino, DSouza, Mark
* To whom correspondence should be addressed. Motivation: The identification of sequence patterns involved in gene regulation and expression is a major challenge in molecular biology. In this paper...
Definition of Analog and Mixed Signal Extensions to (1999)
Graziano Pesole, Sabino Liuni, Giorgio Grillo, Cecilia Saccone
The important role the untranslated regions of eukaryotic mRNAs may play in gene regulation and expression is now widely acknowledged. For this reason we developed UTRdb, a specialized database of...
UTRdb: a specialized database of 5'- and 3'-untranslated regions of eukaryotic mRNAs (1998)
Graziano Pesole, Sabino Liuni, Giorgio Grillo, Cecilia Saccone
The important role the untranslated regions of eukaryotic mRNAs may play in gene regulation and expression is now widely acknowledged. For this reason we developed UTRdb, a specialized database of...
CLEANUP: a fast computer program for removing redundancies from nucleotide sequence databases (1996)
Grillo, Giorgio, Attimonelli, Marcella, Liuni, Sabino, Pesole, Graziano
A key concept in comparing sequence collections is the issue of redundancy. The production of sequence collections free from redundancy is undoubtedly very useful, both in performing statistical...
Liuni, Sabino, Prunella, Nicola, Pesole, Graziano, D'Orazio, Tiziana, Stella, Ettore, Distante, Arcangelo
The development of new techniques in sequencing nucleic acids has produced a great amount of sequence data and has led to the discovery of new relationships. In this paper, we study a method for...
A backtranslation method based on codon usage strategy (1988)
Pesole, Graziano, Attimonelli, Marcella, Liuni, Sabino
This study describes a method for the backtranslation of an aminoacidic sequence, an extremely useful tool for various experimental approaches. It involves two computer programs CLUSTER and BACKTR...
MitoNuc: a database of nuclear genes coding for mitochondrial proteins. Update 2002
Attimonelli, Marcella, Catalano, Domenico, Gissi, Carmela, Grillo, Giorgio, Licciulli, Flavio, Liuni, Sabino, ...
Mitochondria, besides their central role in energy metabolism, have recently been found to be involved in a number of basic processes of cell life and to contribute to the pathogenesis of many...
Pesole, Graziano, Liuni, Sabino, Grillo, Giorgio, Licciulli, Flavio, Mignone, Flavio, Gissi, Carmela, ...
The 5′- and 3′-untranslated regions (5′- and 3′-UTRs) of eukaryotic mRNAs are known to play a crucial role in post-transcriptional regulation of gene expression modulating nucleo-cytoplasmic...
MitoNuc and MitoAln: two related databases of nuclear genes coding for mitochondrial proteins
Pesole, Graziano, Gissi, Carmela, Catalano, Domenico, Grillo, Giorgio, Licciulli, Flavio, Liuni, Sabino, ...
Mitochondria, besides their central role in energy metabolism, have recently been found to be involved in a number of basic processes of cell life and to contribute to the pathogenesis of many...
Pesole, Graziano, Liuni, Sabino, Grillo, Giorgio, Licciulli, Flavio, Larizza, Alessandra, Makalowski, Wojciech, ...
The 5′ and 3′ untranslated regions of eukaryotic mRNAs may play a crucial role in the regulation of gene expression controlling mRNA localization, stability and translational efficiency. For this...
Mignone, Flavio, Gissi, Carmela, Liuni, Sabino, Pesole, Graziano
Gene expression is finely regulated at the post-transcriptional level. Features of the untranslated regions of mRNAs that control their translation, degradation and localization include stem-loop...
Translational control of Scamper expression via a cell-specific internal ribosome entry site
De Pietri Tonelli, Davide, Mihailovich, Marija, Schnurbus, Raphaela, Pesole, Graziano, Grohovaz, Fabio, Zacchetti, Daniele
The mRNA of Scamper, a putative intracellular calcium channel activated by sphingosylphosphocholine, contains a long 5′ transcript leader with several upstream AUGs. In this work we have...
PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences
Grillo, Giorgio, Licciulli, Flavio, Liuni, Sabino, Sbisà, Elisabetta, Pesole, Graziano
Regulation of gene expression at transcriptional and post-transcriptional level involves the interaction between short DNA or RNA tracts and the corresponding trans-acting protein factors. Detection...
Mignone, Flavio, Grillo, Giorgio, Liuni, Sabino, Pesole, Graziano
The identification of conserved sequence tags (CSTs) through comparative genome analysis may reveal important regulatory elements involved in shaping the spatio-temporal expression of genetic...
Transcript Mapping and Genome Annotation of Ascidian mtDNA Using EST Data
Gissi, Carmela, Pesole, Graziano
Mitochondrial transcripts of two ascidian species were reconstructed through sequence assembly of publicly available ESTs resembling mitochondrial DNA sequences (mt-ESTs). This strategy allowed us to...
RNAProfile: an algorithm for finding conserved secondary structure motifs in unaligned RNA sequences
Pavesi, Giulio, Mauri, Giancarlo, Stefani, Marco, Pesole, Graziano
The recent interest sparked due to the discovery of a variety of functions for non-coding RNA molecules has highlighted the need for suitable tools for the analysis and the comparison of RNA...
Pavesi, Giulio, Mereghetti, Paolo, Mauri, Giancarlo, Pesole, Graziano
One of the greatest challenges that modern molecular biology is facing is the understanding of the complex mechanisms regulating gene expression. A fundamental step in this process requires the...
Castrignanò, Tiziana, Canali, Alessandro, Grillo, Giorgio, Liuni, Sabino, Mignone, Flavio, Pesole, Graziano
The identification and characterization of genome tracts that are highly conserved across species during evolution may contribute significantly to the functional annotation of whole-genome sequences....
Boccia, Angelo, Petrillo, Mauro, Di Bernardo, Diego, Guffanti, Alessandro, Mignone, Flavio, Confalonieri, Stefano, ...
The identification and study of evolutionarily conserved genomic sequences that surround disease-related genes is a valuable tool to gain insight into the functional role of these genes and to better...
Mignone, Flavio, Grillo, Giorgio, Licciulli, Flavio, Iacono, Michele, Liuni, Sabino, Kersey, Paul J., ...
The 5′ and 3′ untranslated regions of eukaryotic mRNAs play crucial roles in the post-transcriptional regulation of gene expression through the modulation of nucleo-cytoplasmic mRNA transport,...
ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization
Castrignanò, Tiziana, Rizzi, Raffaella, Talamo, Ivano Giuseppe, De Meo, Paolo D'Onorio, Anselmo, Anna, Bonizzoni, Paola, ...
Alternative splicing (AS) is now emerging as a major mechanism contributing to the expansion of the transcriptome and proteome complexity of multicellular organisms. The fact that a single gene locus...
MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes
Pavesi, Giulio, Mereghetti, Paolo, Zambelli, Federico, Stefani, Marco, Mauri, Giancarlo, Pesole, Graziano
Understanding the complex mechanisms regulating gene expression at the transcriptional and post-transcriptional levels is one of the greatest challenges of the post-genomic era. The MoD (MOtif...
Huntingtin gene evolution in Chordata and its peculiar features in the ascidian Ciona genus
Gissi, Carmela, Pesole, Graziano, Cattaneo, Elena, Tartari, Marzia
MitoNuc: a database of nuclear genes coding for mitochondrial proteins. Update 2002
Attimonelli, Marcella, Catalano, Domenico, Gissi, Carmela, Grillo, Giorgio, Licciulli, Flavio, Liuni, Sabino, ...
Mitochondria, besides their central role in energy metabolism, have recently been found to be involved in a number of basic processes of cell life and to contribute to the pathogenesis of many...
Pesole, Graziano, Liuni, Sabino, Grillo, Giorgio, Licciulli, Flavio, Mignone, Flavio, Gissi, Carmela, ...
The 5′- and 3′-untranslated regions (5′- and 3′-UTRs) of eukaryotic mRNAs are known to play a crucial role in post-transcriptional regulation of gene expression modulating nucleo-cytoplasmic...
MitoNuc and MitoAln: two related databases of nuclear genes coding for mitochondrial proteins
Pesole, Graziano, Gissi, Carmela, Catalano, Domenico, Grillo, Giorgio, Licciulli, Flavio, Liuni, Sabino, ...
Mitochondria, besides their central role in energy metabolism, have recently been found to be involved in a number of basic processes of cell life and to contribute to the pathogenesis of many...
Pesole, Graziano, Liuni, Sabino, Grillo, Giorgio, Licciulli, Flavio, Larizza, Alessandra, Makalowski, Wojciech, ...
The 5′ and 3′ untranslated regions of eukaryotic mRNAs may play a crucial role in the regulation of gene expression controlling mRNA localization, stability and translational efficiency. For this...
Mignone, Flavio, Gissi, Carmela, Liuni, Sabino, Pesole, Graziano
Gene expression is finely regulated at the post-transcriptional level. Features of the untranslated regions of mRNAs that control their translation, degradation and localization include stem-loop...
Translational control of Scamper expression via a cell-specific internal ribosome entry site
De Pietri Tonelli, Davide, Mihailovich, Marija, Schnurbus, Raphaela, Pesole, Graziano, Grohovaz, Fabio, Zacchetti, Daniele
The mRNA of Scamper, a putative intracellular calcium channel activated by sphingosylphosphocholine, contains a long 5′ transcript leader with several upstream AUGs. In this work we have...
PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences
Grillo, Giorgio, Licciulli, Flavio, Liuni, Sabino, Sbisà, Elisabetta, Pesole, Graziano
Regulation of gene expression at transcriptional and post-transcriptional level involves the interaction between short DNA or RNA tracts and the corresponding trans-acting protein factors. Detection...
Mignone, Flavio, Grillo, Giorgio, Liuni, Sabino, Pesole, Graziano
The identification of conserved sequence tags (CSTs) through comparative genome analysis may reveal important regulatory elements involved in shaping the spatio-temporal expression of genetic...
Transcript Mapping and Genome Annotation of Ascidian mtDNA Using EST Data
Gissi, Carmela, Pesole, Graziano
Mitochondrial transcripts of two ascidian species were reconstructed through sequence assembly of publicly available ESTs resembling mitochondrial DNA sequences (mt-ESTs). This strategy allowed us to...
RNAProfile: an algorithm for finding conserved secondary structure motifs in unaligned RNA sequences
Pavesi, Giulio, Mauri, Giancarlo, Stefani, Marco, Pesole, Graziano
The recent interest sparked due to the discovery of a variety of functions for non-coding RNA molecules has highlighted the need for suitable tools for the analysis and the comparison of RNA...
Pavesi, Giulio, Mereghetti, Paolo, Mauri, Giancarlo, Pesole, Graziano
One of the greatest challenges that modern molecular biology is facing is the understanding of the complex mechanisms regulating gene expression. A fundamental step in this process requires the...
Castrignanò, Tiziana, Canali, Alessandro, Grillo, Giorgio, Liuni, Sabino, Mignone, Flavio, Pesole, Graziano
The identification and characterization of genome tracts that are highly conserved across species during evolution may contribute significantly to the functional annotation of whole-genome sequences....
Boccia, Angelo, Petrillo, Mauro, Di Bernardo, Diego, Guffanti, Alessandro, Mignone, Flavio, Confalonieri, Stefano, ...
The identification and study of evolutionarily conserved genomic sequences that surround disease-related genes is a valuable tool to gain insight into the functional role of these genes and to better...
Mignone, Flavio, Grillo, Giorgio, Licciulli, Flavio, Iacono, Michele, Liuni, Sabino, Kersey, Paul J., ...
The 5′ and 3′ untranslated regions of eukaryotic mRNAs play crucial roles in the post-transcriptional regulation of gene expression through the modulation of nucleo-cytoplasmic mRNA transport,...
ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization
Castrignanò, Tiziana, Rizzi, Raffaella, Talamo, Ivano Giuseppe, De Meo, Paolo D'Onorio, Anselmo, Anna, Bonizzoni, Paola, ...
Alternative splicing (AS) is now emerging as a major mechanism contributing to the expansion of the transcriptome and proteome complexity of multicellular organisms. The fact that a single gene locus...
MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes
Pavesi, Giulio, Mereghetti, Paolo, Zambelli, Federico, Stefani, Marco, Mauri, Giancarlo, Pesole, Graziano
Understanding the complex mechanisms regulating gene expression at the transcriptional and post-transcriptional levels is one of the greatest challenges of the post-genomic era. The MoD (MOtif...
Huntingtin gene evolution in Chordata and its peculiar features in the ascidian Ciona genus
Gissi, Carmela, Pesole, Graziano, Cattaneo, Elena, Tartari, Marzia
Horner, David S, Lefkimmiatis, Konstantinos, Reyes, Aurelio, Gissi, Carmela, Saccone, Cecilia, Pesole, Graziano
Regularized Least Squares Cancer Classifiers from DNA microarray data
Ancona, Nicola, Maglietta, Rosalia, D'Addabbo, Annarita, Liuni, Sabino, Pesole, Graziano
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society
Helmer-Citterich, Manuela, Casadio, Rita, Guffanti, Alessandro, Mauri, Giancarlo, Milanesi, Luciano, Pesole, Graziano, ...
The BITS2005 Conference brought together about 200 Italian scientists working in the field of Bioinformatics, students in Biology, Computer Science and Bioinformatics on March 17–19 2005, in Milan....
Bioinformatics in Italy: BITS2006, the third annual meeting of the Italian Society of Bioinformatics
Sbisà, Elisabetta, Catalano, Domenico, Grillo, Giorgio, Licciulli, Flavio, Turi, Antonio, Liuni, Sabino, ...
Exalign: a new method for comparative analysis of exon–intron gene structures
Pavesi, Giulio, Zambelli, Federico, Caggese, Corrado, Pesole, Graziano
The evolution of genes is usually studied and reconstructed at the sequence level, that is, by comparing and aligning their genomic, transcript or protein sequences. However, including the...
Mignone, Flavio, Anselmo, Anna, Donvito, Giacinto, Maggi, Giorgio P, Grillo, Giorgio, Pesole, Graziano
A transcriptional sketch of a primary human breast cancer by 454 deep sequencing
Guffanti, Alessandro, Iacono, Michele, Pelucchi, Paride, Kim, Namshin, Soldà, Giulia, Croft, Larry J, ...
Creanza, Teresa M, Horner, David S, D'Addabbo, Annarita, Maglietta, Rosalia, Mignone, Flavio, Ancona, Nicola, ...
Zambelli, Federico, Pesole, Graziano, Pavesi, Giulio
The first step in gene expression, transcription, is modulated by the interaction of transcription factors with their corresponding binding sites on the DNA sequence. Pscan is a software tool that...
Mangiulli, Marina, Valletti, Alessio, Caratozzolo, Mariano Francesco, Tullo, Apollonia, Sbisà, Elisabetta, Pesole, Graziano, ...
p63 belongs to a family of transcription factors, which, while demonstrating striking conservation of functional domains, regulate distinct biological functions. Its principal role is in the...