Graziano Pesole

Summary

Affiliation: University of Bari
Country: Italy

Publications

  1. ncbi Computational methods for alternative splicing prediction
    Paola Bonizzoni
    Dipartimento di Biochimica e Biologia Molecolare, Universita di Bari, Via Orabona 4, 70126 Bari, Italy
    Brief Funct Genomic Proteomic 5:46-51. 2006
  2. ncbi Motif discovery and transcription factor binding sites before and after the next-generation sequencing era
    Federico Zambelli
    University of Milan
    Brief Bioinform 14:225-37. 2013
  3. ncbi PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text
    Yuri Pirola
    Dipartimento di Informatica Sistemistica e Comunicazione, Univ, degli Studi di Milano Bicocca, Milano, 20126, Italy
    BMC Bioinformatics 13:S2. 2012
  4. ncbi Assessment of orthologous splicing isoforms in human and mouse orthologous genes
    Federico Zambelli
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, Milano, Italia
    BMC Genomics 11:534. 2010
  5. ncbi Genome-wide identification of coding and non-coding conserved sequence tags in human and mouse genomes
    Flavio Mignone
    Department of Structural Chemistry and Inorganic Stereochemistry, School of Pharmacy, University of Milan, Italy
    BMC Genomics 9:277. 2008
  6. ncbi p53FamTaG: a database resource of human p53, p63 and p73 direct target genes combining in silico prediction and microarray data
    Elisabetta Sbisà
    Istituto di Tecnologie Biomediche Sede di Bari, CNR, Via Amendola, 122 D 70126 Bari, Italy
    BMC Bioinformatics 8:S20. 2007
  7. ncbi What is a gene? An updated operational definition
    Graziano Pesole
    Dipartimento di Biochimica e Biologia Molecolare E Quagliariello, Universita di Bari, Via Orabona 4, 70126 Bari, Italy
    Gene 417:1-4. 2008
  8. ncbi High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera
    Erica Mica
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, Milano, Italy
    BMC Genomics 10:558. 2009
  9. ncbi MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes
    Giulio Pavesi
    Dipartimento di Scienze Biomolecolari e Biotecnologie, University of Milano, Milano, Italy
    Nucleic Acids Res 34:W566-70. 2006
  10. ncbi UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs
    Giorgio Grillo
    Istituto Tecnologie Biomediche del Consiglio Nazionale delle Ricerche, Via Amendola 122 D, 70126 Bari, Italy
    Nucleic Acids Res 38:D75-80. 2010

Detail Information

Publications79

  1. ncbi Computational methods for alternative splicing prediction
    Paola Bonizzoni
    Dipartimento di Biochimica e Biologia Molecolare, Universita di Bari, Via Orabona 4, 70126 Bari, Italy
    Brief Funct Genomic Proteomic 5:46-51. 2006
    ..Specific features and limitations of different approaches and software are discussed, particularly those affecting prediction accuracy and assembly of alternative transcripts...
  2. ncbi Motif discovery and transcription factor binding sites before and after the next-generation sequencing era
    Federico Zambelli
    University of Milan
    Brief Bioinform 14:225-37. 2013
    ....
  3. ncbi PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text
    Yuri Pirola
    Dipartimento di Informatica Sistemistica e Comunicazione, Univ, degli Studi di Milano Bicocca, Milano, 20126, Italy
    BMC Bioinformatics 13:S2. 2012
    ..Traditionally, the problem has been faced by combining different tools, not specifically designed for this task...
  4. ncbi Assessment of orthologous splicing isoforms in human and mouse orthologous genes
    Federico Zambelli
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, Milano, Italia
    BMC Genomics 11:534. 2010
    ....
  5. ncbi Genome-wide identification of coding and non-coding conserved sequence tags in human and mouse genomes
    Flavio Mignone
    Department of Structural Chemistry and Inorganic Stereochemistry, School of Pharmacy, University of Milan, Italy
    BMC Genomics 9:277. 2008
    ..This discrimination is often based (thus dependent) on the availability of annotated proteins...
  6. ncbi p53FamTaG: a database resource of human p53, p63 and p73 direct target genes combining in silico prediction and microarray data
    Elisabetta Sbisà
    Istituto di Tecnologie Biomediche Sede di Bari, CNR, Via Amendola, 122 D 70126 Bari, Italy
    BMC Bioinformatics 8:S20. 2007
    ....
  7. ncbi What is a gene? An updated operational definition
    Graziano Pesole
    Dipartimento di Biochimica e Biologia Molecolare E Quagliariello, Universita di Bari, Via Orabona 4, 70126 Bari, Italy
    Gene 417:1-4. 2008
    ....
  8. ncbi High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera
    Erica Mica
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, Milano, Italy
    BMC Genomics 10:558. 2009
    ..The recent annotation of the genome of the grapevine (Vitis vinifera L.) allowed the identification of many putative conserved microRNA precursors, grouped into multiple gene families...
  9. ncbi MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes
    Giulio Pavesi
    Dipartimento di Scienze Biomolecolari e Biotecnologie, University of Milano, Milano, Italy
    Nucleic Acids Res 34:W566-70. 2006
    ..Available at http://www.pesolelab.it/modtools/ and http://www.beacon.unimi.it/modtools/...
  10. ncbi UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs
    Giorgio Grillo
    Istituto Tecnologie Biomediche del Consiglio Nazionale delle Ricerche, Via Amendola 122 D, 70126 Bari, Italy
    Nucleic Acids Res 38:D75-80. 2010
    ..All internet resources implemented for retrieval and functional analysis of 5' and 3' untranslated regions of eukaryotic mRNAs are accessible at http://utrdb.ba.itb.cnr.it/...
  11. ncbi Huntingtin gene evolution in Chordata and its peculiar features in the ascidian Ciona genus
    Carmela Gissi
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita di Milano, Milano, Italy
    BMC Genomics 7:288. 2006
    ....
  12. ncbi Molecular clock and gene function
    Cecilia Saccone
    Dipartimento di Biochimica e Biologia Molecolare, Universita di Bari, Via Orabona 4, 70126, Bari, Italy
    J Mol Evol 57:S277-85. 2003
    ..However, the porin gene redundancy found in invertebrates and possibly in some fishes may indicate a tendency to duplicate the genetic material, rather than a real need for function innovation...
  13. ncbi The mitochondrial genome of Phallusia mammillata and Phallusia fumigata (Tunicata, Ascidiacea): high genome plasticity at intra-genus level
    Fabio Iannelli
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita di Milano, Via Celoria 26, 20133 Milano, Italy
    BMC Evol Biol 7:155. 2007
    ....
  14. ncbi Identification and functional characterization of two new transcriptional variants of the human p63 gene
    Marina Mangiulli
    Dipartimento di Biochimica e Biologia Molecolare E Quagliariello, Universita degli Studi di Bari, Via Orabona 4, 70126 Bari, Italy
    Nucleic Acids Res 37:6092-104. 2009
    ..Taken together, our results demonstrate the existence of novel p63 proteins whose expression should be considered in future studies on the roles of p63 in the regulation of cellular functions...
  15. ncbi WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences
    Giulio Pavesi
    Dipartimento di Scienze Biomolecolari e Biotecnologie, University of Milan, Milan, Italy
    BMC Bioinformatics 8:46. 2007
    ....
  16. ncbi Detecting alternative gene structures from spliced ESTs: a computational approach
    Paola Bonizzoni
    Dipartimento di Informatica Sistemistica e Comunicazione, Universita degli Studi di Milano Bicocca, Milano, Italy
    J Comput Biol 16:43-66. 2009
    ..We propose a graph algorithm for the problem that is linear in the number of predicted isoforms and size of the graph. Finally, an experimental analysis of the method is performed to assess the reliability of the predictions...
  17. ncbi Selection of relevant genes in cancer diagnosis based on their prediction accuracy
    Rosalia Maglietta
    Istituto di Studi sui Sistemi Intelligenti per l Automazione, CNR Via Amendola 122 D I, 70126 Bari, Italy
    Artif Intell Med 40:29-44. 2007
    ..The question we pose is the following: how do we measure the relevance of a single gene in a given pathology?..
  18. ncbi Exalign: a new method for comparative analysis of exon-intron gene structures
    Giulio Pavesi
    Dipartimento di Scienze Biomolecolari e Biotecnologie, University of Milan, Milan, Italy
    Nucleic Acids Res 36:e47. 2008
    ..The web interface for accessing Exalign is available at http://www.pesolelab.it/exalign/ or http://www.beacon.unimi.it/exalign/..
  19. ncbi Computational methods for ab initio and comparative gene finding
    Ernesto Picardi
    Dipartimento di Biochimica e Biologia Molecolare E Quagliariello, University of Bari, Bari, Italy
    Methods Mol Biol 609:269-84. 2010
    ..Finally, we will briefly introduce metrics to in house evaluation of gene predictions in terms of sensitivity and specificity at nucleotide, exon, and gene levels as well...
  20. ncbi A transcriptional sketch of a primary human breast cancer by 454 deep sequencing
    Alessandro Guffanti
    Institute of Biomedical Technologies, National Research Council, Milan, Italy
    BMC Genomics 10:163. 2009
    ..This method utilizes a cDNA library normalization step to diminish the representation of highly expressed transcripts and biology-oriented bioinformatic analyses to facilitate detection of rare and novel transcripts...
  21. ncbi Identification of tumor-associated cassette exons in human cancer through EST-based computational prediction and experimental validation
    Alessio Valletti
    Dipartimento di Biochimica e Biologia Molecolare, University of Bari, Quagliariello, Via Orabona 4, Bari 70126, Italy
    Mol Cancer 9:230. 2010
    ....
  22. ncbi A new strategy to identify novel genes and gene isoforms: Analysis of human chromosomes 15, 21 and 22
    Matteo Rè
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Via Celoria 26, 20133 Milano, Italy
    Gene 365:35-40. 2006
    ..These findings demonstrate the effectiveness and high prediction reliability of the proposed methodology which could specifically be applied to the annotation of novel genome sequences...
  23. ncbi Phylogenetic analyses of complete mitochondrial genome sequences suggest a basal divergence of the enigmatic rodent Anomalurus
    David S Horner
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita di Milano, Via Celoria 26, 20133 Milano, Italy
    BMC Evol Biol 7:16. 2007
    ..While it is now generally agreed that Rodentia constitutes a monophyletic sister-group of Lagomorpha and that this clade (Glires) is sister to Primates and Dermoptera, higher-level relationships within Rodentia remain contentious...
  24. ncbi Phylogenetic comparison of huntingtin homologues reveals the appearance of a primitive polyQ in sea urchin
    Marzia Tartari
    Department of Pharmacological Sciences, University of Milan, Milano, Italy
    Mol Biol Evol 25:330-8. 2008
    ....
  25. ncbi Statistical assessment of discriminative features for protein-coding and non coding cross-species conserved sequence elements
    Teresa M Creanza
    Istituto di Studi sui Sistemi Intelligenti per l Automazione, CNR, Via Amendola 122 D I, Bari, Italy
    BMC Bioinformatics 10:S2. 2009
    ....
  26. ncbi Evolution of nuclearly encoded mitochondrial genes in Metazoa
    Anna De Grassi
    Istituto di Tecnologie Biomediche, Sezione di Bari, CNR, Bari, Italy
    Gene 354:181-8. 2005
    ..These results are consistent with the 'balance hypothesis' and, at least in insects, the expression of duplicate genes is low and strongly testis-biased...
  27. ncbi Molecular strategies in Metazoan genomic evolution
    Cecilia Saccone
    Dipartimento di Biochimica e Biologia Molecolare, Universita degli Studi, Via Orabona 4, Bari, Italy
    Gene 300:195-201. 2002
    ..Here, we report a description of the evolution of the p53 gene family as an example of expansion of both genetic complexity and gene expression of the nuclear genome...
  28. ncbi In silico representation and discovery of transcription factor binding sites
    Giulio Pavesi
    University of Milan, Milano, Italy
    Brief Bioinform 5:217-36. 2004
    ..This paper provides a survey of existing methods proposed for the problem, focusing both on the ideas underlying them and their availability to the scientific community...
  29. ncbi Accurate discrimination of conserved coding and non-coding regions through multiple indicators of evolutionary dynamics
    Matteo Rè
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, Via Celoria 26, 20133 Milano, Italia
    BMC Bioinformatics 10:282. 2009
    ....
  30. ncbi Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes
    Federico Zambelli
    Dipartimento di Scienze Biomolecolari e Biotecnologie, University of Milan, Milan, Italy
    Nucleic Acids Res 37:W247-52. 2009
    ..The website is free and open to all users and there is no login requirement. Address: http://www.beaconlab.it/pscan...
  31. ncbi DNAfan: a software tool for automated extraction and analysis of user-defined sequence regions
    Andreas Gisel
    Sezione di Bioinformatica e Genomica di Bari, Istituto di Tecnologie Biomediche, CNR, Via Amendola 122/D, 70126 Bari, Italy
    Bioinformatics 20:3676-9. 2004
    ..Its filter features restricts the pattern search to a well-defined set of sequences, allowing drastic reduction in false positive hits. AVAILABILITY: http://bighost.ba.itb.cnr.it:8080/Framework...
  32. ncbi The nuclear OXPHOS genes in insecta: a common evolutionary origin, a common cis-regulatory motif, a common destiny for gene duplicates
    Damiano Porcelli
    Dipartimento di Genetica e Microbiologia DIGEMI, Universita di Bari, Italy
    BMC Evol Biol 7:215. 2007
    ....
  33. ncbi A novel computational strategy to identify A-to-I RNA editing sites by RNA-Seq data: de novo detection in human spinal cord tissue
    Ernesto Picardi
    Dipartimento di Bioscienze, Biotecnologie e Scienze Farmacologiche, Universita di Bari, Bari, Italy
    PLoS ONE 7:e44184. 2012
    ..We assessed the suitability of our procedure by confirming A-to-I candidates using conventional Sanger sequencing and performing RNA-Seq as well as whole exome sequencing of human spinal cord tissue from a single individual...
  34. ncbi Mitochondrial phylogeny of Anura (Amphibia): a case study of congruent phylogenetic reconstruction using amino acid and nucleotide characters
    Carmela Gissi
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita di Milano, Via Celoria, 26 20133 Milano, Italy
    Gene 366:228-37. 2006
    ....
  35. ncbi UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs
    Flavio Mignone
    Dipartimento di Scienze Biomolecolari e Biotecnologie, , Via Celoria 26, 20133 Milano, Italy
    Nucleic Acids Res 33:D141-6. 2005
    ..g. GO term, PFAM domain, etc.). All internet resources implemented for retrieval and functional analysis of 5' and 3' untranslated regions of eukaryotic mRNAs are accessible at http://www.ba.itb.cnr.it/UTR/...
  36. ncbi ExpEdit: a webserver to explore human RNA editing in RNA-Seq experiments
    Ernesto Picardi
    Dipartimento di Biochimica e Biologia Molecolare E Quagliariello, Universita di Bari, Bari, Italy
    Bioinformatics 27:1311-2. 2011
    ..Results are shown as dynamic tables containing University of California, Santa Cruz (UCSC) links for a quick examination of the genomic context. AVAILABILITY: ExpEdit is freely available on the web at http://www.caspur.it/ExpEdit/...
  37. ncbi MitoZoa 2.0: a database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa
    Paolo D'Onorio De Meo
    CASPUR, Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Universita e Ricerca, Rome, Italy
    Nucleic Acids Res 40:D1168-72. 2012
    ..MitoZoa is freely accessible at http://www.caspur.it/mitozoa...
  38. ncbi WebVar: A resource for the rapid estimation of relative site variability from multiple sequence alignments
    Flavio Mignone
    Dipartimento di Scienze Biomolecolari e Biotecnologie, , 20113 Milano, Italy
    Bioinformatics 20:1331-3. 2004
    ..WebVar provides a variety of graphic and textual representations of estimates, designed to assist in phylogenetic analysis. AVAILABILITY: The WebVar server is located at http://www.pesolelab.it/Tools/WebVar.html..
  39. ncbi Mitogenomics reveals two cryptic species in Ciona intestinalis
    Fabio Iannelli
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita di Milano, Via Celoria 26, 20133 Milano, Italy
    Trends Genet 23:419-22. 2007
    ....
  40. ncbi Complete mtDNA of Ciona intestinalis reveals extensive gene rearrangement and the presence of an atp8 and an extra trnM gene in ascidians
    Carmela Gissi
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita di Milano, Via Celoria 26, 20133 Milan, Italy
    J Mol Evol 58:376-89. 2004
    ..4%), and the absence of asymmetric base distribution between the two strands suggest that this genome is more similar to those of some protostomes than to deuterostomes...
  41. ncbi EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data
    Ernesto Picardi
    Dipartimento di Biochimica e Biologia Molecolare E, Quagliariello, Universita degli Studi di Bari, 70126 Bari, Italy
    BMC Bioinformatics 10:S10. 2009
    ..Our procedure has been implemented in the software EasyCluster and takes into account the spliced nature of ESTs after an ad hoc genomic mapping...
  42. ncbi Regularized Least Squares Cancer classifiers from DNA microarray data
    Nicola Ancona
    Istituto di Studi sui Sistemi Intelligenti per I Automazione, CNR, Via Amendola 122 D I, 70126 Bari, Italy
    BMC Bioinformatics 6:S2. 2005
    ..The performances of both approaches have been also investigated with respect to the number of selected genes and different gene selection strategies...
  43. ncbi Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing
    Ernesto Picardi
    Dipartimento di Biochimica e Biologia Molecolare E Quagliariello, Universita degli Studi di Bari, Bari, Italy
    Nucleic Acids Res 38:4755-67. 2010
    ....
  44. ncbi Genomic organization and recombinational unit duplication-driven evolution of ovine and bovine T cell receptor gamma loci
    Giovanna Vaccarelli
    Department of Genetics and Microbiology, University of Bari, Via Amendola 165 A, 70126 Bari, Italy
    BMC Genomics 9:81. 2008
    ..2 and appears to be unique to ruminants. The purpose of this study was the sequencing of the genomic regions encompassing both loci in a "gammadelta high" organism and the analysis of their evolutionary history...
  45. ncbi MitoZoa: a curated mitochondrial genome database of metazoans for comparative genomics studies
    Renato Lupi
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, Italy
    Mitochondrion 10:192-9. 2010
    ..The MitoZoa database is available at http://www.caspur.it/mitozoa...
  46. ncbi Expression and genomic analyses of Camelus dromedarius T cell receptor delta (TRD) genes reveal a variable domain repertoire enlargement due to CDR3 diversification and somatic mutation
    Rachele Antonacci
    Department of Genetics and Microbiology, University of Bari, Via Amendola 165 A 70126 Bari, Italy
    Mol Immunol 48:1384-96. 2011
    ....
  47. ncbi uAUG and uORFs in human and rodent 5'untranslated mRNAs
    Michele Iacono
    Dipartimento di Scienze Biomolecolari e Biotecnologie, , Via Celoria, 26, 20133 Milano, Italy
    Gene 349:97-105. 2005
    ....
  48. ncbi Evolutionary dynamics of mammalian mRNA untranslated regions by comparative analysis of orthologous human, artiodactyl and rodent gene pairs
    Alessandra Larizza
    Dipartimento di Biochimica e Biologia Molecolare, Bari, Italy
    Comput Chem 26:479-90. 2002
    ....
  49. ncbi Reference databases for taxonomic assignment in metagenomics
    Monica Santamaria
    Institute of Biomembranes and Bioenergetics, National Research Council, Bari, Italy
    Brief Bioinform 13:682-95. 2012
    ..ITSoneDB is available for download and browsing at http://itsonedb.ba.itb.cnr.it/...
  50. ncbi SpliceAid-F: a database of human splicing factors and their RNA-binding sites
    Matteo Giulietti
    Department of Biosciences, University of Bari, Bari, Italy
    Nucleic Acids Res 41:D125-31. 2013
    ..The data collected in SpliceAid-F can provide significant information to explain an observed splicing pattern as well as the effect of mutations in functional regulatory elements...
  51. ncbi Transcript mapping and genome annotation of ascidian mtDNA using EST data
    Carmela Gissi
    Dipartimento di Scienze Biomolecolari e Biotecnologie, , Milano, Italy
    Genome Res 13:2203-12. 2003
    ....
  52. ncbi Energy biogenesis: one key for coordinating two genomes
    Marco Sardiello
    Dipartimento di Anatomia Patologica e di Genetica, Sezione di Genetica, , Via Amendola 165/A, 70126 Bari, Italy
    Trends Genet 21:12-6. 2005
    ....
  53. ncbi TRIM8 modulates p53 activity to dictate cell cycle arrest
    Mariano Francesco Caratozzolo
    Institute for Biomedical Technologies, National Research Council, Bari, Italy
    Cell Cycle 11:511-23. 2012
    ..Altogether, our results reveal a previously unknown regulatory pathway controlling p53 activity and suggest TRIM8 as a novel therapeutic target to enhance p53 tumor suppressor activity...
  54. ncbi Mitochondrial DNA in metazoa: degree of freedom in a frozen event
    Cecilia Saccone
    Centro di Studio sui Mitocondri e Metabolismo Energetico, CNR, Via Amendola 165 A, 70126 Bari, Italy
    Gene 286:3-12. 2002
    ....
  55. ncbi Translational control of Scamper expression via a cell-specific internal ribosome entry site
    Davide De Pietri Tonelli
    Cellular Neurophysiology Unit, Department of Neuroscience, San Raffaele Scientific Institute, University of Milano, Milano, Italy
    Nucleic Acids Res 31:2508-13. 2003
    ..Finally, the Scamper IRES appears to be the first IRES with specificity for kidney epithelial cells...
  56. ncbi Structural and evolutionary analysis of the ribosomal genes of the parasitic nematode Meloidogyne artiellia suggests its ancient origin
    Carla De Giorgi
    Dipartimento di Biochimica e Biologia Molecolare, , Bari, Italy
    Mol Biochem Parasitol 124:91-4. 2002
  57. ncbi MitoNuc: a database of nuclear genes coding for mitochondrial proteins. Update 2002
    Marcella Attimonelli
    Dipartimento di Biochimica e Biologia Molecolare, Universita di Bari, Via Orabona 4, 70126 Bari, Italy
    Nucleic Acids Res 30:172-3. 2002
    ..The logic scheme of MitoNuc database has been implemented in the ORACLE DBMS. This will allow the end-users to retrieve data through a friendly interface that will be soon implemented...
  58. ncbi Correction: High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera
    Erica Mica
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, Milano, Italy
    BMC Genomics 11:109. 2010
    ..The editors and authors regret the inconvenience caused to readers by premature publication of the original paper...
  59. ncbi Assessing computational tools for the discovery of transcription factor binding sites
    Martin Tompa
    Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, Washington 98195 2350, USA
    Nat Biotechnol 23:137-44. 2005
    ..The purpose of the current assessment is twofold: to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark of data sets for assessing future tools...
  60. ncbi PatSearch: A program for the detection of patterns and structural motifs in nucleotide sequences
    Giorgio Grillo
    Sezione di Bioinformatica e Genomica di Bari, Istituto Tecnologie Biomediche CNR, via Amendola 168/5, 70125 Bari, Italy
    Nucleic Acids Res 31:3608-12. 2003
    ..PatSearch is available on the web at http://bighost.area.ba.cnr.it/BIG/PatSearch/...
  61. ncbi Computational identification of protein coding potential of conserved sequence tags through cross-species evolutionary analysis
    Flavio Mignone
    Dipartimento di Fisiologia e Biochimica Generali, Universita di Milano, Via Celoria 26, 20133 Milano, Italy
    Nucleic Acids Res 31:4639-45. 2003
    ..The application of this method may help the validation of predicted genes, the prediction of alternative splicing patterns in known and unknown genes and the definition of a dictionary of non-coding regulatory elements...
  62. ncbi ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization
    Tiziana Castrignanò
    Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Universita e Ricerca, CASPUR, Rome, Italy
    Nucleic Acids Res 34:W440-3. 2006
    ..The ASPIC web resource-available at http://www.caspur.it/ASPIC/--is dynamically interconnected with the Ensembl and Unigene databases and also implements an upload facility...
  63. ncbi Discrimination of non-protein-coding transcripts from protein-coding mRNA
    Martin C Frith
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, Kanagawa, Japan
    RNA Biol 3:40-8. 2006
    ..Conversely and surprisingly, our analyses also provide evidence that as much as approximately 10% of entries in the manually curated protein database Swiss-Prot are erroneous translations of actually non-coding transcripts...
  64. ncbi Evolution of genes and genomes on the Drosophila phylogeny
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 450:203-18. 2007
    ..These may prove to underlie differences in the ecology and behaviour of these diverse species...
  65. ncbi ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences
    Paola Bonizzoni
    DISCo, University of Milan Bicocca, Via Bicocca degli Arcimboldi, 8, Milan, 20135, Italy
    BMC Bioinformatics 6:244. 2005
    ..Apart from often being computationally expensive, this approach is vulnerable to several problems--hence the need to develop novel strategies...
  66. ncbi Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes
    Giulio Pavesi
    D.I.Co, University of Milan, Milan, Italy
    Nucleic Acids Res 32:W199-203. 2004
    ..The web interface is available at the address www.pesolelab.it by following the 'Tools' link...
  67. ncbi RNAProfile: an algorithm for finding conserved secondary structure motifs in unaligned RNA sequences
    Giulio Pavesi
    Department of Computer Science and Communication D I Co, University of Milan, Via Comelico 39, 20135 Milan, Italy
    Nucleic Acids Res 32:3258-69. 2004
    ..We also show how it can be applied to corrupted datasets in which a motif does not appear in all the input sequences, as well as to the discovery of more complex motifs in the non-coding RNA...
  68. ncbi Phylogenetic analyses: a brief introduction to methods and their application
    David S Horner
    Department of Biomolecular Sciences and Biotechnology, University of Milan, Via Celoria 26, 20133 Milano, Italy
    Expert Rev Mol Diagn 4:339-50. 2004
    ....
  69. ncbi Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita
    Pierre Abad
    INRA, UMR 1301, 400 Route des Chappes, F 06903 Sophia Antipolis, France
    Nat Biotechnol 26:909-15. 2008
    ..Our results provide insights into the adaptations required by metazoans to successfully parasitize immunocompetent plants, and open the way for discovering new antiparasitic strategies...
  70. ncbi GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags
    Tiziana Castrignanò
    Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Universitàe Ricerca, CASPUR, Rome, Italy
    Bioinformatics 22:497-9. 2006
    ..GenoMiner allows the user to search the query sequence against a number of vertebrate genome assemblies in a single run providing a user-friendly graphical output...
  71. ncbi Using Weeder for the discovery of conserved transcription factor binding sites
    Giulio Pavesi
    University of Milan, Milan, Italy
    Curr Protoc Bioinformatics . 2006
    ..The program has been designed to make its usage as simple as possible and to require very little prior knowledge about the length and conservation of the motifs to be found...
  72. ncbi Congruent mammalian trees from mitochondrial and nuclear genes using Bayesian methods
    Aurelio Reyes
    Sezione di Bioinformatica e Genomica, Istituto Tecnologie Biomediche CNR Bari, Italy
    Mol Biol Evol 21:397-403. 2004
    ..Relationships between and within these lineages strongly suggest that the gene trees may also be congruent with the underlying species phylogeny...
  73. ncbi The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
    Olivier Jaillon
    Genoscope CEA and UMR 8030 CNRS Genoscope Université d Evry, 2 rue Gaston Cremieux, BP5706, 91057 Evry, France
    Nature 449:463-7. 2007
    ..Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants...
  74. ncbi UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs. Update 2002
    Graziano Pesole
    Dipartimento di Fisiologia e Biochimica Generali, Universita di Milano, Via Celoria 26, 20133 Milano, Italy
    Nucleic Acids Res 30:335-40. 2002
    ..All Internet resources we implemented for retrieval and functional analysis of 5'- and 3'-UTRs of eukaryotic mRNAs are accessible at http://bighost.area.ba.cnr.it/BIG/UTRHome/...
  75. ncbi A novel additional group II intron distinguishes the mitochondrial rps3 gene in gymnosperms
    Teresa M R Regina
    Dipartimento di Biologia Cellulare, , 87036 Arcavacata di Rende, Italy
    J Mol Evol 60:196-206. 2005
    ..Furthermore, the pattern of the rps3i2 distribution among algae and land plants provides evidence for the evolutionary acquisition of this novel intron in gymnosperms via intragenomic transposition or retrotransposition...
  76. ncbi Finding conserved gene order across multiple genomes
    Giulio Pavesi
    Methods Mol Biol 396:111-9. 2007
    ..This unit explains the usage of GeneSyn, a software tool for the automatic identification of conserved gene order across multiple annotated genomes...
  77. ncbi CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison
    Tiziana Castrignanò
    Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Universita e Ricerca, CASPUR, Rome, Italy
    Nucleic Acids Res 32:W624-7. 2004
    ..The web tool, available at http://www.caspur.it/CSTminer/, is dynamically interconnected with the Ensembl genome resources and produces a graphical output showing a map of detected conserved sequences and annotated gene features...
  78. ncbi rRNA-like sequences in human mRNAs
    Flavio Mignone
    Dipartimento di Fisiologia e Biochimica Generali, , Milan, Italy
    Appl Bioinformatics 1:145-54. 2002
    ....
  79. ncbi Changes in Escherichia coli transcriptome during acclimatization at low temperature
    Alessandra Polissi
    Department of Microbiology, Glaxo Wellcome SpA, Verona, Italy
    Res Microbiol 154:573-80. 2003
    ..Interestingly, we found that PNPase both negatively and positively modulated the transcript abundance of some of these genes, thus suggesting a complex role of PNPase in controlling cold adaptation...