Giulio Pavesi

Summary

Affiliation: University of Milan
Country: Italy

Publications

  1. pmc The histone-like NF-Y is a bifunctional transcription factor
    Michele Ceribelli
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita di Milano, Via Celoria 26, 20133 Milano, Italy
    Mol Cell Biol 28:2047-58. 2008
  2. doi request reprint ChIP-Seq Data Analysis to Define Transcriptional Regulatory Networks
    Giulio Pavesi
    Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
    Adv Biochem Eng Biotechnol . 2017
  3. pmc 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
  4. pmc Hedgehogs, humans and high-school science. The benefits of involving high-school students in university research
    Giulio Pavesi
    Universita degli Studi di Milano, Italy
    EMBO Rep 9:208-11. 2008
  5. pmc 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
  6. pmc Gain-of-function p53 mutants have widespread genomic locations partially overlapping with p63
    Elena Martynova
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, Milano, Italy
    Oncotarget 3:132-43. 2012
  7. ncbi request reprint A perspective of promoter architecture from the CCAAT box
    Diletta Dolfini
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, Milano, Italy
    Cell Cycle 8:4127-37. 2009
  8. pmc Cscan: finding common regulators of a set of genes by using a collection of genome-wide ChIP-seq datasets
    Federico Zambelli
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita di Milano, Italy
    Nucleic Acids Res 40:W510-5. 2012
  9. ncbi request reprint In silico representation and discovery of transcription factor binding sites
    Giulio Pavesi
    University of Milan, Milano, Italy
    Brief Bioinform 5:217-36. 2004
  10. doi request reprint Using Weeder for the discovery of conserved transcription factor binding sites
    Giulio Pavesi
    University of Milan, Milan, Italy
    Curr Protoc Bioinformatics . 2006

Collaborators

Detail Information

Publications33

  1. pmc The histone-like NF-Y is a bifunctional transcription factor
    Michele Ceribelli
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita di Milano, Via Celoria 26, 20133 Milano, Italy
    Mol Cell Biol 28:2047-58. 2008
    ..These data indicate that NF-Y is embedded in positive as well as in negative methyl histone marks, serving a dual function in transcriptional regulation, as an activator or as a repressor...
  2. doi request reprint ChIP-Seq Data Analysis to Define Transcriptional Regulatory Networks
    Giulio Pavesi
    Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
    Adv Biochem Eng Biotechnol . 2017
    ..This chapter provides a survey on how data of this kind are to be processed and integrated with expression and other types of data to infer transcriptional regulatory rules and codes...
  3. pmc 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
    ....
  4. pmc Hedgehogs, humans and high-school science. The benefits of involving high-school students in university research
    Giulio Pavesi
    Universita degli Studi di Milano, Italy
    EMBO Rep 9:208-11. 2008
  5. pmc 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/...
  6. pmc Gain-of-function p53 mutants have widespread genomic locations partially overlapping with p63
    Elena Martynova
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, Milano, Italy
    Oncotarget 3:132-43. 2012
    ..Our data favour a model whereby mutp53 GOF mutants act both by tethering growth-controlling TFs and highjacking p63 to new locations...
  7. ncbi request reprint A perspective of promoter architecture from the CCAAT box
    Diletta Dolfini
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, Milano, Italy
    Cell Cycle 8:4127-37. 2009
    ..In conclusion, the new features of the CCAAT box and the link with the neighbouring elements will help in the functional classification of promoters...
  8. pmc Cscan: finding common regulators of a set of genes by using a collection of genome-wide ChIP-seq datasets
    Federico Zambelli
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita di Milano, Italy
    Nucleic Acids Res 40:W510-5. 2012
    ..The web interface is free for use, and there is no login requirement. Available at: http://www.beaconlab.it/cscan...
  9. ncbi request reprint 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...
  10. doi request reprint 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...
  11. pmc 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...
  12. pmc PscanChIP: Finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments
    Federico Zambelli
    Dipartimento di Bioscienze, Universita di Milano, Via Celoria 26, 20133 Milano, Italy
    Nucleic Acids Res 41:W535-43. 2013
    ..The web interface is free for use, and there is no login requirement. It is available at http://www.beaconlab.it/pscan_chip_dev. ..
  13. ncbi request reprint An acetylation-mono-ubiquitination switch on lysine 120 of H2B
    Raffaella Gatta
    Dipartimento de Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, Milano, Italy
    Epigenetics 6:630-7. 2011
    ..Our data point at acetylation of Lysine 120 of H2B as an early mark of poised or active state and establish a temporal sequence between acetylation and mono-ubiquitination of this H2B residue...
  14. pmc 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...
  15. pmc 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
    ....
  16. pmc 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/..
  17. doi request reprint The short isoform of NF-YA belongs to the embryonic stem cell transcription factor circuitry
    Diletta Dolfini
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, Milano, Italy
    Stem Cells 30:2450-9. 2012
    ..These data indicate that NF-Y belongs to the restricted circle of TFs that govern mESCs, and, specifically, that NF-YAs is the active isoform in these cells...
  18. pmc Transcriptional network of p63 in human keratinocytes
    Silvia Pozzi
    Department of Biomolecular Sciences and Biotechnologies, University of Milan, Milan, Italy
    PLoS ONE 4:e5008. 2009
    ..Rather than a rigid master-slave hierarchical model, our data indicate that p63 connects different hubs involved in the multiple specific functions of the skin...
  19. pmc Phylogenetic analyses suggest multiple changes of substrate specificity within the glycosyl hydrolase 20 family
    Jari Intra
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita di Milano, Via Celoria 26, 20133 Milano, Italy
    BMC Evol Biol 8:214. 2008
    ..Nevertheless, only limited analyses of phylogenetic relationships between GH20 genes have been performed until now...
  20. doi request reprint Expression study of an alpha-l-fucosidase gene in the Drosophilidae family
    Maria E Pasini
    Department of Biomolecular Sciences and Biotechnology, University of Milano, Milano, Italy
    Gene 420:23-33. 2008
    ..These findings support the hypothesis that the enzyme is involved in the molecular events of primary gamete interactions that are conserved among drosophilids belonging to Drosophila genus...
  21. pmc A high definition look at the NF-Y regulome reveals genome-wide associations with selected transcription factors
    Diletta Dolfini
    Dipartimento di Bioscienze, Universita degli Studi di Milano, Milano, Via Celoria 26, 20133, Italy
    Nucleic Acids Res 44:4684-702. 2016
    ..These data define genome-wide rules for the organization of NF-Y-centered regulatory modules, supporting a model of distinct categorization and synergy with well defined sets of TFs. ..
  22. pmc 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...
  23. ncbi request reprint Is renalase a novel player in catecholaminergic signaling? The mystery of the catalytic activity of an intriguing new flavoenzyme
    Sara Baroni
    Dipartimento di Bioscienze, Universita degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
    Curr Pharm Des 19:2540-51. 2013
    ....
  24. pmc 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...
  25. ncbi request reprint Gene trap lines identify Arabidopsis genes expressed in stomatal guard cells
    Massimo Galbiati
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, Via Celoria 26, 20 133 Milano, Italy
    Plant J 53:750-62. 2008
    ....
  26. doi request reprint RIP-Seq data analysis to determine RNA-protein associations
    Federico Zambelli
    Dipartimento di Bioscienze, Universita di Milano, Via Celoria 26, 20133, Milano, Italy
    Methods Mol Biol 1269:293-303. 2015
    ..In this chapter we provide a survey of different approaches that can be taken for the analysis of RIP-Seq data and the identification of the RNAs bound by a given RBP. ..
  27. doi request reprint Genome wide features, distribution and correlations of NF-Y binding sites
    Federico Zambelli
    Dipartimento di Bioscienze, Universita degli Studi di Milano, Milano, Via Celoria 26, 20133, Italy Istituto di Biomembrane e Bioenergetica, Consiglio Nazionale delle Ricerche, Bari, Via Amendola 165 A, 70126, Italy
    Biochim Biophys Acta . 2016
    ..This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani...
  28. doi request reprint Detecting conserved coding genomic regions through signal processing of nucleotide substitution patterns
    Matteo Rè
    Department of Biomolecular Science and Biotechnology, University of Milan, Via Celoria 26, 20133 Milan, Italy
    Artif Intell Med 45:117-23. 2009
    ....
  29. ncbi request reprint Comparative and phylogenetic analysis of alpha-L-fucosidase genes
    Jari Intra
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita di Milano, Via Celoria 26, 20133 Milano, Italy
    Gene 392:34-46. 2007
    ..Phylogenetic analysis suggests a gene duplication event very early in metazoan evolution with the subsequent differential loss of isoforms in various metazoan lineages...
  30. pmc 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...
  31. ncbi request reprint 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...
  32. pmc Genomic organization and evolutionary conservation of plant D-type cyclins
    Margit Menges
    Institute of Biotechnology, University of Cambridge, Cambridge CB2 1QT, United Kingdom
    Plant Physiol 145:1558-76. 2007
    ..Global expression correlation analysis further supports distinct expression patterns for CYCD subgroups...
  33. ncbi request reprint 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...