Graziano Pesole

Graziano Pesole is a Full Professor of molecular biology in the University of Bari. He has since long carried out research activity in the fields of bioinformatics, comparative genomics, and molecular evolution. In particular, his interests are computational approaches for the identification of regulatory elements in noncoding genome regions, alternative splicing, and functional analysis of untranslated regions of eukaryotic mRNAs. He has developed a specialized database (UTRdb/UTRsite), largely used by the scientific community, collecting mRNA untranslated sequences and related regulatory motifs involved in the posttranscriptional regulation of gene expression. He has also developed analysis software and several algorithms largely used by the scientific community and available also through web browsers. Within his studies on molecular evolution, he has contributed to the development of new analysis methodologies and has carried out several studies on the evolution of mitochondrial genome at the intraspecies level, in order to clarify some aspects of the origin of modern man, and at the interspecies one to reconstruct mammal phylogeny and to study the evolutionary dynamics of the mitochondrial genome of Tunicata. He leads an interdisciplinary research group including molecular biologists, computer scientists, and mathematicians. He coordinated research units in several research projects funded by national (MIUR, CNR, Telethon, AIRC) and international (EU, NIH) agencies, and has filed an international patent for the selection of primers for RNA fingerprinting. He is a member of the editorial board of international journals (GENE, BMC Bioinformatics, BMC Genomics, Computational Biology and Chemistry, Briefings in Bioinformatics), author of over 120 papers published in international journals, and coauthor of books on bioinformatics and genomics published by italian (Zanichelli, Gnocchi) and international (Wiley) editors.

Biography Updated on 21 October 2007

Personal Home Page

http://www.pesolelab.it/index.php?mod=00_News

Articles in Scholarly Journals [Incomplete List]

  1. Selection of relevant genes in cancer diagnosis based on their prediction accuracy
    Artificial Intelligence in Medicine, vol. 40, no. 1, pp. 29–44, 2007
  2. A high performance grid-web service framework for the identification of ‘conserved sequence tags’
    Future Generation Computer Systems, vol. 23, no. 3, pp. 371–381, 2007
  3. Mitogenomics reveals two cryptic species in Ciona intestinalis
    Trends in Genetics, vol. 23, no. 9, pp. 419–422, 2007
  4. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
    Nature, vol. 449, no. 7161, Article ID nature06148, 4 pages, 2007
  5. Statistical assessment of functional categories of genes deregulated in pathological conditions by using microarray data
    Bioinformatics, vol. 23, no. 16, pp. 2063–2072, 2007
  6. BMC Bioinformatics, vol. 8, no. 1, p. 46, 2007
  7. BMC Evolutionary Biology, vol. 7, no. 1, p. 16, 2007
  8. BMC Genomics, vol. 7, no. 1, p. 288, 2006
  9. MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes
    Nucleic Acids Research, vol. 34, no. Web Server, pp. W566–W570, 2006
  10. ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization
    Nucleic Acids Research, vol. 34, no. Web Server, pp. W440–W443, 2006
  11. BMC Bioinformatics, vol. 7, no. 1, p. 387, 2006
  12. Computational methods for alternative splicing prediction
    Briefings in Functional Genomics and Proteomics, vol. 5, no. 1, pp. 46–51, 2006
  13. Mitochondrial phylogeny of Anura (Amphibia): A case study of congruent phylogenetic reconstruction using amino acid and nucleotide characters
    Gene, vol. 366, no. 2, pp. 228–237, 2006
  14. A new strategy to identify novel genes and gene isoforms: Analysis of human chromosomes 15, 21 and 22
    Gene, vol. 365, pp. 35–40, 2006
  15. Energy biogenesis: one key for coordinating two genomes
    Trends in Genetics, vol. 21, no. 1, pp. 12–16, 2005
  16. uAUG and uORFs in human and rodent 5?untranslated mRNAs
    Gene, vol. 349, pp. 97–105, 2005
  17. Evolution of nuclearly encoded mitochondrial genes in Metazoa
    Gene, vol. 354, pp. 181–188, 2005
  18. Discovery of 342 putative new genes from the analysis of 5'-end-sequenced full-length-enriched cDNA human transcripts
    Genomics, vol. 85, no. 6, pp. 739–751, 2005
  19. A Novel Additional Group II Intron Distinguishes the Mitochondrial rps3 Gene in Gymnosperms
    Journal of Molecular Evolution, vol. 60, no. 2, pp. 196–206, 2005
  20. Assessing computational tools for the discovery of transcription factor binding sites
    Nature Biotechnology, vol. 23, no. 1, Article ID nbt1053, 7 pages, 2005
  21. GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags
    Bioinformatics, vol. 22, no. 4, pp. 497–499, 2005
  22. BMC Bioinformatics, vol. 6, no. 1, p. 244, 2005
  23. Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society
    BMC Bioinformatics, vol. 6, no. Suppl 4, p. S1, 2005
  24. BMC Bioinformatics, vol. 6, no. Suppl 4, p. S2, 2005
  25. Phylogenetic analyses: a brief introduction to methods and their application
    Expert Review of Molecular Diagnostics, vol. 4, no. 3, pp. 339–350, 2004
  26. Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes
    Nucleic Acids Research, vol. 32, no. Web Server, pp. W199–W203, 2004
  27. CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison
    Nucleic Acids Research, vol. 32, no. Web Server, pp. W624–W627, 2004
  28. RNAProfile: an algorithm for finding conserved secondary structure motifs in unaligned RNA sequences
    Nucleic Acids Research, vol. 32, no. 10, pp. 3258–3269, 2004
  29. DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes
    Nucleic Acids Research, vol. 33, no. Database issue, pp. D505–D510, 2004
  30. UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs
    Nucleic Acids Research, vol. 33, no. Database issue, pp. D141–D146, 2004
  31. WebVar: a resource for the rapid estimation of relative site variability from multiple sequence alignments
    Bioinformatics, vol. 20, no. 8, pp. 1331–1333, 2004
  32. GeneSyn: a tool for detecting conserved gene order across genomes
    Bioinformatics, vol. 20, no. 9, pp. 1472–1474, 2004
  33. DNAfan: a software tool for automated extraction and analysis of user-defined sequence regions
    Bioinformatics, vol. 20, no. 18, pp. 3676–3679, 2004
  34. In silico representation and discovery of transcription factor binding sites
    Briefings in Bioinformatics, vol. 5, no. 3, pp. 217–236, 2004
  35. Complete mtDNA of Ciona intestinalis Reveals Extensive Gene Rearrangement and the Presence of an atp8 and an Extra trnM Gene in Ascidians
    Journal of Molecular Evolution, vol. 58, no. 4, pp. 376–389, 2004
  36. Molecular Clock and Gene Function
    Journal of Molecular Evolution, vol. 57, no. S1, pp. S277–S285, 2003
  37. The estimation of relative site variability among aligned homologous protein sequences
    Bioinformatics, vol. 19, no. 5, pp. 600–606, 2003
  38. Congruent Mammalian Trees from Mitochondrial and Nuclear Genes Using Bayesian Methods
    Molecular Biology and Evolution, vol. 21, no. 2, pp. 397–403, 2003
  39. Erratum to “Structural and evolutionary analysis of the ribosomal genes of the parasitic nematode Meloidogyne artiellia suggests its ancient origin” [Mol Biochem Parasitol 2002; 124: 91–94]
    Molecular and Biochemical Parasitology, vol. 127, no. 1, p. 99, 2003
  40. Changes in Escherichia coli transcriptome during acclimatization at low temperature
    Research in Microbiology, vol. 154, no. 8, pp. 573–580, 2003
  41. Translational control of Scamper expression via a cell-specific internal ribosome entry site
    Nucleic Acids Research, vol. 31, no. 10, pp. 2508–2513, 2003
  42. Computational identification of protein coding potential of conserved sequence tags through cross-species evolutionary analysis
    Nucleic Acids Research, vol. 31, no. 15, pp. 4639–4645, 2003
  43. PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences
    Nucleic Acids Research, vol. 31, no. 13, pp. 3608–3612, 2003
  44. p53 Gene Family: Structural, Functional and Evolutionary Features
    Current Genomics, vol. 4, no. 1, pp. 13–26, 2003
  45. Transcript Mapping and Genome Annotation of Ascidian mtDNA Using EST Data
    Genome Research, vol. 13, no. 9, pp. 2203–2212, 2003
  46. MitoNuc: a database of nuclear genes coding for mitochondrial proteins. Update 2002
    Nucleic Acids Research, vol. 30, no. 1, pp. 172–173, 2002
  47. UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs. Update 2002
    Nucleic Acids Research, vol. 30, no. 1, pp. 335–340, 2002
  48. Structural and evolutionary analysis of the ribosomal genes of the parasitic nematode Meloidogyne artiellia suggests its ancient origin
    Molecular and Biochemical Parasitology, vol. 124, no. 1-2, pp. 91–94, 2002
  49. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
    Nature, vol. 420, no. 6915, Article ID nature01266, 10 pages, 2002
  50. Mitochondrial DNA in metazoa: degree of freedom in a frozen event
    Gene, vol. 286, no. 1, pp. 3–12, 2002
  51. Molecular strategies in Metazoan genomic evolution
    Gene, vol. 300, no. 1-2, pp. 195–201, 2002
  52. Lineage Specificity of the Evolutionary Dynamics of the mtDNA D-Loop Region in Rodents
    Journal of Molecular Evolution, vol. 54, no. 2, pp. 145–155, 2002
  53. Identification, molecular characterization, and tissue expression of OVCOV1
    Mammalian Genome, vol. 13, no. 11, pp. 619–624, 2002
  54. Evolutionary dynamics of mammalian mRNA untranslated regions by comparative analysis of orthologous human, artiodactyl and rodent gene pairs
    Computers & Chemistry, vol. 26, no. 5, pp. 479–490, 2002
  55. Nature, vol. 409, no. 6821, pp. 685–690, 2001
  56. Structural and functional features of eukaryotic mRNA untranslated regions
    Gene, vol. 276, no. 1-2, pp. 73–81, 2001
  57. Long-branch attraction phenomenon and the impact of among-site rate variation on rodent phylogeny
    Gene, vol. 259, no. 1-2, pp. 177–187, 2000
  58. Analysis of oligonucleotide AUG start codon context in eukariotic mRNAs
    Gene, vol. 261, no. 1, pp. 85–91, 2000
  59. Evolution of the mitochondrial genetic system: an overview
    Gene, vol. 261, no. 1, pp. 153–159, 2000
  60. MitoNuc and MitoAln: two related databases of nuclear genes coding for mitochondrial proteins
    Nucleic Acids Research, vol. 28, no. 1, pp. 163–165, 2000
  61. UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs
    Nucleic Acids Research, vol. 28, no. 1, pp. 193–196, 2000
  62. PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance
    Bioinformatics, vol. 16, no. 5, pp. 439–450, 2000
  63. The untranslated regions of eukaryotic mRNAs: Structure, function, evolution and bioinformatic tools for their analysis
    Briefings in Bioinformatics, vol. 1, no. 3, pp. 236–249, 2000
  64. Global immune disregulation in multiple sclerosis: from the adaptive response to the innate immunity
    Journal of Neuroimmunology, vol. 107, no. 2, pp. 216–219, 2000
  65. Isochore specificity of AUG initiator context of human genes
    FEBS Letters, vol. 464, no. 1-2, pp. 60–62, 1999
  66. The Members of the RH Gene Family (RH50 and RH30) Followed Different Evolutionary Pathways
    Journal of Molecular Evolution, vol. 48, no. 2, pp. 151–159, 1999
  67. Inclusion of Cetaceans Within the Order Artiodactyla Based on Phylogenetic Analysis of Pancreatic Ribonuclease Genes
    Journal of Molecular Evolution, vol. 48, no. 3, pp. 360–368, 1999
  68. Nucleotide Substitution Rate of Mammalian Mitochondrial Genomes
    Journal of Molecular Evolution, vol. 48, no. 4, pp. 427–434, 1999
  69. Guinea Pig p53 mRNA: Identification of New Elements in Coding and Untranslated Regions and Their Functional and Evolutionary Implications
    Genomics, vol. 58, no. 1, pp. 50–64, 1999
  70. UTRdb: a specialized database of 5' and 3' untranslated regions of eukaryotic mRNAs
    Nucleic Acids Research, vol. 27, no. 1, pp. 188–191, 1999
  71. Internet resources for the functional analysis of 5' and 3' untranslated regions of eukaryotic mRNAs
    Trends in Genetics, vol. 15, no. 9, p. 378, 1999
  72. Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system
    Gene, vol. 238, no. 1, pp. 195–209, 1999
  73. Biotechnology Techniques, vol. 12, no. 10, pp. 783–786, 1998
  74. UTRdb: a specialized database of 5'- and 3'-untranslated regions of eukaryotic mRNAs
    Nucleic Acids Research, vol. 26, no. 1, pp. 192–195, 1998
  75. Journal of Bioenergetics and Biomembranes, vol. 29, no. 3, pp. 233–239, 1997
  76. Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications
    Gene, vol. 205, no. 1-2, pp. 125–140, 1997
  77. Structural and compositional features of untranslated regions of eukaryotic mRNAs
    Gene, vol. 205, no. 1-2, pp. 95–102, 1997
  78. Apolipoprotein(a): A Puzzling Evolutionary Story
    Journal of Molecular Evolution , vol. 44 , no. 2 , pp. 234 –236 , 1997
  79. Gypsy/Ty3-like elements in the genome of the terrestrial salamanderHydromantes (Amphibia, Urodela)
    Journal of Molecular Evolution, vol. 43, no. 6, pp. 584–593, 1996
  80. The evolution of the RNase P- and RNase MRP-associated RNAs: Phylogenetic analysis and nucleotide substitution rate
    Journal of Molecular Evolution, vol. 43, no. 1, pp. 46–57, 1996
  81. Databases of mRNA untranslated regions for metazoa
    Computers & Chemistry, vol. 20, no. 1, pp. 141–144, 1996
  82. The guinea-pig is not a rodent
    Nature, vol. 381, no. 6583, Article ID 381597a0, 3 pages, 1996
  83. CLEANUP: a fast computer program for removing redundancies from nucleotide sequence databases
    Bioinformatics, vol. 12, no. 1, pp. 1–8, 1996
  84. A tandemly repeated DNA family originated from SINE-related elements in the European plethodontid salamanders (Amphibia, Urodela)
    Journal of Molecular Evolution, vol. 40, no. 6, pp. 608–615, 1995
  85. Molecular classification of living organisms
    Journal of Molecular Evolution, vol. 40, no. 3, pp. 273–279, 1995
  86. Evolutionary analysis of cytochrome b sequences in some perciformes: Evidence for a slower rate of evolution than in mammals
    Journal of Molecular Evolution, vol. 39, no. 6, pp. 589–597, 1994
  87. Linguistic approaches to the analysis of sequence information
    Trends in Biotechnology, vol. 12, no. 10, pp. 401–408, 1994
  88. Sequence analysis and compositional properties of untranslated regions of human mRNAs
    Gene, vol. 140, no. 2, pp. 219–225, 1994
  89. A statistical method for detecting regions with different evolutionary dynamics in multialigned sequences
    Molecular Phylogenetics and Evolution, vol. 1, no. 2, pp. 91–96, 1992
  90. The main regulatory region of mammalian mitochondrial DNA: Structure-function model and evolutionary pattern
    Journal of Molecular Evolution, vol. 33, no. 1, pp. 83–91, 1991
  91. The branching order of mammuals: Phylogenetic trees inferred from nuclear and mitochrondrial molecular data
    Journal of Molecular Evolution, vol. 33, no. 6, pp. 537–542, 1991
  92. Glutamine Synthetase Gene Evolution: A Good Molecular Clock
    Proceedings of the National Academy of Sciences, vol. 88, no. 2, pp. 522–526, 1991
  93. Evolutionary analysis of the nucleus-encoded subunits of mammalian cytochrome c oxidase
    European Journal of Biochemistry, vol. 195, no. 1, pp. 151–156, 1991
  94. Direct evidence that restriction endonucleases may under estimate the degree of divergence between molecules
    Current Genetics, vol. 18, no. 2, pp. 167–168, 1990
  95. DNA microenvironments and the molecular clock
    Journal of Molecular Evolution, vol. 29, no. 5, pp. 407–411, 1989