2001-2010

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  • Bernardi G. (2009-2010). Anton Dohrn e la Stazione Zoologica di Napoli. Atti Ist. Veneto 168: 55-64. (PDF)
  • Bernardi G., Varriale A. (2010). Distribution of DNA methylation, CpGs, and CpG islands in human isochores. Genomics: 95: 25-28. (PDF)
  • Bernardi G. (2010). La teoria neoselezionista dell’evoluzione. Enciclopedia Italiana. XXI Secolo 5: 297-307. (PDF)
  • Bernardi G. (2009). Anton Dohrn. Marine Genomics 2: 81-83. (PDF)
  • Di Filippo M., Bernardi G. (2009). The early apoptotic DNA fragmentation targets a small number of specific open chromatin region.Plos One 4: 1-7. (PDF)
  • Cammarano R., Costantini M., Bernardi G. (2009). The isochore patterns of invertebrate genomes. BMC Genomics 10: 538-550. (PDF)
  • Bucciarelli G., Di Filippo M., Costagliola D., Alvarez-Valin F., Bernardi G., Bernardi G. (2009). Environmental genomics: a tale of two fishes. Mol. Biol. Evol. 26: 1235-1243. (PDF)
  • Costantini M., Bernardi G. (2009). Mapping insertions, deletions and SNPs in Venter’s chromosomes. Plos One 4: 1-11. (PDF)
  • Costantini M., Cammarano R., Bernardi G. (2009). The evolution of isochore patterns in vertebrate genomes. BMC Genomics 10: 146. (PDF)
  • Bernardi G. (2009). The role of chance in evolution of Science. In Scientific Insights into the Evolution of the Universe and of Life. The Proceedings of the Plenary Session 31 Oct.- 4 Nov. 2008. Pontificial Academy Scientarium. Acta 20 pp.228-239. (PDF)
  • Saccone S., Bernardi G. (2008). GC-rich isochores in the interphase nucleus. In Encyclopedia of Life Sciences, John Wiley & Sons, Ltd, Chichester, UK. (PDF)
  • Costantini M., Di Filippo M., Bernardi G. (2008). Extrapolating ENCODE data to the whole human genome. Gene 419: 66-69. (PDF)
  • Costantini M., Bernardi G. (2008a). Correlations between coding and contiguous non-coding sequences in isochore families from vertebrate genomes. Gene 410: 241-248. (PDF)
  • Bernardi G. (2008). Evolutionary history of the human genome. In Encyclopedia of Life Sciences, John Wiley & Sons, Ltd, Chichester, UK. (PDF)
  • Bernardi G. (2008). Fish genomics: A mini-review on some structural and evolutionary issues. Marine Genomics 1: 3-7. (PDF)
  • Bernardi G. (2008). The neo-selectionist theory of genome evolution. In Encyclopedia of Life Sciences, John Wiley & Sons, Ltd, Chichester, UK. (PDF)
  • Varriale A., Torelli G., Bernardi G. (2008). Compositional properties and thermal adaptation of 18S rRNA in vertebrates. RNA 14:1-9. (PDF)
  • Saccone S., Bernardi G. (2008). Gene distribution in human chromosomes. In Encyclopedia of Life Sciences, John Wiley & Sons, Ltd, Chichester, UK. (PDF)
  • Di Filippo M., Bernardi G. (2008). Mapping DNase I-hypersensitive sites on human isochores. Gene 419: 62-65. (PDF)
  • Arhondakis S., Clay O., Bernardi G. (2008). GC level and expression of human coding sequences. Biochem. Biophys. Res. Commun. 367: 542-545. (PDF)
  • Costantini M., Bernardi G. (2008b). Replication timing, chromosomal bands and isochores. Proc. Natl. Acad. Sci. USA 105: 3433-3437. (PDF)
  • Costantini M., Bernardi G. (2008c). The short sequence design of isochores from the human genome. Proc. Natl. Acad. Sci. USA. 105: 13971-13976. (PDF)
  • Bernardi G. (2008). Genome organization of vertebrates. In Encyclopedia of Life Sciences, John Wiley & Sons, Ltd, Chichester, UK. (PDF)
  • Mahmud A.AM., Amore G., Bernardi G. (2008). Compositional genome contexts affect gene expression control in sea urchin embryo. Plos ONE 3: 1-8. (PDF)
  • Costantini M., Clay O., Federico C., Saccone S., Auletta F., Bernardi G. (2007). Human chromosomal bands: nested structure, high-definition map and molecular basis. Chromosoma 116: 29-40. (PDF)
  • Costantini M., Di Filippo M., Auletta F., Bernardi G. (2007). Isochore pattern and gene distribution in the chicken genome. Gene 400: 9-15. (PDF)
  • Cruveiller S., Clay O., Jari K., Bernardi G. (2007). Simple proteomic checks for detecting noncoding RNA. Proteomics 7: 361-363. (PDF)
  • Bernardi G. (2007). The neo-selectionist theory of genome evolution. Proc. Natl. Acad. Sci. USA 104: 8385-8390. (PDF)
  • Costantini M., Auletta F., Bernardi G. (2007). Isochore patterns and gene distributions in fish genomes. Genomics 90: 364-371. (PDF)
  • Varriale A., Bernardi G. (2006b). DNA methylation in reptiles. Gene 385: 122-127. (PDF)
  • Costantini M., Clay O., Auletta F., Bernardi G. (2006). An isochore map of human chromosomes. Genome Res. 16: 536-541. (PDF)
  • Musto H., Naya H., Zavala A., Romero H., Alvarez-Valín F., Bernardi G. (2006). Genomic GC level, optimal growth temperature and genome size in prokaryotes. Biochem. Biophys. Res. Commun. 374: 1-3. (PDF)
  • Clay O., Carels N., Douady C.J., Bernardi G. (2006). Density gradient ultracentrifugation and whole genome sequences: fine-tuning the correspondence. In Progress in Colloid and Polymer Science. Analytical Ultracentrifugation VIII (Wandrey C., Cölfen H.) (PDF)
  • Arhondakis S., Clay O., Bernardi G. (2006). Compositional properties of human cDNA libraries: Practical implications. FEBS Lett. 580: 5772-5778. (PDF)
  • Rayko E., Jabbari K., Bernardi G. (2006). The evolution of introns in human duplicated genes. Gene 365: 41-47. (PDF)
  • Varriale A., Bernardi G. (2006a). DNA methylation and body temperature in fishes. Gene 385: 111-121. (PDF)
  • Federico C., Scavo C., Cantarella C.D., Motta S., Saccone S., Bernardi G. (2006). Gene-rich and gene-poor chromosomal regions have different locations in the interphase nuclei of cold-blooded vertebrates. Chromosoma 115: 123-128. (PDF)
  • Bernardi G, (2005). The distribution of genes in human genome. In Encyclopedia of Life Sciences. John Wiley & Sons Ltd. (PDF)
  • Federico C., Cantarella D.C., Scavo C., Saccone S., Bed’Hom B., Bernardi G. (2005). Avian genomes: different karyotypes but a similar distribution of the GC-richest chromosome regions at interphase. Chromosome Res. 13: 785-793. (PDF)
  • Bernardi G. (2005). Lessons from a small, dispensable genome: the mitochondrial genome of yeast – review. Gene 354: 189-200. (PDF)
  • Santini S., Bernardi G. (2005). Organization and base composition of tilapia Hox genes: implications for the evolution of Hox clusters in fish. Gene 346: 51-61. (PDF)
  • Bernardi G. (2005). Una visione ultra-darwiniana dell’evoluzione del genoma. Rendiconti Accad. Naz. Delle Sccienze detta dei XL Memoire Di Scienze Fisiche e Naturali 123º Vol. XXIX: pp. 7-17. (PDF)
  • Clay O., Bernardi G. (2005). How not to search for isochores: a reply to Cohen et al.. Mol. Biol. Evol. 22: 2315-2317. (PDF)
  • Saccone S., Bernardi G. (2005). Chromosomes 21 and 22: gene density. In Encyclopedia of Life Sciences. John Wiley & Sons Ltd. (PDF)
  • Bernardi G. (2005). Genome oganization of vertebrates In Encyclopedia of Life Sciences. John Wiley & Sons Ltd. (PDF)
  • Bernardi G. (2005). The distribution of genes in human genome. In Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics (Dunn M.J., Jorde L.B., Little P.F.R., Subramaniam S., eds.), John Wiley & Sons, UK. (PDF)
  • Clay O., Carels N., Douady C.J., Bernardi G. (2005). Using analytical ultracentrifugation of DNA in CsCl gradients to explore large-scale properties of genomes. In Analytical Ultracentrifugation: Techniques and Methods (Scott D., Harding S.E., Rowe A.J.,eds.), RSC Publishing  (PDF)
  • Musto H., Naya H., Zavala A., Romero H., Alvarez-Valin F., Bernardi G (2005). The correlation between genomic G+C and optimal growth temperature of prokaryotes is robust: a reply to Marashi and Ghalanbor. Biochem. Biophys. Res. Commun. 330: 357-360. (PDF)
  • Bernardi G. (2005). Isochores. In: Encyclopedia of Life Sciences John Wiley & Sons Ltd. (PDF)
  • Bernardi G. (2005). La distribuzione dei geni nel genoma umano. In I Venerdì delle Accademie Napoletane nell’Anno Accademico 2003-2004 (Garzya A., Tessitore F., eds.) pp. 21-31, Giannini Editore, Napoli. (PDF)
  • Wronka G., Bernardi G., Doerfler W. (2004). Localization of Integrated Adenovirus DNA in the Hamster Genome. Cell Mol. Life Sci. 61: 2983-2990. (PDF)
  • Tsyba L., Rynditch A.V., Boeri E., Jabbari K., Bernardi G. (2004). Distribution of HIV-1 in the genomes of AIDS patients. Cell. Mol. Life Sci. 61: 721-726. (PDF)
  • Jabbari K., Bernardi G. (2004b). Body temperature and evolutionary genomics of vertebrates: a lesson from the genomes of Takifugu rubripes and Tetraodon nigroviridis. Gene 333: 179-181. (PDF)
  • Federico C., Saccone S., Andreozzi L., Motta S., Russo V., Carels N., Bernardi G. (2004). The pig genome: compositional analysis and identification of the gene-richest regions in chromosomes and nuclei. Gene 343: 245-251. (PDF)
  • Musto H., Naya H., Zavala A., Romero H., Alvarez-Valin F., Bernardi G. (2004). Correlations between genomic GC levels and optimal growth temperatures in prokaryotes. FEBS Lett. 573: 73-77. (PDF)
  • Bernardi G. (2004). Structural and evolutionary fish genomics. Mar. Biotechnol. 6: S1-S3. (PDF)
  • Cruveiller S., Jabbari K., Clay O., Bernardi G. (2004b). Incorrectly predicted genes in rice? Gene 333:187-188. (PDF)
  • Paces J., Zíka R., Paces V., Pavlícek A., Clay O., Bernardi G. (2004). Representing GC variation along eukaryotic chromosomes. Gene 333:135-141. (PDF)
  • Alvarez-Valin F., Clay O., Cruveiller S., Bernardi G. (2004). Inaccurate reconstruction of ancestral GC levels creates a ‘vanishing isochores’ effect. Mol. Phylogenet. Evol. 31: 788-793. (PDF)
  • Jabbari K., Bernardi G. (2004a). Cytosine methylation and CpG, TpG (CpA) and TpA frequencies. Gene 333: 143-149. (PDF)
  • Cruveiller S., Jabbari K., Clay O., Bernardi G. (2004a). Compositional gene landscapes in vertebrates. Genome Res. 14: 886-892. (PDF)
  • Jabbari K., Bernardi G. (2004c). Comparative genomics of Anopheles gambiae and Drosophila melanogaster. Gene 333: 183-186. (PDF)
  • Bernardi G.  2004; reprinted in 2005. Structural and Evolutionary Genomics: Natural Selection in Genome Evolution. Elsevier, Amsterdam. (PDF)
  • Jabbari K., Cruveiller S., Clay O., Le Saux J., Bernardi G. (2004). The new genes of rice: a closer look. Trends Plant Sci. 9: 281-285. (PDF)
  • Bernaola-Galvan P., Oliver J.L., Carpena P., Clay O., Bernardi G. (2004). Quantifying intrachromosomal GC heterogeneity in prokaryotic genomes. Gene 333: 121-133. (PDF)
  • Jabbari K., Rayko E., Bernardi G. (2003). The major shifts of human duplicated genes. Gene 317: 203-208. (PDF)
  • Bernardi G. and Saccone S. (2003). Gene distribution on human chromosomes. In Encyclopedia of the human genome, 2: 617-620. Nature Publishing Group, London, UK. (PDF)
  • Jabbari K., Cruveiller S., Clay O., Bernardi G. (2003). The correlation between GC3 and hydropathy in human genes. Gene 317: 137-140. (PDF)
  • Saccone S., Bernardi G. (2003). GC-rich isochores: origin. In Encyclopedia of the human genome, 2: 583-587. Nature Publishing Group, London, UK. (PDF)
  • Clay O., Arhondakis S., D’Onofrio G., Bernardi G. (2003). LDH-A and a-actin as tools to assess the effects of temperature on the vertebrate genome: some problems. Gene 317: 157-160. (PDF)
  • Romero H., Zavala A., Musto H., Bernardi G. (2003). The influence of translational selection on codon usage in fishes from the family Cyprinidae. Gene 317: 141-147. (PDF)
  • Jabbari K., Clay O., Bernardi G. (2003). GC3 heterogeneity and body temperature in vertebrates. Gene 317: 161-163. (PDF)
  • Clay O., Douady C.J., Carels N., Hughes S., Bucciarelli G., Bernardi G. (2003). Using analytical ultracentrifugation to study compositional variation in vertebrate genomes. European Biophysics Journal 32: 418-426. (PDF)
  • Sazanov A.A., Sazanova A.L., Kozyreva A.A., Smirnov A.F., Federico C., Motta S., Saccone S., Bernardi G. (2003). Comparative compositional mapping of chicken and quail chromosomes. Genetika 39: 819-825. (PDF)
  • Cruveiller S., Jabbari K., Clay O., Bernardi G. (2003). Compositional features of eukaryotic genomes for checking predicted genes. Brief. Bioinform. 4 (1): 43-52. (PDF)
  • de Luca di Roseto G., Bucciarelli G., Bernardi G. (2002). An analysis of the genome of Ciona intestinalis. Gene 295: 311-316. (PDF)
  • Pavlicek A., Paces J., Clay O., Bernardi G. (2002). A compact view of isochores in the draft human genome sequence. FEBS Lett. 511: 165-169. (PDF)
  • Hughes S., Clay O., Bernardi G. (2002). Compositional patterns in reptilian genomes. Gene 295: 323-329. (PDF)
  • Pavlicek A., Clay O., Jabbari K., Paces J., Bernardi G. (2002). Isochore conservation between MHC regions on human chromosome 6 and mouse chromosome 17. FEBS Lett. 511: 175-177. (PDF)
  • Alvarez-Valin F., Lamolle G., Bernardi G. (2002). Isochores, GC3 and mutation biases in the human genome. Gene 300: 161-168. (PDF)
  • Saccone S., Federico C., Bernardi G. (2002). Localization of the gene-richest and the gene-poorest isochores in the interphase nuclei of mammals and birds. Gene 300: 169-178. (PDF)
  • D’Onofrio G., Ghosh T.C., Bernardi G. (2002). The base composition of the genes is correlated with the secondary structures of the encoded proteins. Gene 300: 179-187. (PDF)
  • Pavlicek A., Clay O., Bernardi G. (2002). Transposable elements encoding functional proteins: pitfalls in unprocessed genomic data? FEBS Lett. 523: 252-253. (PDF)
  • Clay O., Bernardi G. (2002). Isochores: dream or reality? Trends Biotechnol. 20 (6): 237. (PDF)
  • Bucciarelli G., Bernardi G., Bernardi G. (2002). An ultracentrifugation analysis of two hundred fish genomes. Gene 295: 153-162. (PDF)
  • Bernardi G. (2001a). Les isochores: mythe ou réalité? Médecine/Sciences 17:1097. (PDF)
  • Andreozzi L., Federico C., Motta S., Saccone S., Sazanova A.L., Sazanov A.A., Smirnov A.F., Galkina S.A., Lukina N.A., Rodionov A.V., Carels N., Bernardi G. (2001). Compositional mapping of chicken chromosomes and identification of the gene-richest region. (PDF)
  • Bernardi G. (2001). Genome organization of vertebrates. In Encyclopedia of the human genome, 3: 19-27. Nature Publishing Group, London, UK. (PDF)
  • Bernardi G. (2001b). Misunderstandings about isochores. Part 1. Gene 276: 3-13. (PDF)
  • Saccone S., Pavlicek A., Federico C., Paces J., Bernardi G. (2001). Genes, isochores and bands in human chromosomes 21 and 22. Chromosome Res. 9: 533-539. (PDF)
  • Saccone S., Bernardi G. (2001). Human chromosomal banding by in situ hybridization of isochores. Methods in Cell Science 23: 7-15. (PDF)
  • Clay O., Carels N., Douady C., Macaya G., Bernardi G. (2001). Compositional heterogeneity within and among isochores in mammalian genomes. I. CsCl and sequence analyses. Gene 276: 15-24. (PDF)
  • Pavlicek A., Jabbari K., Paces J., Paces V., Hejnar J., Bernardi G. (2001). Similar integration but different stability of Alus and LINEs in the human genome. Gene 276: 39-45. (PDF)
  • Bernardi G. (2001). Isochores. In Encyclopedia of the human genome, 3: 586-591. Nature Publishing Group, London, UK. (PDF)
  • Clay O., Bernardi G. (2001). Compositional heterogeneity within and among isochores in mammalian genomes. II. Some general comments. Gene 276: 25-31. (PDF)
  • Clay O., Bernardi G. (2001). The isochores in human chromosomes 21 and 22. Biochem. Biophys. Res. Commun. 285: 855-856. (PDF)
  • Musto H., Cruveiller S., D’Onofrio G., Romero H., Bernardi G. (2001). Translational selection on codon usage in Xenopus laevis. Mol. Biol. Evol. 18: 1703-1707. (PDF)
  • Bernardi G. (2001). The evolutionary history of the human genome. In Encyclopedia of the human genome, 2: 363-367. Nature Publishing Group, London, UK. (PDF)