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Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae.
Percudani R, Pavesi A, Ottonello S. Percudani R, et al. J Mol Biol. 1997 May 2;268(2):322-30. doi: 10.1006/jmbi.1997.0942. J Mol Biol. 1997. PMID: 9159473
A total of 274 transfer RNA genes, representing the entire tRNA gene set of the yeast Saccharomyces cerevisiae, has been extracted from the whole genome sequence of this organism using a dedicated search algorithm (Pol3scan). ...A significantly stronger co-ad
A total of 274 transfer RNA genes, representing the entire tRNA gene set of the yeast Saccharomyces cerevisiae, has been extracted fr
A new insight into the suggestion of a possible antigenic role of a member of the 70 kD heat shock proteins.
Rocchi G, Pavesi A, Ferrari C, Bolchi A, Manara GC. Rocchi G, et al. Cell Biol Int. 1993 Jan;17(1):83-92. doi: 10.1006/cbir.1993.1008. Cell Biol Int. 1993. PMID: 7684294
A weak reactivity of the anti-hsp72/hsc73 MoAb was found in the cytoplasm of the unstressed human epidermal cells, while stressed cells showed an enhanced reactivity at the cytoplasmic level and the expression of the molecules on the cell surface. ...
A weak reactivity of the anti-hsp72/hsc73 MoAb was found in the cytoplasm of the unstressed human epidermal cells, while stressed cel
Identification of new eukaryotic tRNA genes in genomic DNA databases by a multistep weight matrix analysis of transcriptional control regions.
Pavesi A, Conterio F, Bolchi A, Dieci G, Ottonello S. Pavesi A, et al. Nucleic Acids Res. 1994 Apr 11;22(7):1247-56. doi: 10.1093/nar/22.7.1247. Nucleic Acids Res. 1994. PMID: 8165140 Free PMC article.
A linear method for the search of eukaryotic nuclear tRNA genes in DNA databases is described. Based on a modified version of the general weight matrix procedure, our algorithm relies on the recognition of two intragenic control regions known as A and B boxes
A linear method for the search of eukaryotic nuclear tRNA genes in DNA databases is described. Based on a modified version of
On the informational content of overlapping genes in prokaryotic and eukaryotic viruses.
Pavesi A, De Iaco B, Granero MI, Porati A. Pavesi A, et al. J Mol Evol. 1997 Jun;44(6):625-31. doi: 10.1007/pl00006185. J Mol Evol. 1997. PMID: 9169554 Free PMC article.
Using information theory indices, we identified in the regions of overlap a first pattern, exhibiting a more uniform base composition and more severe constraints in base ordering with respect to the nonoverlapping regions. ...At the level of codon usage, a lo …
Using information theory indices, we identified in the regions of overlap a first pattern, exhibiting a more uniform base comp …
A novel algorithm for the search of 5S rRNA genes in DNA databases: comparison with other methods and identification of new potential 5S rRNA genes.
Pavesi A, Percudani R, Conterio F. Pavesi A, et al. DNA Seq. 1997;7(3-4):165-77. doi: 10.3109/10425179709034032. DNA Seq. 1997. PMID: 9254010
This combined strategy, which includes a fast, but poorly selective, preliminary search procedure and an auxiliary step, that is slow but highly selective, strongly reduces the number of false positive instances, yielding a total false positive rate of 0.00076%. ... …
This combined strategy, which includes a fast, but poorly selective, preliminary search procedure and an auxiliary step, that is slow …
Relationships between transcriptional and translational control of gene expression in Saccharomyces cerevisiae: a multiple regression analysis.
Pavesi A. Pavesi A. J Mol Evol. 1999 Feb;48(2):133-41. doi: 10.1007/pl00006451. J Mol Evol. 1999. PMID: 9929381
Using a representative set of yeast genes with a known level of transcription, the relationship between transcriptional and translational steps was evaluated by a multiple linear regression model. ...This finding suggests a close association of the cel …
Using a representative set of yeast genes with a known level of transcription, the relationship between transcriptional and tr …
Detection of signature sequences in overlapping genes and prediction of a novel overlapping gene in hepatitis G virus.
Pavesi A. Pavesi A. J Mol Evol. 2000 Mar;50(3):284-95. doi: 10.1007/s002399910033. J Mol Evol. 2000. PMID: 10754072 Free PMC article.
In this work, a novel feature peculiar to overlapping coding regions is presented. It was detected by analysis of a sample set of 21 virus genomic sequences and consisted in the repeated occurrence of a cluster of basic amino acid residues, encoded by a
In this work, a novel feature peculiar to overlapping coding regions is presented. It was detected by analysis of a sample set …
Cloning of two glutamate dehydrogenase cDNAs from Asparagus officinalis: sequence analysis and evolutionary implications.
Pavesi A, Ficarelli A, Tassi F, Restivo FM. Pavesi A, et al. Genome. 2000 Apr;43(2):306-16. doi: 10.1139/g99-127. Genome. 2000. PMID: 10791819
A first phylogenetic analysis including only GDHs from plants suggested that the two GDH genes of A. officinalis arose by an ancient duplication event, pre-dating the divergence of monocots and dicots. Codon usage analysis showed a bias towards A/T end
A first phylogenetic analysis including only GDHs from plants suggested that the two GDH genes of A. officinalis arose by an a
Origin and evolution of GBV-C/hepatitis G virus and relationships with ancient human migrations.
Pavesi A. Pavesi A. J Mol Evol. 2001 Aug;53(2):104-13. doi: 10.1007/s002390010198. J Mol Evol. 2001. PMID: 11479681
Due to the absence of a real pathogenic role of GBV-C/HGV in liver disease and its extremely low mutation rate, this virus is a potential marker to trace prehistoric links between human populations. In this study, origin and evolution of GBV-C/HGV were examined usin …
Due to the absence of a real pathogenic role of GBV-C/HGV in liver disease and its extremely low mutation rate, this virus is a
African origin of polyomavirus JC and implications for prehistoric human migrations.
Pavesi A. Pavesi A. J Mol Evol. 2003 May;56(5):564-72. doi: 10.1007/s00239-002-2425-y. J Mol Evol. 2003. PMID: 12698293
This discrepancy places into question the effectiveness of JCV as a marker of human population history. The present study investigates the evolution of JCV using a large set of fully sequenced strains. ...Further credit to the African origin of JCV is provided by …
This discrepancy places into question the effectiveness of JCV as a marker of human population history. The present study investigate …
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