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Publications

Perrini S, Ficarella R, Picardi E, Cignarelli A, Barbaro M, Nigro P, Peschechera A, Palumbo O, Carella M, De Fazio M, Natalicchio A, Laviola L, Pesole G., Giorgino F.
Differences in gene expression and cytokine release profiles highlight the heterogeneity of distinct subsets of adipose tissue-derived stem cells in the subcutaneous and visceral adipose tissue in humans.
PLoS One. 2013;8(3):e57892. doi: 10.1371/journal.pone.0057892. Epub 2013 Mar 5.

Giulietti M, Piva F, D'Antonio M, D'Onorio De Meo P, Paoletti D, Castrignanò T, D'Erchia AM, Picardi E, Zambelli F, Principato G, Pavesi G, Pesole G.
SpliceAid-F: a database of human splicing factors and their RNA-binding sites.
Nucleic Acids Res. 2013 Jan;41(Database issue):D125-31. doi: 10.1093/nar/gks997. Epub 2012 Oct 30.

Picardi E, Gallo A, Galeano F, Tomaselli S, Pesole G.
A novel computational strategy to identify A-to-I RNA editing sites by RNA-Seq data: de novo detection in human spinal cord tissue.
PLoS One. 2012;7(9):e44184. doi: 10.1371/journal.pone.0044184. Epub 2012 Sep 5.

Valiente G, Pesole G.
Bioinformatics approaches and tools for metagenomic analysis. Editorial.
Brief Bioinform. 2012 Nov;13(6):645. doi: 10.1093/bib/bbs079.

Santamaria M, Fosso B, Consiglio A, De Caro G, Grillo G, Licciulli F, Liuni S, Marzano M, Alonso-Alemany D, Valiente G, Pesole G.
Reference databases for taxonomic assignment in metagenomics.
Brief Bioinform. 2012 Jul 10. [Epub ahead of print]

Chiara M, Pesole G., Horner DS.
SVM2: an improved paired-end-based tool for t
he detection of small genomic structural variations using high-throughput single-genome resequencing data.
Nucleic Acids Res. 2012 Jun 25. [Epub ahead of print]

Zambelli F, Prazzoli GM, Pesole G., Pavesi G.
Cscan: finding common regulators of a set of genes by using a collection of genome-wide ChIP-seq datasets.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W510-5.

Picardi E, Pesole G.
Mitochondrial genomes gleaned from human whole-exome sequencing.
Nat Methods. 2012 May 30;9(6):523-4.

Pesole G., Allen JF, Lane N, Martin W, Rand DM, Schatz G, Saccone C.
The neglected genome.
EMBO Rep. 2012 Jun 1;13(6):473-4.

Pirola Y, Rizzi R, Picardi E, Pesole G., Della Vedova G, Bonizzoni P.
PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text.
BMC Bioinformatics. 2012 Apr 12;13 Suppl 5:S2.

Zambelli F, Pesole G., Pavesi G.
Motif discovery and transcription factor binding sites before and after the next-generation sequencing era.
Brief Bioinform. 2012 Apr 19. [Epub ahead of print]

Chiarella P, Summa V, De Santis S, Signori E, Picardi E, Pesole G., Saglio G, Fazio VM.
BCR/ABL1 Fusion Transcripts Generated from Alternative Splicing: Implications for Future Targeted Therapies in Ph+ Leukaemias.
Curr Mol Med. 2012 Jun 1;12(5):547-65.

Caratozzolo MF, Micale L, Turturo MG, Cornacchia S, Fusco C, Marzano F, Augello B, D'Erchia AM, Guerrini L, Pesole G., Sbisà E, Merla G, Tullo A.
TRIM8 modulates p53 activity to dictate cell cycle arrest.
Cell Cycle. 2012 Feb 1;11(3):511-23.

D'Onorio de Meo P, D'Antonio M, Griggio F, Lupi R, Borsani M, Pavesi G, Castrignanò T, Pesole G., Gissi C.
MitoZoa 2.0: a database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa.
Nucleic Acids Res. 2012 Jan;40(Database issue):D1168-72.

Bartolini B, Chillemi G, Abbate I, Bruselles A, Rozera G, Castrignanò T, Paoletti D, Picardi E, Desideri A, Pesole G., Capobianchi MR.
Assembly and characterization of pandemic influenza A H1N1 genome in nasopharyngeal swabs using high-throughput pyrosequencing.
New Microbiol. 2011 Oct;34(4):391-7

Botti E, Spallone G, Moretti F, Marinari B, Pinetti V, Galanti S, De Meo PD, De Nicola F, Ganci F, Castrignanò T, Pesole G., Chimenti S, Guerrini L, Fanciulli M, Blandino G, Karin M, Costanzo A.
Developmental factor IRF6 exhibits tumor suppressor activity in squamous cell carcinomas.
Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13710-5.

Antonacci R, Mineccia M, Lefranc MP, Ashmaoui HM, Lanave C, Piccinni B, Pesole G., Hassanane MS, Massari S, Ciccarese S.
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.
Mol Immunol. 2011 Jul;48(12-13):1384-96.

Picardi E, D'Antonio M, Carrabino D, Castrignanò T, Pesole G.
ExpEdit: a webserver to explore human RNA editing in RNA-Seq experiments.
Bioinformatics. 2011 May 1;27(9):1311-2.

Martelli PL, D'Antonio M, Bonizzoni P, Castrignanò T, D'Erchia AM, D'Onorio De Meo P, Fariselli P, Finelli M, Licciulli F, Mangiulli M, Mignone F, Pavesi G, Picardi E, Rizzi R, Rossi I, Valletti A, Zauli A, Zambelli F, Casadio R, Pesole G.
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing.
Nucleic Acids Res. 2011 Jan;39(Database issue):D80-5.

Zambelli F, Pavesi G, Gissi C, Horner DS, Pesole G.
Assessment of orthologous splicing isoforms in human and mouse orthologous genes.
BMC Genomics. 2010 Oct 1;11:534.

Valletti A, Anselmo A, Mangiulli M, Boria I, Mignone F, Merla G, D'Angelo V, Tullo A, Sbisà E, D'Erchia AM, Pesole G.
Identification of tumor-associated cassette exons in human cancer through EST-based computational prediction and experimental validation.
Mol Cancer. (2010) Sep 2;9:230.

Picardi, E. and Pesole G.
Computational methods for ab initio and comparative gene finding.
Methods Mol Biol 609 (2010) 269-84.

Picardi, E., Horner, D.S., Chiara, M., Schiavon, R., Valle, G. and Pesole G.
Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing.
Nucleic Acids Res (2010) 38(14):4755-67.

Lupi, R., de Meo, P.D., Picardi, E., D'Antonio, M., Paoletti, D., Castrignano, T., Pesole G. and Gissi, C.:
MitoZoa: a curated mitochondrial genome database of metazoans for comparative genomics studies.
Mitochondrion (2010) 10: 192-9.

Horner, D.S., Pavesi, G., Castrignano, T., De Meo, P.D., Liuni, S., Sammeth, M., Picardi, E. and Pesole G.
Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing.
Brief Bioinform (2010) 11:181-97.

Grillo, G., Turi, A., Licciulli, F., Mignone, F., Liuni, S., Banfi, S., Gennarino, V.A., Horner, D.S., Pavesi, G., Picardi, E. and Pesole G.
UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs.
Nucleic Acids Res 38 (2010) D75-80.

Gissi, C., Pesole G., Mastrototaro, F., Iannelli, F., Guida, V. and Griggio, F.
Hypervariability of ascidian mitochondrial gene order: exposing the myth of deuterostome organelle genome stability.
Mol Biol Evol 27 (2010) 211-5.

Mica, E., Piccolo, V., Delledonne, M., Ferrarini, A., Pezzotti, M., Casati, C., Del Fabbro, C., Valle, G., Policriti, A., Morgante, M., Pesole G., Pe, M.E. and Horner, D.S.
Correction: High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera.
BMC Genomics 11 (2010) 109.

Riva, A. and Pesole G.
A unique, consistent identifier for alternatively spliced transcript variants.
PLoS One 4 (2009) e7631.

Mica, E., Piccolo, V., Delledonne, M., Ferrarini, A., Pezzotti, M., Casati, C., Del Fabbro, C., Valle, G., Policriti, A., Morgante, M., Pesole G., Pe, M.E. and Horner, D.S.
High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera.
BMC Genomics 10 (2009) 558.

Rè M, Pesole G., Horner DS.
Accurate discrimination of conserved coding and non-coding regions through multiple indicators of evolutionary dynamics.
BMC Bioinformatics. 2009 Sep 8;10:282.

Mangiulli M, Valletti A, Caratozzolo MF, Tullo A, Sbisà E, Pesole G., D'Erchia AM.
Identification and functional characterization of two new transcriptional variants of the human p63 gene.
Nucleic Acids Res. 2009 Oct;37(18):6092-104.

Picardi E, Mignone F, Pesole G.
EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data.
BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S10.

Creanza TM, Horner DS, D'Addabbo A, Maglietta R, Mignone F, Ancona N, Pesole G.
Statistical assessment of discriminative features for protein-coding and non coding cross-species conserved sequence elements.
BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S2.

Zambelli F, Pesole G., Pavesi G.
Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes.
Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W247-52. Epub 2009 May 31.

Guffanti A, Iacono M, Pelucchi P, Kim N, Soldà G, Croft LJ, Taft RJ, Rizzi E, Askarian-Amiri M, Bonnal RJ, Callari M, Mignone F, Pesole G., Bertalot G, Bernardi LR, Albertini A, Lee C, Mattick JS, Zucchi I, De Bellis G.
A transcriptional sketch of a primary human breast cancer by 454 deep sequencing.
BMC Genomics. 2009 Apr 20;10:163.

Bonizzoni P, Mauri G, Pesole G., Picardi E, Pirola Y, Rizzi R. J.
Detecting alternative gene structures from spliced ESTs: a computational approach.
J. Comput Biol. 2009 Jan;16(1):43-66.

Abad P, Gouzy J, Aury JM, Castagnone-Sereno P, Danchin EG, Deleury E, Perfus-Barbeoch L, Anthouard V, Artiguenave F, Blok VC, Caillaud MC, Coutinho PM, Dasilva C, De Luca F, Deau F, Esquibet M, Flutre T, Goldstone JV, Hamamouch N, Hewezi T, Jaillon O, Jubin C, Leonetti P, Magliano M, Maier TR, Markov GV, McVeigh P, Pesole G., Poulain J, Robinson-Rechavi M, Sallet E, Ségurens B, Steinbach D, Tytgat T, Ugarte E, van Ghelder C, Veronico P, Baum TJ, Blaxter M, Bleve-Zacheo T, Davis EL, Ewbank JJ, Favery B, Grenier E, Henrissat B, Jones JT, Laudet V, Maule AG, Quesneville H, Rosso MN, Schiex T, Smant G, Weissenbach J, Wincker P.
Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita.
Nat Biotechnol. 2008 Aug;26(8):909-15. Epub 2008 Jul 27. PMID: 18660804 [PubMed - in process]

Gissi C, Iannelli F, Pesole G.
Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species.
Heredity. 2008 Jul 9. [Epub ahead of print] PMID: 18612321 [PubMed - as supplied by publisher]

Mignone F, Anselmo A, Donvito G, Maggi GP, Grillo G, Pesole G.
Genome-wide identification of coding and non-coding conserved sequence tags in human and mouse genomes.
BMC Genomics. 2008 Jun 11;9:277.

Pesole G.
What is a gene? An updated operational definition.
Gene. 2008 Jul 1;417(1-2):1-4. Epub 2008 Mar 26.

Pavesi G, Zambelli F, Caggese C, Pesole G.
Exalign: a new method for comparative analysis of exon-intron gene structures.
Nucleic Acids Res. 2008 Apr 8; May;36(8):e47

Castrignanò T, D'Antonio M, Anselmo A, Carrabino D, D'Onorio DM, D'Erchia A, Licciulli F, Mangiulli M, Mignone F, Pavesi G, Picardi E, Riva A, Rizzi R, Bonizzoni P, Pesole G.
ASPicDB: A database resource for alternative splicing analysis.
Bioinformatics. 24:1300-1304, 2008 PMID: 18388144

Vaccarelli G, Miccoli MC, Antonacci R, Pesole G., Ciccarese S.
Genomic organization and recombinational unit duplication-driven evolution of ovine and bovine T cell receptor gamma loci.
BMC Genomics. 2008 Feb 18;9(1):81 [Epub ahead of print] PMID: 18282289 [PubMed - as supplied by publisher]

Tartari M, Gissi C, Lo Sardo V, Zuccato C, Picardi E, Pesole G., Cattaneo E.
Phylogenetic comparison of huntingtin homologues reveals the appearance of a primitive polyQ in sea urchin.
Mol Biol Evol. 2008 Feb;25(2):330-8. Epub 2007 Nov 28. PMID: 18048403 [PubMed - in process]

Horner DS, Pirovano W, Pesole G.
Correlated substitution analysis and the prediction of amino acid structural contacts.
Brief Bioinform. 2008 vol. 9(1) 46-56.

Pavesi G, Pesole G.
Finding conserved gene order across multiple genomes.
Methods Mol Biol. 2007, 396:111-20.

Porcelli D, Barsanti P, Pesole G., Caggese C.
The nuclear OXPHOS genes in insecta: a common evolutionary origin, a common cis-regulatory motif, a common destiny for gene duplicates.
BMC Evol Biol. 2007 Nov 8;7:215.

Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, .., Pesole G., .., Kleber M, Mauceli E, MacCallum I.
Evolution of genes and genomes on the Drosophila phylogeny.
Nature. 2007 Nov 8;450(7167):203-18.

Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyere C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G., Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pe ME, Valle G, Morgante M, Caboche M, Adam-Blondon AF, Weissenbach J, Quetier F, Wincker P.
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.
Nature. 2007 Sep 27;449(7161):463-7.

Iannelli F, Pesole G., Sordino P, Gissi C.
Mitogenomics reveals two cryptic species in Ciona intestinalis.
Trends Genet. 2007 23(9): 419-422.

Maglietta R, Piepoli A, Catalano D, Licciulli F, Carella M, Liuni S, Pesole G., Perri F, Ancona N.
Statistical assessment of functional categories of genes deregulated in pathological conditions by using microarray data.
Bioinformatics. 2007, Aug 15;23(16):2063-72

D’Onorio De Meo P, Carrabino D, Sanna N, Castrignanò T, Grillo G, Licciulli F, Liuni S, Re M, Mignone F, Pesole G.
A high-performance grid-web service framework for the identification of ”conserved sequence tags”.
Future Generation Computer Systems, 2007, 23: 371-381.

Sbisà E, Catalano D, Grillo G, Licciulli F, Turi A, Liuni S, Pesole G., De Grassi A, Caratozzolo MF, D'Erchia AM, Navarro B, Tullo A, Saccone C, Gisel A.
p53FamTaG: a database resource of human p53, p63 and p73 direct target genes combining in silico prediction and microarray data.BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S20.

Horner DS, Lefkimmiatis K, Reyes A, Gissi C, Saccone C, Pesole G.
Phylogenetic analyses of complete mitochondrial genome sequences suggest a basal divergence of the enigmatic rodent Anomalurus.
BMC Evol Biol. 2007 Feb 8;7:16.

Pavesi G, Zambelli F, Pesole G.
WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences.
BMC Bioinformatics. 2007 Feb 7;8:46.

Maglietta R, D'Addabbo A, Piepoli A, Perri F, Liuni S, Pesole G., Ancona N.
Selection of relevant genes in cancer diagnosis based on their prediction accuracy.
Artif Intell Med. 2007 40: 29-44

Pavesi G, Pesole G.
Using weeder for the discovery of conserved transcription factor binding sites.
Curr Protoc Bioinformatics. 2006 Oct;Chapter 2:Unit 2.11. PMID: 18428764 [PubMed - in process]

Gissi C, Pesole G., Cattaneo E, Tartari M.
Huntingtin gene evolution in Chordata and its peculiar features in the ascidian Ciona genus.
BMC Genomics. 2006 Nov 8;7:288.

Ancona N, Maglietta R, Piepoli A, D'Addabbo A, Cotugno R, Savino M, Liuni S, Carella M, Pesole G., Perri F.
On the statistical assessment of classifiers using DNA microarray data.
BMC Bioinformatics. 2006 Aug 19;7(1):387

Pavesi G, Mereghetti P, Zambelli F, Stefani M, Mauri G, Pesole G.
MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W566-70.

Castrignano T, Rizzi R, Talamo IG, De Meo PD, Anselmo A, Bonizzoni P, Pesole G.
ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W440-3.

Bonizzoni P, Rizzi R, Pesole G.
Computational methods for alternative splicing prediction.
Brief Funct Genomic Proteomic. 2006 Mar;5(1):46-51.

Frith MC, Bailey TL, Kasukawa T, Mignone F, Kummerfeld SK, Madera M, Sunkara S, Furono M, Bult CJ, Quakenbush J, Kai C, Kawai J, Carninci P, Hayashizaki Y, Pesole G., Mattick JS.
Discrimination of non-protein coding transcripts drom protein-coding mRNAs.
RNA Biology 3:1-40, 2006.

Gissi C, San Mauro D, Pesole G., Zardoya R.
Mitochondrial phylogeny of Anura (Amphibia): A case study of congruent phylogenetic reconstruction using amino acid and nucleotide characters.
Gene 366:228-237, 2006.

Re M, Mignone F, Iacono M, Grillo G, Liuni S, Pesole G.
A new strategy to identify novel genes and gene isoforms: Analysis of human chromosomes 15, 21 and 22.
Gene. 365: 35-40, 2006.

Castrignano T, De Meo PD, Grillo G, Liuni S, Mignone F, Talamo IG, Pesole G.
GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags.
Bioinformatics. 22: 497-499, 2006.

Ancona N, Maglietta R, D'Addabbo A, Liuni S, Pesole G.
Regularized Least Squares Cancer classifiers from DNA microarray data.
BMC Bioinformatics. 2005 Dec 1;6 Suppl 4:S2.

Helmer-Citterich M, Casadio R, Guffanti A, Mauri G, Milanesi L, Pesole G., Valle G, Saccone C.
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society.
BMC Bioinformatics. 2005 Dec 1;6 Suppl 4:S1.

Bonizzoni P, Rizzi R, Pesole G.
ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences.
BMC Bioinformatics. 2005 Oct 5;6:244.

Carninci P, Kasukawa T, .., Pavesi G, Pesole G., et al.
The transcriptional landscape of the mammalian genome.
Science. 2005 Sep 2;309(5740):1559-63.

De Grassi A, Caggese C, D'Elia D, Lanave C, Pesole G., Saccone C.
Evolution of nuclearly encoded mitochondrial genes in Metazoa.
Gene. 2005 Jul 18;354:181-8.

Dalla E, Mignone F, Verardo R, Marchionni L, Marzinotto S, Lazarevic D, Reid JF, Marzio R, Klaric E, Licastro D, Marcuzzi G, Gambetta R, Pierotti MA, Pesole G., Schneider C.
Discovery of 342 putative new genes from the analysis of 5'-end-sequenced full-length-enriched cDNA human transcripts.
Genomics. 2005 Jun;85(6):739-51.

Regina TM, Picardi E, Lopez L, Pesole G., Quagliariello C.
A novel additional group II intron distinguishes the mitochondrial rps3 gene in gymnosperms.
J Mol Evol. (2005) 60:196-206.

Michele Iacono, Flavio Mignone and Graziano Pesole.
uAUG and uORFs in human and rodent 5’untranslated mRNAs.
GENE (2005) 349:97-105

Marco Sardiello, Gaetano Tripoli, Antonio Romito, Crescenzio Minervini, Luigi Viggiano, Corrado Caggese and Graziano Pesole.
Energy biogenesis: one key for coordinating two genomes.
Trends in Genetics 2005 21:12-16.

Martin Tompa, Nan Li, Timothy L. Bailey, George M. Church, Bart De Moor, Eleazar Eskin, Alexander V. Favorov, Martin C. Frith, Yutao Fu, W. James Kent, Vsevolod J. Makeev, Andrei A. Mironov, William Stafford Noble, Giulio Pavesi, Graziano Pesole, Mireille Régnier, Nicolas Simonis, Saurabh Sinha, Gert Thijs, Jacques van Helden, Mathias Vandenbogaert, Zhiping Weng, Christopher Workman, Chun Ye & Zhou Zhu
Assessing Computational Tools for the Discovery of Transcription Factor Binding Sites.
Nature Biotech. (2005) 23: 137-144.

Flavio Mignone, Giorgio Grillo, Flavio Licciulli, Michele Iacono, Sabino Liuni, Paul J. Kersey, Gorge J. Duarte, Cecilia Saccone and Graziano Pesole.
UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs.
Nucl. Acids Res. 2005 33: D141-D146.

Angelo Boccia, Mauro Petrillo, Diego di Bernardo, Alessandro Guffanti, Flavio Mignone, Stefano Confalonieri, Lucilla Luzi, Graziano Pesole, Giovanni Paolella, Andrea Ballabio, and Sandro Banfi.
DG-CST (Disease Gene Conserved Sequence Tags), a database of human–mouse conserved elements associated to disease genes.
Nucl. Acids Res. 2005 33: D505-D510

Pavesi G, Mauri G, Pesole G.
In silico representation and discovery of transcription factor binding sites.
Brief Bioinform. 2004 Sep;5(3):217-36.

Gisel A, Panetta M, Grillo G, Licciulli VF, Liuni S, Saccone C, Pesole G.
DNAfan: a software tool for automated extraction and analysis of user-defined sequence regions.
Bioinformatics. 2004: 18: 3676-3679.

Pavesi G, Mereghetti P, Mauri G, Pesole G.
Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W199-203.

Castrignano T, Canali A, Grillo G, Liuni S, Mignone F, Pesole G.
CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W624-7.

Pavesi G, Mauri G, Stefani M, Pesole G.
RNAProfile: an algorithm for finding conserved secondary structure motifs in unaligned RNA sequences.
Nucleic Acids Res. 2004 Jun 15;32(10):3258-69. Print 2004.

Pavesi G, Mauri G, Iannelli F, Gissi C, Pesole G.
GeneSyn: a tool for detecting conserved gene order across genomes.
Bioinformatics. 2004 Jun 12;20(9):1472-4. Epub 2004 Feb 19

Mignone F, Horner DS, Pesole G.
WebVar: a resource for the rapid estimation of relative site variability from multiple sequence alignments.
Bioinformatics. 2004 May 22;20(8):1331-3.

Horner DS, Pesole G.
Phylogenetic analyses: a brief introduction to methods and their application.
Expert Rev Mol Diagn. 2004 May;4(3):339-50.

Gissi C, Iannelli F, Pesole G.
Complete mtDNA of Ciona intestinalis reveals extensive gene rearrangement and the presence of an atp8 and an extra trnM gene in ascidians.
J Mol Evol. 2004 Apr;58(4):376-89.

Reyes A, Gissi C, Catzeflis F, Nevo E, Pesole G., Saccone C.
Congruent Mammalian trees from mitochondrial and nuclear genes using bayesian methods.
Mol Biol Evol. 2004 Feb;21(2):397-403.

Pavesi G, Mauri G, Pesole G.
An algorithm for finding conserved secondary structure motifs in unaligned RNA sequences
J COMPUT SCI TECHNOL 19 (1): 2-12 JAN 2004

Saccone C., Caggese C., D’Erchia AM, Lanave C., Oliva M., Pesole G.
Molecular Clock and gene function.
J. Mol. Evol. (2003) 57-S277-S285.

Polissi A, De Laurentis W, Zangrossi S, Briani F, Longhi V, Pesole G. and Deho G.
Changes in Escherichia coli transcriptome during acclimatation at low temperature
(2003) Research in Microbiology 154: 573-580.

Grillo G, Licciulli F, Liuni S, Sbisa E, Pesole G.
PatSearch: A program for the detection of patterns and structural motifs in nucleotide sequences.
Nucleic Acids Res. (2003) 31(13):3608-12.

Mignone F, Grillo G, Liuni S, Pesole G.
Computational identification of protein coding potential of conserved sequence tags through cross-species evolutionary analysis.
Nucleic Acids Res. (2003) 31(15):4639-45.

Gissi C and Pesole G.
Transcript Mapping and Genome Annotation of Ascidian mtDNA Using EST Data.
Genome Res. (2003) 13(9):2203-12.

D’Erchia AM, Tullo A, Pesole G., Saccone C and Sbisà E.
p53 gene family: structural and evolutionary features.
Current Genomics (2003) 4: 13-26.

De Pietri Tonelli D., Mihailovich M., Schnurbus R., Pesole G., Grohovaz F. and Zacchetti D.
Translational control of Scamper expression via a cell-specific internal ribosome entry site.
Nucleic Acids Res. (2003) 31: 2508-2513.

Horner DS and Pesole G.
The estimation of relative site variability among aligned homologous protein sequences.
Bioinformatics (2003) 19: 600-606.

Mignone F. and Pesole G.
rRNA-like sequences in human mRNAs.
Applied Bioinformatics (2002) 1:145-154.

Saccone C, Barome PO, D'Erchia AM, D'Errico I, Pesole G., Sbisa E, Tullo A.
Molecular strategies in Metazoan genomic evolution.
Gene. 2002 Oct 30;300(1-2):195-201

Okazaki Y, Furuno M, and Pesole G. et al.
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.
Nature. 2002 Dec 5;420(6915):563-73.

De Giorgi C, Veronico P, De Luca F, Natilla A, Lanave C, Pesole G.
Structural and evolutionary analysis of the ribosomal genes of the parasitic nematode Meloidogyne artiellia suggests its ancient origin.
Mol Biochem Parasitol. 2002 Sep-Oct;124(1-2):91-4.

Leach RE, Duniec-Dmuchowski ZM, Pesole G., Tanaka TS, Ko MS, Armant RD, Krawetz SA.
Identification, molecular characterization, and tissue expression of OVCOV1.
Mamm Genome. 2002 Nov;13(11):619-24.

Mignone F, Gissi C, Liuni S, Pesole G.
Untranslated regions of mRNAs.
Genome Biol. 2002;3(3):REVIEWS0004.

Larizza A., Pesole G., Reyes A., Sbisà E. and Saccone C.
Lineage specificity of the evolutionary dynamics of the mtDNA D-loop region in rodents.
J. Mol. Evol. 2002, 54: 145-155.

Larizza A., Makalowski W., Pesole G., Saccone C.
Evolutionary dynamics of mammalian mRNA untranslated regions by comparative analysis of orthologous human, artiodactyl and rodent gene pairs.
Comp. Chem. 2002, 26: 479-490.

Attimonelli M, Catalano D, Gissi C, Grillo G, Licciulli F, Liuni S, Santamaria M, Pesole G., Saccone C.
MitoNuc: a database of nuclear genes coding for mitochondrial proteins.
Update 2002. Nucleic Acids Res. 2002 Jan 1;30(1):172-3.

Pesole G., Liuni S., Grillo G., Licciulli F., Larizza A., Makalowski W., Saccone C.
UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs – update 2002.
Nucleic Acids Res. 2002, 30:335-340.

Saccone C., Gissi C., Reyes A., Larizza A., Sbisà E. and Pesole G.
Mitochondrial DNA in Metazoa: degree of freedom in a frozen event.
GENE 2002, 286: 3-12

Pavesi G., Mauri G. and Pesole G.
Methods for pattern discovery in unaligned biological sequences.
Briefings in Bioinformatics 2001, 2: 1-14.

Pesole G., Mignone F., Gissi C., Grillo G., Licciulli F. and Liuni S.
Structural and functional features of eukaryotic mRNA untranslated regions.
GENE 2001, 276: 73-81.

Pavesi G, Mauri G, Pesole G.
An algorithm for finding signals of unknown length in DNA sequences.
Bioinformatics. 2001 Jun;17 Suppl 1:S207-14.

Pesole G. among other Authors of FANTOM Consortium and the RIKEN Genome Exploration Research Group.
Functional annotation of a full length mouse cDNA collection.
Nature 2001, 409: 685-690.

Pesole G. and Saccone C.
A novel method to estimate the substitution rate variation among sites in large dataset of homologous DNA sequences.
Genetics, 2001, 157: 859-865

Pesole G., Gissi C., Grillo G., Licciulli F., Liuni S. and Saccone C.
Analysis of oligonucleotide AUG start codon context in eukaryotic mRNAs.
GENE 2000, 261: 85-91.

Saccone C., Gissi C., Lanave C., Larizza A., Pesole G. and Reyes A.
Evolution of the mitochondrial genetic system: an overview.
GENE, 2000 261: 153-159.

Reyes A., Pesole G. and Saccone C.
Long-branch attraction phenomenon and the impact of among-site variation on rodent phylogeny.
GENE 2000 259: 177-187. 70

Pesole G., Grillo G., Larizza A. and Liuni S.
The untranslated regions of eukariotic mRNAs: structure, function, evolution and bioinformatics tools for their analysis.
Briefings in Bioinformatics 2000, 1:236-249 [Review Article]

Reyes A, Gissi C, Pesole G., Catzeflis FM, Saccone C.
Where do rodents fit? Evidence from the complete mitochondrial genome of Sciurus vulgaris.
Mol Biol Evol. 2000 Jun;17(6):979-83.

Ristori G, Montesperelli C, Perna A, Cannoni S, Battistini L, Borsellino G, Riccio P, Pesole G., Chersi A, Pozzilli C, Buttinelli C, Salvetti M.
Global immune disregulation in multiple sclerosis: from the adaptive response to the innate immunity.
J Neuroimmunol. 2000 Jul 24;107(2):216-9.

Gissi C, Reyes A, Pesole G., Saccone C.
Lineage-specific evolutionary rate in mammalian mtDNA.
Mol Biol Evol. 2000 Jul;17(7):1022-31.

Pesole G., Liuni S. and D’Souza M.
PatSearch: a pattern matcher software to find functional elements in nucleotide and protein sequences and to assess statistical significance.
Bioinformatics (2000) 16(5):439-50.

Ristori G., Salvetti M., Pesole G., Attimonelli M., Buttinelli C., Martin R. and Riccio P.
Compositional bias and mimicry toward the nonself proteome in immunodominant T-cell epitopes of self and nonself antigens.
Faseb J. (2000) 14: 431-438

Pesole G., Gissi C., Catalano D., Grillo G., Licciulli F., Liuni S., Attimonelli M., Saccone C.
MitoNuc and MitoAln: two related databases of nuclear genes coding for mitochondrial proteins.
Nucleic Acids Res (2000) 28: 163-165

Pesole G., Liuni S., Grillo G., Licciulli F., Larizza A., Makalowski W., Saccone C.
UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs.
Nucleic Acids Res. (2000) 28: 193-196

Reyes A, Paraggio M, Pesole G. and Romano P.
Genetic characterization of dsRNA plasmids in italian Saccharomyces cerevisiae wine yeasts.
Food technol. Biotechnol. (1999) 37: 229-234

Saccone C., De Giorgi C., Gissi C., Pesole G., Reyes A.
Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system.
Gene (1999) 238: 195-209

Pesole G., Bernardi G., Saccone C.
Isochore specificity of AUG initiator context of human genes.
FEBS Lett (1999) 464: 60-62

Pesole G. and Liuni S.
Internet resources for the functional analysis of 5' and 3' untranslated regions of eukaryotic mRNAs.
(1999) Trends Genet. 15:378.

D'Erchia A.M., Pesole G., Tullo A., Saccone C., Sbisà E.
Guinea pig p53 mRNA: identification of new elements in coding and untranslated regions and their functional and evolutionary
implications.(1999) Genomics 58: 50-64.

Pesole G., Gissi C., De Chirico A., Saccone C.
Nucleotide substitution rate of mammalian mitochondrial genomes.
(1999) J. Mol. Evol. 48: 427-34.

Kleineidam R.G., Pesole G., Breukelman H.J., Beintema J.J. and Kastelein R.A.
Inclusion of Cetaceans within the order artiodactyla based on phylogenetic analysis of Pancreatic Ribonuclease genes.
J. Mol. Evol. (1999) 48: 360:368.

Matassi G., Cherif-Zahar B., Pesole G., Raynal V., Cartron J.P.
The members of the RH gene family (RH50 and RH30) followed different evolutionary pathways.
J. Mol. Evol. (1999) 48: 151-159.

Pesole G., Liuni S., Grillo G., Ippedico M., Larizza A., Makalowski W., Saccone C.
UTRdb: a specialized database of 5’ and 3’ untranslated regions of eukaryotic mRNAs.
Nucleic Acids Res. (1999) 27: 188-191.

Ardini E., Pesole G., Tagliabue E., Magnifico A., Castronovo V., Bobel M.E., Colnaghi M.I. and Menard S.
The 67-kDa laminin receptor originated from a ribosomal protein that acquired a dual function during evolution.
Mol. Biol. Evol. (1998) 15: 1017-1025.

Rossano R., Del Fiore A., D’Elia A., Pesole G., Parente E., Riccio P.
New procedure for the determination of nisin in milk.
Biotechnology Techniques (1998) 12: 783-786.

Reyes A., Gissi C., Pesole G. and Saccone C.
Asymmetric directional mutation pressure in the mitochondrial genome of mammals.
Mol. Biol. Evol. (1998) 15: 957-966.

Pesole G., Liuni S., Grillo G., Belichard P., Trenkle T., Welsh J. and McClelland M.
GeneUP: a program to select short PCR primer pairs that occur in multiple members of sequence lists.
BioTechniques (1998) 25: 112-123.

Reyes A., Pesole G. and Saccone C.
Complete Mitochondrial DNA Sequence of the Fat Dormouse, Glis glis: Further Evidence of Rodent Paraphyly.
Mol. Biol. Evol. (1998) 15: 499-505.

Pesole G., Liuni S., Grillo G., Saccone C.
UTRdb: a specialized database of 5'- and 3'-untranslated regions of eukaryotic mRNAs.
Nucleic Acids Res (1998) 26(1):194-198.

Sbisà E., Tanzariello F., Reyes A., Pesole G. and Saccone C.
Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications.
Gene (1997) 205: 125-140.

Pesole G., Liuni S., Grillo G. and Saccone C.
Structural and compositional features of untranslated regions of eukaryotic mRNAs.
Gene (1997) 205: 95-102.

De Giorgi C., Martiradonna A., Pesole G. and Saccone C.
Lineage specific evolution of mitochondrial ATP synthase subunit 8. J. Bioenerg.
Biomembranes (1997) 29: 233-239.

Madsen O., Deen P.M.T., Pesole G., Saccone C., de Jong W.W.
Molecular evolution of mammalian aquaporin-2. Further evidence that elephant shrew and aardvark join the paenungulate clade.
Mol. Biol. Evol. (1997) 14:363-371.

Lawn R., Patthy L., Pesole G. and Saccone C.
Apolipoprotein(a): a puzzling evolutionary story. J.
Mol. Evol. (1997) 44: 234-236.

Marracci S., Batistoni R., Pesole G., Citti L., Loreti S. and Nardi I.
Gypsy/Ty3-like elements in the genome of the terrestrial salamander Hydromantes (Amphibia, Urodela)
J. Mol. Evol. (1996) 43: 584-593.

D’Erchia A.M., Gissi C., Pesole G., Saccone C. and Arnason U.
The guinea-pig is not a rodent.
NATURE (1996) 381: 597-600.

Pesole G., Ceci L.R., Gissi C., Saccone C. and Quagliariello C.
Evolution of the nad3-rps12 gene cluster in angiosperm mitochondria: comparison of edited and unedited sequences.
J. Mol. Evol. (1996) 43:447-452.

Sbisà E., Pesole G., Tullo A. and Saccone C.
The evolution of Rnase P and Rnase MRP associated RNAs: phylogenetic analysis and nucleotide substitution rate.
J. Mol. Evol. (1996) 43: 46-57.

Grillo G., Attimonelli M., Liuni S. and Pesole G.
CLEANUP: a fast computer program for removing redundancies from nucleotide sequence databases.
Comput. Applic. Biosci. (1996) 12: 1-8.

Pesole G., Attimonelli M. and Saccone C.
Linguistic analysis of nucleotide sequences: algorithms for pattern recognition and analysis of codon strategy.
Methods in Enzymology (1996) 266: 281-294.

Pesole G., Grillo G. and Liuni S.
Databases of mRNA untranslated regions for Metazoa.
Computers & Chemistry (1996) 20: 141-144.

Pesole G., Lotti M., Alberghina L. and Saccone C.
Evolutionary origin of non-universal CUG(Ser) codon in some Candida species as inferred from a molecular phylogeny.
Genetics (1995) 141: 903-907.

Pesole G., Dellisanti G., Preparata G. and Saccone C.
The importance of base composition in the correct assessment of genetic distance.
J. Mol. Evol. (1995) 41: 1124-1127.

Saccone C., Lanave C., Pesole G. and Preparata G.
The reversible stationary Markov process for estimating the pattern of nucleotide substitution: a reply to Ziheng Yang.
J. Mol. Evol. (1995) 41: 253 [Letter to the Editor]

Batistoni R., Pesole G., Marracci S. and Nardi I.
A tandemly repeated DNA family originated from SINE-related elements in the European plethodontid salamanders (Anphibia, Urodela).
J. Mol. Evol. (1995) 40: 608-615.

Saccone C., Gissi C., Lanave C. and Pesole G.
Molecular classification of living organisms.
J. Mol. Evol. (1995) 40: 273-279.

Pesole G., Gissi C., Lanave C. and Saccone C.
Glutamine synthetase gene evolution in bacteria.
Molecular Biology and Evolution (1995) 12: 189-197.

Pesole G., Attimonelli M. and Saccone C.
Linguistic approaches to the analysis of sequence information.
Trends in Biotechnology (1994) 12: 401-408.

Pesole G., Saccone C. and Quagliariello E.
Molecular Evolution: from past to future.
Bulletin of Molecular Biology and Medicine (1994) 19: 93-102.

Cantatore P., Roberti M., Pesole G., Ludovico A., Milella F., Gadaleta M.N. and Saccone C.
Evolutionary analysis of cytochrome b sequences in some perciformes: evidence for a slower rate of evolution than in mammals.v
J. Mol. Evol (1994) 39: 589-597.

Pesole G., Saccone C. and Quagliariello E.
From the molecules the history of life.
Accountability in Research (1994) 3: 1-13.

Pesole G., Fiormarino G. and Saccone C.
Sequence analysis and compositional properties of untranslated regions of human mRNAs.
Gene (1994) 140: 219-225.

Pesole G., Gerardi A., di Jeso F. and Saccone C.
The peculiar evolution of apolipoprotein(a) in human and rhesus macaque.
Genetics (1994) 136: 255-260.

Lanave C. and Pesole G.
Stationary Markov processes in the evolution of biological macromolecules.
BINARY (1993) 5: 191-194.

Liuni S., Prunella N., Pesole G., D'Orazio T., Stella E. and Distante A.
SIMD parallelization of the WORDUP algorithm for detecting statistically significant patterns in DNA sequences.
Comput. Applic. Biosci. (1993) 9:701-707.

Saccone C., Lanave C. and Pesole G.
Time and biosequences
J. Mol. Evol. (1993) 37: 154-159.

Prunella N., Liuni S., Attimonelli M. and Pesole G.
FASTPAT: a fast and efficient algorithm for string searching in DNA sequences.
Comput. Applic. Biosci. (1993) 9: 541-545.

Saccone C, Pesole G., Sbisà E and Preparata G.
Time and biosequences: a contribution to the origin of modern man.
Human Evolution (1992) 7: 37-46.

Pesole G., Prunella N., Liuni S., Attimonelli M. and Saccone C.
WORDUP: an efficient algorithm for discovering statistically significant patterns in DNA sequences.
Nucleic Acids Res. (1992) 20: 2871-2875.

Pesole G., Attimonelli M., Preparata G. and Saccone C.
A statistical method for detecting regions with different evolutionary dynamics in multialigned sequences.
Molecular Phylogenetics and Evolution (1992) 2: 91-96.

Pesole G., Sbisa' E., Preparata G. and Saccone C.
The evolution of the mitochondrial D-loop region and the origin of modern man.
Mol. Biol. Evol. (1992) 9: 587-598

Pesole G., Sbisa' E., Mignotte F. and Saccone C.
The branching order of mammals: phylogenetic trees inferred from nuclear and mitochondrial molecular data.
J. Mol. Evol. (1991) 33: 537-542

Saccone C., Pesole G. and Sbisà E.
The main regulatory region of mammalian mitochondrial DNA: structure-function model and evolutionary pattern.
J. Mol. Evol. (1991) 33: 83-91

Saccone C., Pesole G. and Kadenbach B.
Evolutionary analysis of the nucleus encoded subunits of mammalian cytochrome c oxidase.
Eur. J. Biochem. (1991) 195: 151-156

Pesole G., Bozzetti M.P., Lanave C., Preparata G. and Saccone C.
Glutamine Synthetase Gene Evolution: A good example of a Molecular Clock.
Proc. Natl. Acad. Sci. USA (1991) 88: 522-526.

De Giorgi C., De Luca F., Stefanile C., Pesole G., and Saccone C.
Direct evidence that restriction endonuclease may under estimate the degree of divergence between molecules.
Curr. Genetics (1990) 18: 167-168.

Saccone C., Lanave C., Pesole G. and Preparata G.
The Influence of Base Composition on Quantitative Estimates of Gene Evolution.
Methods in Enzymology (1990) 183: 570-583

Holmes E.C., Pesole G. and Saccone C.
Stochastic models of molecular evolution and the estimation of phylogeny and rates of nucleotide substitution in the hominoid primates.
J. Human Evolution (1989) 18: 775-794

Saccone C., Pesole G. and Preparata G.
DNA Microenvironments and the Molecular Clock.
J. Mol. Evol. (1989) 29: 407-411

Pesole G., Attimonelli M. and Liuni S.
A backtranslation method based on codon usage strategy.
Nucleic Acids Res. (1988) 16: 1715-1728

Attimonelli M., Lanave C., Liuni S. and Pesole G.
MERGE: a software package for generating a single data-base starting from EMBL and GenBank collections.
Nucleic Acids Res. (1988) 16: 1681-1682

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