Works by Pesole, Graziano

Results: 200

Congruent Mammalian Trees from Mitochondrial and Nuclear Genes Using Bayesian Methods.

Published in:

Molecular Biology & Evolution, 2004, v. 21, n. 2, p. 397

By:

Reyes, Aurelio;
Gissi, Carmela;
Catzeflis, Francois;
Nevo, Eviatar;
Pesole, Graziano;
Saccone, Cecilia

Publication type:

Article

Lineage-Specific Evolutionary Rate in Mammalian mtDNA.

Published in:

Molecular Biology & Evolution, 2000, v. 17, n. 7, p. 1022, doi. 10.1093/oxfordjournals.molbev.a026383

By:

Gissi, Carmela;
Reyes, Aurelio;
Pesole, Graziano;
Saccone, Cecilia

Publication type:

Article

Where Do Rodents Fit? Evidence from the Complete Mitochondrial Genome of Sciurus vulgaris.

Published in:

Molecular Biology & Evolution, 2000, v. 17, n. 6, p. 979, doi. 10.1093/oxfordjournals.molbev.a026379

By:

Reyes, Aurelio;
Gissi, Carmela;
Pesole, Graziano;
Catzeflis, François M.;
Saccone, Cecilia

Publication type:

Article

Profile of microbial communities on carbonate stones of the medieval church of San Leonardo di Siponto (Italy) by Illumina-based deep sequencing.

Published in:

Applied Microbiology & Biotechnology, 2016, v. 100, n. 19, p. 8537, doi. 10.1007/s00253-016-7656-8

By:

Chimienti, Guglielmina;
Piredda, Roberta;
Pepe, Gabriella;
Werf, Inez;
Sabbatini, Luigia;
Crecchio, Carmine;
Ricciuti, Patrizia;
D'Erchia, Anna;
Manzari, Caterina;
Pesole, Graziano

Publication type:

Article

Diversity of hydrolases from hydrothermal vent sediments of the Levante Bay, Vulcano Island (Aeolian archipelago) identified by activity-based metagenomics and biochemical characterization of new esterases and an arabinopyranosidase.

Published in:

Applied Microbiology & Biotechnology, 2015, v. 99, n. 23, p. 10031, doi. 10.1007/s00253-015-6873-x

By:

Placido, Antonio;
Hai, Tran;
Ferrer, Manuel;
Chernikova, Tatyana;
Distaso, Marco;
Armstrong, Dale;
Yakunin, Alexander;
Toshchakov, Stepan;
Yakimov, Michail;
Kublanov, Ilya;
Golyshina, Olga;
Pesole, Graziano;
Ceci, Luigi;
Golyshin, Peter

Publication type:

Article

The lifeblood of LifeWatch ERIC: national in-kind contributions.

Published in:

Research Ideas & Outcome Journal, 2024, p. 1, doi. 10.3897/rio.10.e121887

By:

Los, Wouter;
Năpăruş-Aljančič, Magdalena;
Bileva, Tatyana;
Chatzinikolaou, Eva;
Graber-Soudry, Ohad;
de Moncuit, Lucas;
Neto, Marta;
Pesole, Graziano;
Abascal, Maria Vallejo;
Grozdanova, Dafinka

Publication type:

Article

Laniakea: an open solution to provide Galaxy "on-demand" instances over heterogeneous cloud infrastructures.

Published in:

GigaScience, 2020, v. 9, n. 4, p. N.PAG, doi. 10.1093/gigascience/giaa033

By:

Tangaro, Marco Antonio;
Donvito, Giacinto;
Antonacci, Marica;
Chiara, Matteo;
Mandreoli, Pietro;
Pesole, Graziano;
Zambelli, Federico

Publication type:

Article

The metagenomic data life-cycle: standards and best practices.

Published in:

GigaScience, 2017, v. 6, n. 8, p. 1, doi. 10.1093/gigascience/gix047

By:

Hoopen, Petra ten;
Finn, Robert D.;
Bongo, Lars Ailo;
Corre, Erwan;
Fosso, Bruno;
Meyer, Folker;
Mitchell, Alex;
Pelletier, Eric;
Pesole, Graziano;
Santamaria, Monica;
Willassen, Nils Peder;
Cochrane, Guy

Publication type:

Article

Quantifying RNA Editing in Deep Transcriptome Datasets.

Published in:

Frontiers in Genetics, 2020, v. 11, p. 1, doi. 10.3389/fgene.2020.00194

By:

Lo Giudice, Claudio;
Silvestris, Domenico Alessandro;
Roth, Shalom Hillel;
Eisenberg, Eli;
Pesole, Graziano;
Gallo, Angela;
Picardi, Ernesto

Publication type:

Article

Identification of deregulated lncRNAs in Alzheimer's disease: an integrated gene co-expression network analysis of hippocampus and fusiform gyrus RNA-seq datasets.

Published in:

Frontiers in Aging Neuroscience, 2024, p. 1, doi. 10.3389/fnagi.2024.1437278

By:

Filomena, Ermes;
Picardi, Ernesto;
Tullo, Apollonia;
Pesole, Graziano;
D'Erchia, Anna Maria

Publication type:

Article

Genomic Surveillance of Circulating SARS-CoV-2 in South East Italy: A One-Year Retrospective Genetic Study.

Published in:

Viruses (1999-4915), 2021, v. 13, n. 5, p. 731, doi. 10.3390/v13050731

By:

Capozzi, Loredana;
Bianco, Angelica;
Del Sambro, Laura;
Simone, Domenico;
Lippolis, Antonio;
Notarnicola, Maria;
Pesole, Graziano;
Pace, Lorenzo;
Galante, Domenico;
Parisi, Antonio;
Martinez-Sobrido, Luis;
Toral, Fernando Almazan

Publication type:

Article

Dynamic inosinome profiles reveal novel patient stratification and gender-specific differences in glioblastoma.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1647-x

By:

Silvestris, Domenico Alessandro;
Picardi, Ernesto;
Cesarini, Valeriana;
Fosso, Bruno;
Mangraviti, Nicolò;
Massimi, Luca;
Martini, Maurizio;
Pesole, Graziano;
Locatelli, Franco;
Gallo, Angela

Publication type:

Article

Assessing computational tools for the discovery of transcription factor binding sites.

Published in:

Nature Biotechnology, 2005, v. 23, n. 1, p. 137, doi. 10.1038/nbt1053

By:

Tompa, Martin;
Li, Nan;
Bailey, Timothy L.;
Church, George M.;
De Moor, Bart;
Eskin, Eleazar;
Favorov, Alexander V.;
Frith, Martin C.;
Fu, Yutao;
Kent, W. James;
Makeev, Vsevolod J.;
Mironov, Andrei A.;
Noble, William Stafford;
Pavesi, Giulio;
Pesole, Graziano;
Régnier, Mireille;
Simonis, Nicolas;
Sinha, Saurabh;
Thijs, Gert;
van Helden, Jacques

Publication type:

Article

A Novel Additional Group II Intron Distinguishes the Mitochondrialrps3Gene in Gymnosperms.

Published in:

Journal of Molecular Evolution, 2005, v. 60, n. 2, p. 196, doi. 10.1007/s00239-004-0098-4

By:

Regina, Teresa M. R.;
Picardi, Ernesto;
Lopez, Loredana;
Pesole, Graziano;
Quagliariello, Carla

Publication type:

Article

Complete mtDNA of Ciona intestinalis Reveals Extensive Gene Rearrangement and the Presence of an atp8 and an Extra trnM Gene in Ascidians.

Published in:

Journal of Molecular Evolution, 2004, v. 58, n. 4, p. 376, doi. 10.1007/s00239-003-2559-6

By:

Gissi, Carmela;
Iannelli, Fabio;
Pesole, Graziano

Publication type:

Article

Molecular Clock and Gene Function.

Published in:

Journal of Molecular Evolution, 2003, v. 57, p. S277, doi. 10.1007/s00239-003-0037-9

By:

Saccone, Cecilia;
Caggese, Corrado;
D'Erchia, Anna Maria;
Lanave, Cecilia;
Oliva, Marta;
Pesole, Graziano

Publication type:

Article

Lineage Specificity of the Evolutionary Dynamics of the mtDNA D-Loop Region in Rodents.

Published in:

Journal of Molecular Evolution, 2002, v. 54, n. 2, p. 145, doi. 10.1007/s00239-001-0063-4

By:

Larizza, Alessandra;
Pesole, Graziano;
Reyes, Aurelio;
Sbisà, Elisabetta;
Saccone, Cecilia

Publication type:

Article

ITSoneWB: profiling global taxonomic diversity of eukaryotic communities on Galaxy.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4253, doi. 10.1093/bioinformatics/btab431

By:

Tangaro, Marco A;
Defazio, Giuseppe;
Fosso, Bruno;
Licciulli, Vito Flavio;
Grillo, Giorgio;
Donvito, Giacinto;
Lavezzo, Enrico;
Baruzzo, Giacomo;
Pesole, Graziano;
Santamaria, Monica

Publication type:

Article

VINYL: Variant prIoritizatioN bY survivaL analysis.

Published in:

Bioinformatics, 2020, v. 36, n. 24, p. 5590, doi. 10.1093/bioinformatics/btaa1067

By:

Chiara, Matteo;
Mandreoli, Pietro;
Tangaro, Marco Antonio;
D'Erchia, Anna Maria;
Sorrentino, Sandro;
Forleo, Cinzia;
Horner, David S;
Zambelli, Federico;
Pesole, Graziano

Publication type:

Article

CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes.

Published in:

Bioinformatics, 2020, v. 36, n. 22/23, p. 5522, doi. 10.1093/bioinformatics/btaa1047

By:

Chiara, Matteo;
Zambelli, Federico;
Tangaro, Marco Antonio;
Mandreoli, Pietro;
Horner, David S;
Pesole, Graziano

Publication type:

Article

Machine Learning Data Analysis Highlights the Role of Parasutterella and Alloprevotella in Autism Spectrum Disorders.

Published in:

Biomedicines, 2022, v. 10, n. 8, p. N.PAG, doi. 10.3390/biomedicines10082028

By:

Pietrucci, Daniele;
Teofani, Adelaide;
Milanesi, Marco;
Fosso, Bruno;
Putignani, Lorenza;
Messina, Francesco;
Pesole, Graziano;
Desideri, Alessandro;
Chillemi, Giovanni

Publication type:

Article

TRIM Proteins in Colorectal Cancer: TRIM8 as a Promising Therapeutic Target in Chemo Resistance.

Published in:

Biomedicines, 2021, v. 9, n. 3, p. 241, doi. 10.3390/biomedicines9030241

By:

Marzano, Flaviana;
Caratozzolo, Mariano Francesco;
Pesole, Graziano;
Sbisà, Elisabetta;
Tullo, Apollonia;
Baud, Veronique

Publication type:

Article

Comparison of ovarian mRNA expression levels in wild and hatchery-produced greater amberjack Seriola dumerili.

Published in:

Scientific Reports, 2024, v. 14, n. 1, p. 1, doi. 10.1038/s41598-024-69091-2

By:

Lavecchia, Anna;
De Virgilio, Caterina;
Mansi, Luigi;
Manzari, Caterina;
Mylonas, Constantinos C.;
Picardi, Ernesto;
Pousis, Chrysovalentinos;
Cox, Sharon N.;
Ventriglia, Gianluca;
Zupa, Rosa;
Pesole, Graziano;
Corriero, Aldo

Publication type:

Article

Upregulation of YKL-40 Promotes Metastatic Phenotype and Correlates with Poor Prognosis and Therapy Response in Patients with Colorectal Cancer.

Published in:

Cells (2073-4409), 2022, v. 11, n. 22, p. 3568, doi. 10.3390/cells11223568

By:

De Robertis, Mariangela;
Greco, Maria Raffaella;
Cardone, Rosa Angela;
Mazza, Tommaso;
Marzano, Flaviana;
Mehterov, Nikolay;
Kazakova, Maria;
Belev, Nikolay;
Tullo, Apollonia;
Pesole, Graziano;
Sarafian, Victoria;
Signori, Emanuela

Publication type:

Article

Emerging Roles of TRIM8 in Health and Disease.

Published in:

Cells (2073-4409), 2021, v. 10, n. 3, p. 561, doi. 10.3390/cells10030561

By:

Marzano, Flaviana;
Guerrini, Luisa;
Pesole, Graziano;
Sbisà, Elisabetta;
Tullo, Apollonia;
Meroni, Germana

Publication type:

Article

Corrigendum: Genome Sequencing and Comparative Analysis of Three Hanseniaspora uvarum Indigenous Wine Strains Reveal Remarkable Biotechnological Potential.

Published in:

2020

By:

Guaragnella, Nicoletta;
Chiara, Matteo;
Capece, Angela;
Romano, Patrizia;
Pietrafesa, Rocchina;
Siesto, Gabriella;
Manzari, Caterina;
Pesole, Graziano

Publication type:

Correction Notice

Genome Sequencing and Comparative Analysis of Three Hanseniaspora uvarum Indigenous Wine Strains Reveal Remarkable Biotechnological Potential.

Published in:

Frontiers in Microbiology, 2020, v. 10, p. 1, doi. 10.3389/fmicb.2019.03133

By:

Guaragnella, Nicoletta;
Chiara, Matteo;
Capece, Angela;
Romano, Patrizia;
Pietrafesa, Rocchina;
Siesto, Gabriella;
Manzari, Caterina;
Pesole, Graziano

Publication type:

Article

PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W535, doi. 10.1093/nar/gkt448

By:

Zambelli, Federico;
Pesole, Graziano;
Pavesi, Giulio

Publication type:

Article

SpliceAid-F: a database of human splicing factors and their RNA-binding sites.

Published in:

Nucleic Acids Research, 2013, v. 41, p. D125, doi. 10.1093/nar/gks997

By:

Giulietti, Matteo;
Piva, Francesco;
D’Antonio, Mattia;
De Meo, Paolo D’Onorio;
Paoletti, Daniele;
Castrignanò, Tiziana;
D’Erchia, Anna Maria;
Picardi, Ernesto;
Zambelli, Federico;
Principato, Giovanni;
Pavesi, Giulio;
Pesole, Graziano

Publication type:

Article

SVM2: an improved paired-end-based tool for the detection of small genomic structural variations using high-throughput single-genome resequencing data.

Published in:

Nucleic Acids Research, 2012, v. 40, n. 18, p. e145, doi. 10.1093/nar/gks606

By:

Chiara, Matteo;
Pesole, Graziano;
Horner, David S.

Publication type:

Article

Cscan: finding common regulators of a set of genes by using a collection of genome-wide ChIP-seq datasets.

Published in:

Nucleic Acids Research, 2012, v. 40, p. W510, doi. 10.1093/nar/gks483

By:

Zambelli, Federico;
Prazzoli, Gian Marco;
Pesole, Graziano;
Pavesi, Giulio

Publication type:

Article

MitoZoa 2.0: a database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa.

Published in:

Nucleic Acids Research, 2012, p. D1168, doi. 10.1093/nar/gkr1144

By:

D'Onorio de Meo, Paolo;
D'Antonio, Mattia;
Griggio, Francesca;
Lupi, Renato;
Borsani, Massimiliano;
Pavesi, Giulio;
Castrignanò, Tiziana;
Pesole, Graziano;
Gissi, Carmela

Publication type:

Article

ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_1, p. D80, doi. 10.1093/nar/gkq1073

By:

Martelli, Pier L.;
D’Antonio, Mattia;
Bonizzoni, Paola;
Castrignanò, Tiziana;
D’Erchia, Anna M.;
D’Onorio De Meo, Paolo;
Fariselli, Piero;
Finelli, Michele;
Licciulli, Flavio;
Mangiulli, Marina;
Mignone, Flavio;
Pavesi, Giulio;
Picardi, Ernesto;
Rizzi, Raffaella;
Rossi, Ivan;
Valletti, Alessio;
Zauli, Andrea;
Zambelli, Federico;
Casadio, Rita;
Pesole, Graziano

Publication type:

Article

Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing.

Published in:

Nucleic Acids Research, 2010, v. 38, n. 14, p. 4755, doi. 10.1093/nar/gkq202

By:

Picardi, Ernesto;
Horner, David S.;
Chiara, Matteo;
Schiavon, Riccardo;
Valle, Giorgio;
Pesole, Graziano

Publication type:

Article

UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs.

Published in:

Nucleic Acids Research, 2010, v. 38, p. D75, doi. 10.1093/nar/gkp902

By:

Grillo, Giorgio;
Turi, Antonio;
Licciulli, Flavio;
Mignone, Flavio;
Liuni, Sabino;
Banfi, Sandro;
Gennarino, Vincenzo Alessandro;
Horner, David S.;
Pavesi, Giulio;
Picardi, Ernesto;
Pesole, Graziano

Publication type:

Article

Identification and functional characterization of two new transcriptional variants of the human p63 gene.

Published in:

Nucleic Acids Research, 2009, v. 37, n. 18, p. 6092, doi. 10.1093/nar/gkp674

By:

Mangiulli, Marina;
Valletti, Alessio;
Caratozzolo, Mariano Francesco;
Tullo, Apollonia;
Sbisà, Elisabetta;
Pesole, Graziano;
D’Erchia, Anna Maria

Publication type:

Article

Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes.

Published in:

Nucleic Acids Research, 2009, v. 37, n. suppl_2, p. W247, doi. 10.1093/nar/gkp464

By:

Zambelli, Federico;
Pesole, Graziano;
Pavesi, Giulio

Publication type:

Article

Exalign: a new method for comparative analysis of exon–intron gene structures.

Published in:

Nucleic Acids Research, 2008, v. 36, n. 8, p. e47, doi. 10.1093/nar/gkn153

By:

Pavesi, Giulio;
Zambelli, Federico;
Caggese, Corrado;
Pesole, Graziano

Publication type:

Article

ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization.

Published in:

Nucleic Acids Research, 2006, v. 34, n. 11, p. w440, doi. 10.1093/nar/gkl324

By:

Castrignanò, Tiziana;
Rizzi, Raffaella;
Talamo, Ivano Giuseppe;
De Meo, Paolo D'Onorio;
Anselmo, Anna;
Bonizzoni, Paola;
Pesole, Graziano

Publication type:

Article

MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes.

Published in:

Nucleic Acids Research, 2006, v. 34, n. 11, p. w566, doi. 10.1093/nar/gkl285

By:

Pavesi, Giulio;
Mereghetti, Paolo;
Zambelli, Federico;
Stefani, Marco;
Mauri, Giancarlo;
Pesole, Graziano

Publication type:

Article

UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs.

Published in:

Nucleic Acids Research, 2005, v. 33, n. suppl 1, p. d141

By:

Mignone, Flavio;
Grillo, Giorgio;
Licciulli, Flavio;
Iacono, Michele;
Liuni, Sabino;
Kersey, Paul J.;
Duarte, Jorge;
Saccone, Cecilia;
Pesole, Graziano

Publication type:

Article

DG-CST (Disease Gene Conserved Sequence Tags), a database of human–mouse conserved elements associated to disease genes.

Published in:

Nucleic Acids Research, 2005, v. 33, n. suppl 1, p. d505

By:

Boccia, Angelo;
Petrillo, Mauro;
di Bernardo, Diego;
Guffanti, Alessandro;
Mignone, Flavio;
Confalonieri, Stefano;
Luzi, Lucilla;
Pesole, Graziano;
Paolella, Giovanni;
Ballabio, Andrea;
Banfi, Sandro

Publication type:

Article

CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison.

Published in:

Nucleic Acids Research, 2004, v. 32, n. suppl 2, p. w624, doi. 10.1093/nar/gkh486

By:

Castrignanò, Tiziana;
Canali, Alessandro;
Grillo, Giorgio;
Liuni, Sabino;
Mignone, Flavio;
Pesole, Graziano

Publication type:

Article

Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes.

Published in:

Nucleic Acids Research, 2004, v. 32, n. suppl 2, p. w199, doi. 10.1093/nar/gkh465

By:

Pavesi, Giulio;
Mereghetti, Paolo;
Mauri, Giancarlo;
Pesole, Graziano

Publication type:

Article

RNAProfile: an algorithm for finding conserved secondary structure motifs in unaligned RNA sequences.

Published in:

Nucleic Acids Research, 2004, v. 32, n. 10, p. 3258, doi. 10.1093/nar/gkh650

By:

Pavesi, Giulio;
Mauri, Giancarlo;
Stefani, Marco;
Pesole, Graziano

Publication type:

Article

Computational identification of protein coding potential of conserved sequence tags through cross‐species evolutionary analysis.

Published in:

Nucleic Acids Research, 2003, v. 31, n. 15, p. 4639, doi. 10.1093/nar/gkg483

By:

Mignone, Flavio;
Grillo, Giorgio;
Liuni, Sabino;
Pesole, Graziano

Publication type:

Article

PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences.

Published in:

Nucleic Acids Research, 2003, v. 31, n. 13, p. 3608, doi. 10.1093/nar/gkg548

By:

Grillo, Giorgio;
Licciulli, Flavio;
Liuni, Sabino;
Sbisà, Elisabetta;
Pesole, Graziano

Publication type:

Article

Translational control of Scamper expression via a cell‐specific internal ribosome entry site.

Published in:

Nucleic Acids Research, 2003, v. 31, n. 10, p. 2508, doi. 10.1093/nar/gkg357

By:

De Pietri Tonelli, Davide;
Mihailovich, Marija;
Schnurbus, Raphaela;
Pesole, Graziano;
Grohovaz, Fabio;
Zacchetti, Daniele

Publication type:

Article

UTRdb and UTRsite: specialized databases of sequences and functional elements of 5′ and 3′ untranslated regions of eukaryotic mRNAs. Update 2002.

Published in:

Nucleic Acids Research, 2002, v. 30, n. 1, p. 335, doi. 10.1093/nar/30.1.335

By:

Pesole, Graziano;
Liuni, Sabino;
Grillo, Giorgio;
Licciulli, Flavio;
Mignone, Flavio;
Gissi, Carmela;
Saccone, Cecilia

Publication type:

Article

MitoNuc: a database of nuclear genes coding for mitochondrial proteins. Update 2002.

Published in:

Nucleic Acids Research, 2002, v. 30, n. 1, p. 172, doi. 10.1093/nar/30.1.172

By:

Attimonelli, Marcella;
Catalano, Domenico;
Gissi, Carmela;
Grillo, Giorgio;
Licciulli, Flavio;
Liuni, Sabino;
Santamaria, Monica;
Pesole, Graziano;
Saccone, Cecilia

Publication type:

Article