Graziano Pesole

According to our database1, Graziano Pesole authored at least 79 papers between 1993 and 2018.

Collaborative distances:
  • Dijkstra number2 of five.
  • Erdős number3 of four.



In proceedings 
PhD thesis 





ITSoneDB: a comprehensive collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences.
Nucleic Acids Research, 2018

REDIportal: a comprehensive database of A-to-I RNA editing events in humans.
Nucleic Acids Research, 2017

MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data.
Bioinformatics, 2017

Unbiased Taxonomic Annotation of Metagenomic Samples.
Proceedings of the Bioinformatics Research and Applications - 13th International Symposium, 2017

BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS.
BMC Bioinformatics, 2015

MSA-PAD: DNA multiple sequence alignment framework based on PFAM accessed domain information.
Bioinformatics, 2015

EasyCluster2: an improved tool for clustering and assembling long transcriptome reads.
BMC Bioinformatics, 2014

MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing.
Bioinformatics, 2014

ODESSA: A high performance analysis pipeline for Ultra Deep targeted Exome Sequencing data.
Proceedings of the International Conference on High Performance Computing & Simulation, 2014

PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments.
Nucleic Acids Research, 2013

SpliceAid-F: a database of human splicing factors and their RNA-binding sites.
Nucleic Acids Research, 2013

WEP: a high-performance analysis pipeline for whole-exome data.
BMC Bioinformatics, 2013

NGS-Trex: Next Generation Sequencing Transcriptome profile explorer.
BMC Bioinformatics, 2013

REDItools: high-throughput RNA editing detection made easy.
Bioinformatics, 2013

Motif discovery and transcription factor binding sites before and after the next-generation sequencing era.
Briefings in Bioinformatics, 2013

Clustering and Assembling Large Transcriptome Datasets by EasyCluster2.
Proceedings of the Emerging Intelligent Computing Technology and Applications, 2013

Cscan: finding common regulators of a set of genes by using a collection of genome-wide ChIP-seq datasets.
Nucleic Acids Research, 2012

MitoZoa 2.0: a database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa.
Nucleic Acids Research, 2012

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

Briefings in Bioinformatics, 2012

Reference databases for taxonomic assignment in metagenomics.
Briefings in Bioinformatics, 2012

ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing.
Nucleic Acids Research, 2011

ExpEdit: a webserver to explore human RNA editing in RNA-Seq experiments.
Bioinformatics, 2011

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

Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing.
Briefings in Bioinformatics, 2010

New Tools for Expression Alternative Splicing Validation.
Proceedings of the Advanced Intelligent Computing Theories and Applications, 2010

Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes.
Nucleic Acids Research, 2009

Detecting Alternative Gene Structures from Spliced ESTs: A Computational Approach.
Journal of Computational Biology, 2009

Accurate discrimination of conserved coding and non-coding regions through multiple indicators of evolutionary dynamics.
BMC Bioinformatics, 2009

EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data.
BMC Bioinformatics, 2009

Statistical assessment of discriminative features for protein-coding and non coding cross-species conserved sequence elements.
BMC Bioinformatics, 2009

Bioinformatics in Italy: BITS2007, the fourth annual meeting of the Italian Society of Bioinformatics.
BMC Bioinformatics, 2008

ASPicDB: A database resource for alternative splicing analysis.
Bioinformatics, 2008

Correlated substitution analysis and the prediction of amino acid structural contacts.
Briefings in Bioinformatics, 2008

HT-RLS: High-Throughput Web Tool for Analysis of DNA Microarray Data Using RLS classifiers.
Proceedings of the 8th IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2008), 2008

GenePC and ASPIC Integrate Gene Predictions with Expressed Sequence Alignments To Predict Alternative Transcripts.
Proceedings of the 6th Asia-Pacific Bioinformatics Conference, 2008

A high performance grid-web service framework for the identification of 'conserved sequence tags'.
Future Generation Comp. Syst., 2007

p53FamTaG: a database resource of human p53, p63 and p73 direct target genes combining in silico prediction and microarray data.
BMC Bioinformatics, 2007

WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences.
BMC Bioinformatics, 2007

Bioinformatics in Italy: BITS2006, the third annual meeting of the Italian Society of Bioinformatics.
BMC Bioinformatics, 2007

Statistical assessment of functional categories of genes deregulated in pathological conditions by using microarray data.
Bioinformatics, 2007

Selection of relevant genes in cancer diagnosis based on their prediction accuracy.
Artificial Intelligence in Medicine, 2007

MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes.
Nucleic Acids Research, 2006

ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization.
Nucleic Acids Research, 2006

On the statistical assessment of classifiers using DNA microarray data.
BMC Bioinformatics, 2006

GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags.
Bioinformatics, 2006

Classification error as a measure of gene relevance in cancer diagnosis.
Proceedings of the International Joint Conference on Neural Networks, 2006

UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs.
Nucleic Acids Research, 2005

DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes.
Nucleic Acids Research, 2005

Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society.
BMC Bioinformatics, 2005

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

Regularized Least Squares Cancer Classifiers from DNA microarray data.
BMC Bioinformatics, 2005

SVM and RLS Models for Cancer Classification.
Proceedings of the IASTED International Conference on Computational Intelligence, 2005

Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes.
Nucleic Acids Research, 2004

CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison.
Nucleic Acids Research, 2004

An Algorithm for Finding Conserved Secondary Structure Motifs in Unaligned RNA Sequences.
J. Comput. Sci. Technol., 2004

WebVar: a resource for the rapid estimation of relative site variability from multiple sequence alignments.
Bioinformatics, 2004

DNAfan: a software tool for automated extraction and analysis of user-defined sequence regions.
Bioinformatics, 2004

In silico representation and discovery of transcription factor binding sites.
Briefings in Bioinformatics, 2004

PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences.
Nucleic Acids Research, 2003

The estimation of relative site variability among aligned homologous protein sequences.
Bioinformatics, 2003

A Method to Detect Gene Structure and Alternative Splice Sites by Agreeing ESTs to a Genomic Sequence.
Proceedings of the Algorithms in Bioinformatics, Third International Workshop, 2003

Predicting Conserved Hairpin Motifs in Unaligned RNA Sequences.
Proceedings of the 15th IEEE International Conference on Tools with Artificial Intelligence (ICTAI 2003), 2003

Handbook of Comparative Genomics - Principles and Methodology.
Wiley, ISBN: 978-0-471-39128-9, 2003

UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs. Update 2002.
Nucleic Acids Research, 2002

MitoNuc: a database of nuclear genes coding for mitochondrial proteins. Update 2002.
Nucleic Acids Research, 2002

Evolutionary Dynamics of Mammalian MRNA Untranslated Regions by Comparative Analysis of Orthologous Human, Artiodactyl and Rodent Gene Pairs.
Computers & Chemistry, 2002

Methods for Pattern Discovery in Unaligned Biological Sequences.
Briefings in Bioinformatics, 2001

An algorithm for finding signals of unknown length in DNA sequences.
Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, 2001

UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs.
Nucleic Acids Research, 2000

MitoNuc and MitoAln: two related databases of nuclear genes coding for mitochondrial proteins.
Nucleic Acids Research, 2000

PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance.
Bioinformatics, 2000

The Untranslated Regions of Eukaryotic MRNAs: Structure, Function, Evolution and Bioinformatic Tools for Their Analysis.
Briefings in Bioinformatics, 2000

UTRdb: a specialized database of 5' and 3' untranslated regions of eukaryotic mRNAs.
Nucleic Acids Research, 1999

UTRdb: a specialized database of 5'- and 3'-untranslated regions of eukaryotic mRNAs.
Nucleic Acids Research, 1998

Databases of MRNA Untranslated Regions for Metazoa.
Computers & Chemistry, 1996

CLEANUP: a fast computer program for removing redundancies from nucleotide sequence databases.
Computer Applications in the Biosciences, 1996

FASTPAT: a fast and efficient algorithm for string searching in DNA sequences.
Computer Applications in the Biosciences, 1993

SIMD parallelization of the WORDUP algorithm for detecting statistically significant patterns in DNA sequences.
Computer Applications in the Biosciences, 1993