WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences

gan Pavesi, Giulio, Zambelli, Federico, Pesole, Graziano
Cyhoeddwyd 2007

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

gan Zambelli, Federico, Pesole, Graziano, Pavesi, Giulio
Cyhoeddwyd 2009

Motif discovery and transcription factor binding sites before and after the next-generation sequencing era

gan Zambelli, Federico, Pesole, Graziano, Pavesi, Giulio
Cyhoeddwyd 2013

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

gan Zambelli, Federico, Pesole, Graziano, Pavesi, Giulio
Cyhoeddwyd 2013

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

gan Pavesi, Giulio, Zambelli, Federico, Caggese, Corrado, Pesole, Graziano
Cyhoeddwyd 2008

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

gan Zambelli, Federico, Prazzoli, Gian Marco, Pesole, Graziano, Pavesi, Giulio
Cyhoeddwyd 2012

Assessment of orthologous splicing isoforms in human and mouse orthologous genes

gan Zambelli, Federico, Pavesi, Giulio, Gissi, Carmela, Horner, David S, Pesole, Graziano
Cyhoeddwyd 2010

A high definition look at the NF-Y regulome reveals genome-wide associations with selected transcription factors

gan Dolfini, Diletta, Zambelli, Federico, Pedrazzoli, Maurizio, Mantovani, Roberto, Pavesi, Giulio
Cyhoeddwyd yn Nucleic Acids Res (2016)

Integrating Peak Colocalization and Motif Enrichment Analysis for the Discovery of Genome-Wide Regulatory Modules and Transcription Factor Recruitment Rules

gan Ronzio, Mirko, Zambelli, Federico, Dolfini, Diletta, Mantovani, Roberto, Pavesi, Giulio
Cyhoeddwyd yn Front Genet (2020)

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

gan Pavesi, Giulio, Mereghetti, Paolo, Zambelli, Federico, Stefani, Marco, Mauri, Giancarlo, Pesole, Graziano
Cyhoeddwyd 2006

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

gan Chiara, Matteo, Zambelli, Federico, Tangaro, Marco Antonio, Mandreoli, Pietro, Horner, David S, Pesole, Graziano
Cyhoeddwyd yn Bioinformatics (2020)

RNentropy: an entropy-based tool for the detection of significant variation of gene expression across multiple RNA-Seq experiments

gan Zambelli, Federico, Mastropasqua, Francesca, Picardi, Ernesto, D’Erchia, Anna Maria, Pesole, Graziano, Pavesi, Giulio
Cyhoeddwyd yn Nucleic Acids Res (2018)

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

gan Tangaro, Marco Antonio, Donvito, Giacinto, Antonacci, Marica, Chiara, Matteo, Mandreoli, Pietro, Pesole, Graziano, Zambelli, Federico
Cyhoeddwyd yn Gigascience (2020)

Gain-of-function p53 mutants have widespread genomic locations partially overlapping with p63

gan Martynova, Elena, Pozzi, Silvia, Basile, Valentina, Dolfini, Diletta, Zambelli, Federico, Imbriano, Carol, Pavesi, Giulio, Mantovani, Roberto
Cyhoeddwyd 2012

PIPE-T: a new Galaxy tool for the analysis of RT-qPCR expression data

gan Zanardi, Nicolò, Morini, Martina, Tangaro, Marco Antonio, Zambelli, Federico, Bosco, Maria Carla, Varesio, Luigi, Eva, Alessandra, Cangelosi, Davide
Cyhoeddwyd yn Sci Rep (2019)

Transcriptional Network of p63 in Human Keratinocytes

gan Pozzi, Silvia, Zambelli, Federico, Merico, Daniele, Pavesi, Giulio, Robert, Amélie, Maltère, Peggy, Gidrol, Xavier, Mantovani, Roberto, Vigano, M. Alessandra
Cyhoeddwyd 2009

Widespread generation of alternative UTRs contributes to sex-specific RNA binding by UNR

gan Mihailovich, Marija, Wurth, Laurence, Zambelli, Federico, Abaza, Irina, Militti, Cristina, Mancuso, Francesco M., Roma, Guglielmo, Pavesi, Giulio, Gebauer, Fátima
Cyhoeddwyd 2012

Widespread generation of alternative UTRs contributes to sex-specific RNA binding by UNR

gan Mihailovic, Marija, Wurth, Laurence, Zambelli, Federico, Abaza, Irina, Militti, Cristina, Mancuso, Francesco M., Roma, Guglielmo, Pavesi, Giulio, Gebauer, Fátima
Cyhoeddwyd 2013

CoVaCS: a consensus variant calling system

gan Chiara, Matteo, Gioiosa, Silvia, Chillemi, Giovanni, D’Antonio, Mattia, Flati, Tiziano, Picardi, Ernesto, Zambelli, Federico, Horner, David Stephen, Pesole, Graziano, Castrignanò, Tiziana
Cyhoeddwyd yn BMC Genomics (2018)

Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities

gan Chiara, Matteo, D’Erchia, Anna Maria, Gissi, Carmela, Manzari, Caterina, Parisi, Antonio, Resta, Nicoletta, Zambelli, Federico, Picardi, Ernesto, Pavesi, Giulio, Horner, David S, Pesole, Graziano
Cyhoeddwyd yn Brief Bioinform (2020)