MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes. - Giulio Pavesi; Paolo Mereghetti; Federico Zambelli; Marco Stefani; Giancarlo Mauri; Graziano Pesole (Nucleic Acids Res., 2006)

Prediction of over Represented Transcription Factor Binding Sites in Co-regulated Genes Using Whole Genome Matching Statistics. - Giulio Pavesi; Federico Zambelli (WILF, 2007)

WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences. - Giulio Pavesi; Federico Zambelli; Graziano Pesole (BMC Bioinform., 2007)

Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes. - Federico Zambelli; Graziano Pesole; Giulio Pavesi (Nucleic Acids Res., 2009)

A Faster Algorithm for Motif Finding in Sequences from ChIP-Seq Data. - Federico Zambelli; Giulio Pavesi (CIBB, 2011)

ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. - Pier Luigi Martelli; Mattia D'Antonio; Paola Bonizzoni; Tiziana Castrignanò; Anna Maria D'Erchia; Paolo D'Onorio De Meo; Piero Fariselli; Michele Finelli; Flavio Licciulli; Marina Mangiulli; Flavio Mignone; Giulio Pavesi; et al. (Nucleic Acids Res., 2011)

Cscan: finding common regulators of a set of genes by using a collection of genome-wide ChIP-seq datasets. - Federico Zambelli; Gian Marco Prazzoli; Graziano Pesole; Giulio Pavesi (Nucleic Acids Res., 2012)

Motif discovery and transcription factor binding sites before and after the next-generation sequencing era. - Federico Zambelli; Graziano Pesole; Giulio Pavesi (Briefings Bioinform., 2013)

SpliceAid-F: a database of human splicing factors and their RNA-binding sites. - Matteo Giulietti; Francesco Piva; Mattia D'Antonio; Paolo D'Onorio De Meo; Daniele Paoletti; Tiziana Castrignanò; Anna Maria D'Erchia; Ernesto Picardi; Federico Zambelli; Giovanni Principato; Giulio Pavesi; Graziano Pesole (Nucleic Acids Res., 2013)

PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments. - Federico Zambelli; Graziano Pesole; Giulio Pavesi (Nucleic Acids Res., 2013)

Tools and data services registry: a community effort to document bioinformatics resources. - Jon C. Ison; Kristoffer Rapacki; Hervé Ménager; Matús Kalas; Emil Rydza; Piotr Chmura; Christian Anthon; Niall Beard; Karel Berka; Dan M. Bolser; Tim Booth; Anthony Bretaudeau; et al. (Nucleic Acids Res., 2016)

INDIGO-DataCloud: a Platform to Facilitate Seamless Access to E-Infrastructures. - Davide Salomoni; Isabel Campos Plasencia; Luciano Gaido; Jesús E. Marco de Lucas; P. Solagna; Jorge Gomes 001; Ludek Matyska; P. Fuhrman; Marcus Hardt; Giacinto Donvito; Lukasz Dutka; Marcin Plóciennik; et al. (J. Grid Comput., 2018)

Critical assessment of bioinformatics methods for the characterization of pathological repeat expansions with single-molecule sequencing data. - Matteo Chiara; Federico Zambelli; Ernesto Picardi; David Stephen Horner; Graziano Pesole (Briefings Bioinform., 2020)

ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community. - Tiziana Castrignanò; Silvia Gioiosa; Tiziano Flati; Mirko Cestari; Ernesto Picardi; Matteo Chiara; Maddalena Fratelli; Stefano Amente; Marco Cirilli; Marco Antonio Tangaro; Giovanni Chillemi; Graziano Pesole; et al. (BMC Bioinform., 2020)

Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities. - Matteo Chiara; Anna Maria D'Erchia; Carmela Gissi; Caterina Manzari; Antonio Parisi; Nicoletta Resta; Federico Zambelli; Ernesto Picardi; Giulio Pavesi; David Stephen Horner; Graziano Pesole (Briefings Bioinform., 2021)

VINYL: Variant prIoritizatioN bY survivaL analysis. - Matteo Chiara; Pietro Mandreoli; Marco Antonio Tangaro; Anna Maria D'Erchia; Sandro Sorrentino; Cinzia Forleo; David Stephen Horner; Federico Zambelli; Graziano Pesole (Bioinform., 2021)

CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes. - Matteo Chiara; Federico Zambelli; Marco Antonio Tangaro; Pietro Mandreoli; David Stephen Horner; Graziano Pesole (Bioinform., 2021)

Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service. - Marco Antonio Tangaro; Pietro Mandreoli; Matteo Chiara; Giacinto Donvito; Marica Antonacci; Antonio Parisi; Angelica Bianco; Angelo Romano; Daniela Manila Bianchi; Davide Cangelosi; Paolo Uva; Ivan Molineris; et al. (BMC Bioinform., 2021)

The Laniakea Dashboard and Storage Encryption Components: A Foundation for Developing On-Demand Cloud Services for Life Science. - Marco Antonio Tangaro; Marica Antonacci; Pietro Mandreoli; Daniele Colombo; Nadina Foggetti; Giacinto Donvito; Graziano Pesole; Federico Zambelli (ICWE Workshops, 2022)

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. - Enis Afgan; Anton Nekrutenko; Björn A. Grüning; Daniel J. Blankenberg; Jeremy Goecks; Michael C. Schatz; Alexander E. Ostrovsky; Alexandru Mahmoud; Andrew J. Lonie; Anna Syme; Anne Fouilloux; Anthony Bretaudeau; et al. (Nucleic Acids Res., 2022)

UTRdb 2.0: a comprehensive, expert curated catalog of eukaryotic mRNAs untranslated regions. - Claudio Lo Giudice; Federico Zambelli; Matteo Chiara; Giulio Pavesi; Marco Antonio Tangaro; Ernesto Picardi; Graziano Pesole (Nucleic Acids Res., 2023)