Federico Zambelli

Publication Activity (10 Years)

Years Active: 2006-2023
Publications (10 Years): 10

Top Topics

Genomic Sequences

Computing Resources

Top Venues

Nucleic Acids Res.

Briefings Bioinform.

Publications

Claudio Lo Giudice, Federico Zambelli, Matteo Chiara, Giulio Pavesi, Marco Antonio Tangaro, Ernesto Picardi, Graziano Pesole
UTRdb 2.0: a comprehensive, expert curated catalog of eukaryotic mRNAs untranslated regions. Nucleic Acids Res. 51 (D1) (2023)
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, Anup Kumar, Arthur C. Eschenlauer, Assunta D. Desanto, Aysam Guerler, Beatriz Serrano-Solano, Bérénice Batut, Bradley W. Langhorst, Bridget Carr, Bryan A. Raubenolt, Cameron J. Hyde, Catherine J. Bromhead, Christopher B. Barnett, Coline Royaux, Cristóbal Gallardo, Daniel J. Fornika, Dannon Baker, Dave Bouvier, Dave Clements, David A. de Lima Morais, David Lopez Tabernero, Delphine Larivière, Engy Nasr, Federico Zambelli, Florian Heyl, Fotis Psomopoulos, Frederik Coppens, Gareth R. Price, Gianmauro Cuccuru, Gildas Le Corguillé, Gregory Von Kuster, Gulsum Gudukbay, Helena Rasche, Hans-Rudolf Hotz, Ignacio Eguinoa, Igor V. Makunin, Isuru Ranawaka, James Taylor, Jayadev Joshi, Jennifer Hillman-Jackson, John Chilton, Kaivan Kamali, Keith Suderman, Krzysztof Poterlowicz, Yvan Le Bras, Lucille Lopez-Delisle, Luke Sargent, Madeline E. Bassetti, Marco Antonio Tangaro, Marius van den Beek, Martin Cech, Matthias Bernt, Matthias Fahrner, Mehmet Tekman, Melanie Christine Föll, Michael R. Crusoe, Miguel Roncoroni, Natalie Kucher, Nate Coraor, Nicholas Stoler, Nick Rhodes, Nicola Soranzo, Niko Pinter, Nuwan Goonasekera, Pablo A. Moreno, Pavankumar Videm, Petera Melanie, Pietro Mandreoli, Pratik D. Jagtap, Qiang Gu, Ralf J. M. Weber, Ross Lazarus, Ruben H. P. Vorderman, Saskia Hiltemann, Sergey Golitsynskiy, Shilpa Garg, Simon A. Bray, Simon L. Gladman, Simone Leo, Subina P. Mehta, Timothy J. Griffin, Vahid Jalili, Yves Vandenbrouck, Victor Wen, Vijay K. Nagampalli, Wendi A. Bacon, Willem L. De Koning, Wolfgang Maier, Peter J. Briggs
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic Acids Res. 50 (W1) (2022)
Marco Antonio Tangaro, Marica Antonacci, Pietro Mandreoli, Daniele Colombo, Nadina Foggetti, Giacinto Donvito, Graziano Pesole, Federico Zambelli
The Laniakea Dashboard and Storage Encryption Components: A Foundation for Developing On-Demand Cloud Services for Life Science. ICWE Workshops (2022)
Matteo Chiara, Federico Zambelli, Marco Antonio Tangaro, Pietro Mandreoli, David Stephen Horner, Graziano Pesole
CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes. Bioinform. 36 (22-23) (2021)
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
Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities. Briefings Bioinform. 22 (2) (2021)
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, Vladimir Nosi, Raffaele A. Calogero, Luca Alessandri, Elena Pedrini, Marina Mordenti, Emanuele Bonetti, Luca Sangiorgi, Graziano Pesole, Federico Zambelli
Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service. BMC Bioinform. (15) (2021)
Matteo Chiara, Pietro Mandreoli, Marco Antonio Tangaro, Anna Maria D'Erchia, Sandro Sorrentino, Cinzia Forleo, David Stephen Horner, Federico Zambelli, Graziano Pesole
VINYL: Variant prIoritizatioN bY survivaL analysis. Bioinform. 36 (24) (2021)
Matteo Chiara, Federico Zambelli, Ernesto Picardi, David Stephen Horner, Graziano Pesole
Critical assessment of bioinformatics methods for the characterization of pathological repeat expansions with single-molecule sequencing data. Briefings Bioinform. 21 (6) (2020)
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, Federico Zambelli
ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community. BMC Bioinform. (10) (2020)
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, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn A. Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael C. Jimenez, Nick S. Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Micetic, Rune Møllegaard Friborg, Sébastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter M. Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vareková, Silvio C. E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen E. Parkinson, Peter Løngreen, Søren Brunak
Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. 44 (Database-Issue) (2016)
Federico Zambelli, Graziano Pesole, Giulio Pavesi
Motif discovery and transcription factor binding sites before and after the next-generation sequencing era. Briefings Bioinform. 14 (2) (2013)
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
SpliceAid-F: a database of human splicing factors and their RNA-binding sites. Nucleic Acids Res. 41 (Database-Issue) (2013)
Federico Zambelli, Graziano Pesole, Giulio Pavesi
PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
Federico Zambelli, Gian Marco Prazzoli, Graziano Pesole, Giulio Pavesi
Cscan: finding common regulators of a set of genes by using a collection of genome-wide ChIP-seq datasets. Nucleic Acids Res. 40 (Web-Server-Issue) (2012)
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, Ernesto Picardi, Raffaella Rizzi, Ivan Rossi, Alessio Valletti, Andrea Zauli, Federico Zambelli, Rita Casadio, Graziano Pesole
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. Nucleic Acids Res. 39 (Database-Issue) (2011)
Federico Zambelli, Giulio Pavesi
A Faster Algorithm for Motif Finding in Sequences from ChIP-Seq Data. CIBB (2011)
Federico Zambelli, Graziano Pesole, Giulio Pavesi
Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
Giulio Pavesi, Federico Zambelli, Graziano Pesole
WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences. BMC Bioinform. 8 (2007)
Giulio Pavesi, Federico Zambelli
Prediction of over Represented Transcription Factor Binding Sites in Co-regulated Genes Using Whole Genome Matching Statistics. WILF (2007)
Giulio Pavesi, Paolo Mereghetti, Federico Zambelli, Marco Stefani, Giancarlo Mauri, Graziano Pesole
MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)