Federico Zambelli

21 papers Journal 18Unranked 3
YearRankTypeTitle / Venue / Authors
2023 J jnl
UTRdb 2.0: a comprehensive, expert curated catalog of eukaryotic mRNAs untranslated regions.
Nucleic Acids Res.
Claudio Lo Giudice, Federico Zambelli, Matteo Chiara, Giulio Pavesi, Marco Antonio Tangaro, Ernesto Picardi, Graziano Pesole
2022 J jnl
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update.
Nucleic Acids Res.
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 E. 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 D. 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
2022 — conf
The Laniakea Dashboard and Storage Encryption Components: A Foundation for Developing On-Demand Cloud Services for Life Science.
ICWE Workshops
Marco Antonio Tangaro, Marica Antonacci, Pietro Mandreoli, Daniele Colombo, Nadina Foggetti, Giacinto Donvito, Graziano Pesole, Federico Zambelli
2021 J jnl
CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes.
Bioinform.
Matteo Chiara, Federico Zambelli, Marco Antonio Tangaro, Pietro Mandreoli, David Stephen Horner, Graziano Pesole
2021 J jnl
Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service.
BMC Bioinform.
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 Alessandrì, Elena Pedrini, Marina Mordenti, Emanuele Bonetti, Luca Sangiorgi, Graziano Pesole, Federico Zambelli
2021 J jnl
Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities.
Briefings Bioinform.
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
2021 J jnl
VINYL: Variant prIoritizatioN bY survivaL analysis.
Bioinform.
Matteo Chiara, Pietro Mandreoli, Marco Antonio Tangaro, Anna Maria D'Erchia, Sandro Sorrentino, Cinzia Forleo, David Stephen Horner, Federico Zambelli, Graziano Pesole
2020 J jnl
Critical assessment of bioinformatics methods for the characterization of pathological repeat expansions with single-molecule sequencing data.
Briefings Bioinform.
Matteo Chiara, Federico Zambelli, Ernesto Picardi, David Stephen Horner, Graziano Pesole
2020 J jnl
ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community.
BMC Bioinform.
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
2018 J jnl
INDIGO-DataCloud: a Platform to Facilitate Seamless Access to E-Infrastructures.
J. Grid Comput.
Davide Salomoni, Isabel Campos Plasencia, Luciano Gaido, Jesús E. Marco de Lucas, P. Solagna, Jorge Gomes, Ludek Matyska, P. Fuhrman, Marcus Hardt, Giacinto Donvito, Lukasz Dutka, Marcin Plóciennik, Roberto Barbera, Ignacio Blanquer, Andrea Ceccanti, Eva Cetinic, Mário David, Doina Cristina Duma, Álvaro López García, Germán Moltó, Pablo Orviz Fernández, Zdenek Sustr, Matthew Viljoen, Fernando Aguilar, Luís Alves, Marica Antonacci, Lucio Angelo Antonelli, Stefano Bagnasco, A. Bonving, Riccardo Bruno, Y. Chen, Alessandro Costa, Davor Davidovic, Benjamin Ertl, Marco Fargetta, Sandro Fiore, S. Gallozzi, Z. Kurkcuoglu, Lara Lloret Iglesias, J. Martins, Alessandra Nuzzo, Paola Nassisi, Cosimo Palazzo, João Murta Pina, Eva Sciacca, Daniele Spiga, Marco Antonio Tangaro, Michal Urbaniak, Sara Vallero, Bas Wegh, Valentina Zaccolo, Federico Zambelli, Tomasz Zok
2016 J jnl
Tools and data services registry: a community effort to document bioinformatics resources.
Nucleic Acids Res.
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. Jiménez, 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
2013 J jnl
Motif discovery and transcription factor binding sites before and after the next-generation sequencing era.
Briefings Bioinform.
Federico Zambelli, Graziano Pesole, Giulio Pavesi
2013 J jnl
PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments.
Nucleic Acids Res.
Federico Zambelli, Graziano Pesole, Giulio Pavesi
2013 J jnl
SpliceAid-F: a database of human splicing factors and their RNA-binding sites.
Nucleic Acids Res.
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
2012 J jnl
Cscan: finding common regulators of a set of genes by using a collection of genome-wide ChIP-seq datasets.
Nucleic Acids Res.
Federico Zambelli, Gian Marco Prazzoli, Graziano Pesole, Giulio Pavesi
2011 — conf
A Faster Algorithm for Motif Finding in Sequences from ChIP-Seq Data.
CIBB
Federico Zambelli, Giulio Pavesi
2011 J jnl
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing.
Nucleic Acids Res.
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
2009 J jnl
Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes.
Nucleic Acids Res.
Federico Zambelli, Graziano Pesole, Giulio Pavesi
2007 — conf
Prediction of over Represented Transcription Factor Binding Sites in Co-regulated Genes Using Whole Genome Matching Statistics.
WILF
Giulio Pavesi, Federico Zambelli
2007 J jnl
WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences.
BMC Bioinform.
Giulio Pavesi, Federico Zambelli, Graziano Pesole
2006 J jnl
MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes.
Nucleic Acids Res.
Giulio Pavesi, Paolo Mereghetti, Federico Zambelli, Marco Stefani, Giancarlo Mauri, Graziano Pesole