Whole-Genome Pyrosequencing of an Epidemic Multidrug-Resistant Acinetobacter baumannii Strain Belonging to the European Clone II Group
IACONO, Michele, VILLA, Laura, CARATTOLI, Alessandra, FORTINI, Daniela, BORDONI, Roberta, IMPERI, Francesco, BONNAL, Raoul J. P, SICHERITZ-PONTEN, Thomas, DE BELLIS, Gianluca, VISCA, Paolo, CASSONE, Antonio
Published in Antimicrobial Agents and Chemotherapy (01.07.2008)
Published in Antimicrobial Agents and Chemotherapy (01.07.2008)
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Novel interferon-sensitive genes unveiled by correlation-driven gene selection and systems biology
Cheroni, Cristina, Manganaro, Lara, Donnici, Lorena, Bevilacqua, Valeria, Bonnal, Raoul J. P., Rossi, Riccardo L., De Francesco, Raffaele
Published in Scientific reports (10.09.2021)
Published in Scientific reports (10.09.2021)
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Publisher Correction: Novel interferon-sensitive genes unveiled by correlation-driven gene selection and systems biology
Cheroni, Cristina, Manganaro, Lara, Donnici, Lorena, Bevilacqua, Valeria, Bonnal, Raoul J. P., Rossi, Riccardo L., De Francesco, Raffaele
Published in Scientific reports (30.09.2021)
Published in Scientific reports (30.09.2021)
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Transcriptional Landscape of Human Tissue Lymphocytes Unveils Uniqueness of Tumor-Infiltrating T Regulatory Cells
De Simone, Marco, Arrigoni, Alberto, Rossetti, Grazisa, Gruarin, Paola, Ranzani, Valeria, Politano, Claudia, Bonnal, Raoul J.P., Provasi, Elena, Sarnicola, Maria Lucia, Panzeri, Ilaria, Moro, Monica, Crosti, Mariacristina, Mazzara, Saveria, Vaira, Valentina, Bosari, Silvano, Palleschi, Alessandro, Santambrogio, Luigi, Bovo, Giorgio, Zucchini, Nicola, Totis, Mauro, Gianotti, Luca, Cesana, Giancarlo, Perego, Roberto A., Maroni, Nirvana, Pisani Ceretti, Andrea, Opocher, Enrico, De Francesco, Raffaele, Geginat, Jens, Stunnenberg, Hendrik G., Abrignani, Sergio, Pagani, Massimiliano
Published in Immunity (Cambridge, Mass.) (15.11.2016)
Published in Immunity (Cambridge, Mass.) (15.11.2016)
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Clonally expanded EOMES+ Tr1-like cells in primary and metastatic tumors are associated with disease progression
Bonnal, Raoul J. P., Rossetti, Grazisa, Lugli, Enrico, De Simone, Marco, Gruarin, Paola, Brummelman, Jolanda, Drufuca, Lorenzo, Passaro, Marco, Bason, Ramona, Gervasoni, Federica, Della Chiara, Giulia, D’Oria, Claudia, Martinovic, Martina, Curti, Serena, Ranzani, Valeria, Cordiglieri, Chiara, Alvisi, Giorgia, Mazza, Emilia Maria Cristina, Oliveto, Stefania, Silvestri, Ylenia, Carelli, Elena, Mazzara, Saveria, Bosotti, Roberto, Sarnicola, Maria Lucia, Godano, Chiara, Bevilacqua, Valeria, Lorenzo, Mariangela, Siena, Salvatore, Bonoldi, Emanuela, Sartore-Bianchi, Andrea, Amatu, Alessio, Veronesi, Giulia, Novellis, Pierluigi, Alloisio, Marco, Giani, Alessandro, Zucchini, Nicola, Opocher, Enrico, Ceretti, Andrea Pisani, Mariani, Nicolò, Biffo, Stefano, Prati, Daniele, Bardelli, Alberto, Geginat, Jens, Lanzavecchia, Antonio, Abrignani, Sergio, Pagani, Massimiliano
Published in Nature immunology (01.06.2021)
Published in Nature immunology (01.06.2021)
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The coding and long noncoding single-cell atlas of the developing human fetal striatum
Bocchi, Vittoria Dickinson, Conforti, Paola, Vezzoli, Elena, Besusso, Dario, Cappadona, Claudio, Lischetti, Tiziana, Galimberti, Maura, Ranzani, Valeria, Bonnal, Raoul J P, De Simone, Marco, Rossetti, Grazisa, He, Xiaoling, Kamimoto, Kenji, Espuny-Camacho, Ira, Faedo, Andrea, Gervasoni, Federica, Vuono, Romina, Morris, Samantha A, Chen, Jian, Felsenfeld, Dan, Pavesi, Giulio, Barker, Roger A, Pagani, Massimiliano, Cattaneo, Elena
Published in Science (American Association for the Advancement of Science) (07.05.2021)
Published in Science (American Association for the Advancement of Science) (07.05.2021)
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FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation
Bolleman, Jerven T, Mungall, Christopher J, Strozzi, Francesco, Baran, Joachim, Dumontier, Michel, Bonnal, Raoul J P, Buels, Robert, Hoehndorf, Robert, Fujisawa, Takatomo, Katayama, Toshiaki, Cock, Peter J A
Published in Journal of biomedical semantics (13.06.2016)
Published in Journal of biomedical semantics (13.06.2016)
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Role of microRNAs and long-non-coding RNAs in CD4+ T-cell differentiation
Pagani, Massimiliano, Rossetti, Grazisa, Panzeri, Ilaria, de Candia, Paola, Bonnal, Raoul J. P., Rossi, Riccardo L., Geginat, Jens, Abrignani, Sergio
Published in Immunological reviews (01.05.2013)
Published in Immunological reviews (01.05.2013)
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Journal Article
miRiadne: a web tool for consistent integration of miRNA nomenclature
Bonnal, Raoul J P, Rossi, Riccardo L, Carpi, Donatella, Ranzani, Valeria, Abrignani, Sergio, Pagani, Massimiliano
Published in Nucleic acids research (01.07.2015)
Published in Nucleic acids research (01.07.2015)
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Complete genome sequence of a serotype 11A, ST62 Streptococcus pneumoniae invasive isolate
Camilli, Romina, Bonnal, Raoul J P, Del Grosso, Maria, Iacono, Michele, Corti, Giorgio, Rizzi, Ermanno, Marchetti, Magda, Mulas, Laura, Iannelli, Francesco, Superti, Fabiana, Oggioni, Marco R, De Bellis, Gianluca, Pantosti, Annalisa
Published in BMC microbiology (01.02.2011)
Published in BMC microbiology (01.02.2011)
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Community-driven development for computational biology at Sprints, Hackathons and Codefests
Möller, Steffen, Afgan, Enis, Banck, Michael, Bonnal, Raoul J P, Booth, Timothy, Chilton, John, Cock, Peter J A, Gumbel, Markus, Harris, Nomi, Holland, Richard, Kalaš, Matúš, Kaján, László, Kibukawa, Eri, Powel, David R, Prins, Pjotr, Quinn, Jacqueline, Sallou, Olivier, Strozzi, Francesco, Seemann, Torsten, Sloggett, Clare, Soiland-Reyes, Stian, Spooner, William, Steinbiss, Sascha, Tille, Andreas, Travis, Anthony J, Guimera, Roman, Katayama, Toshiaki, Chapman, Brad A
Published in BMC bioinformatics (27.11.2014)
Published in BMC bioinformatics (27.11.2014)
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Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics
BONNAL, Raoul J. P, AERTS, Jan, STROZZI, Francesco, SYME, Rob, VOS, Rutger, WENNBLOM, Trevor J, WOODCROFT, Ben J, KATAYAMA, Toshiaki, PRINS, Pjotr, GITHINJI, George, GOTO, Naohisa, MACLEAN, Dan, MILLER, Chase A, MISHIMA, Hiroyuki, PAGANI, Massimiliano, RAMIREZ-GONZALEZ, Ricardo, SMANT, Geert
Published in Bioinformatics (Oxford, England) (01.04.2012)
Published in Bioinformatics (Oxford, England) (01.04.2012)
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Journal Article
De novo transcriptome profiling of highly purified human lymphocytes primary cells
Bonnal, Raoul J.P., Ranzani, Valeria, Arrigoni, Alberto, Curti, Serena, Panzeri, Ilaria, Gruarin, Paola, Abrignani, Sergio, Rossetti, Grazisa, Pagani, Massimiliano
Published in Scientific data (29.09.2015)
Published in Scientific data (29.09.2015)
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The Ruby UCSC API: accessing the UCSC genome database using Ruby
Mishima, Hiroyuki, Aerts, Jan, Katayama, Toshiaki, Bonnal, Raoul J P, Yoshiura, Koh-ichiro
Published in BMC bioinformatics (21.09.2012)
Published in BMC bioinformatics (21.09.2012)
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The long intergenic noncoding RNA landscape of human lymphocytes highlights the regulation of T cell differentiation by linc-MAF-4
Ranzani, Valeria, Rossetti, Grazisa, Panzeri, Ilaria, Arrigoni, Alberto, Bonnal, Raoul J P, Curti, Serena, Gruarin, Paola, Provasi, Elena, Sugliano, Elisa, Marconi, Maurizio, De Francesco, Raffaele, Geginat, Jens, Bodega, Beatrice, Abrignani, Sergio, Pagani, Massimiliano
Published in Nature immunology (01.03.2015)
Published in Nature immunology (01.03.2015)
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Computational pan-genomics: status, promises and challenges
Marschall, Tobias, Marz, Manja, Abeel, Thomas, Dijkstra, Louis, Dutilh, Bas E, Ghaffaari, Ali, Kersey, Paul, Kloosterman, Wigard P, Mäkinen, Veli, Novak, Adam M, Paten, Benedict, Porubsky, David, Rivals, Eric, Alkan, Can, Baaijens, Jasmijn A, Paul I W De Bakker, Boeva, Valentina, Bonnal, Raoul J P, Chiaromonte, Francesca, Chikhi, Rayan, Ciccarelli, Francesca D, Cijvat, Robin, Datema, Erwin, Van Duijn, Cornelia M, Eichler, Evan E, Ernst, Corinna, Eskin, Eleazar, Garrison, Erik, El-Kebir, Mohammed, Klau, Gunnar W, Korbel, Jan O, Eric-Wubbo Lameijer, Langmead, Benjamin, Martin, Marcel, Medvedev, Paul, Mu, John C, Neerincx, Pieter, Ouwens, Klaasjan, Peterlongo, Pierre, Pisanti, Nadia, Rahmann, Sven, Raphael, Ben, Reinert, Knut, de Ridder, Dick, de Ridder, Jeroen, Schlesner, Matthias, Schulz-Trieglaff, Ole, Sanders, Ashley D, Sheikhizadeh, Siavash, Shneider, Carl, Smit, Sandra, Valenzuela, Daniel, Wang, Jiayin, Wessels, Lodewyk, Zhang, Ying, Guryev, Victor, Vandin, Fabio, Ye, Kai, Schönhuth, Alexander
Published in Briefings in bioinformatics (01.01.2018)
Published in Briefings in bioinformatics (01.01.2018)
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Distinct microRNA signatures in human lymphocyte subsets and enforcement of the naive state in CD4 + T cells by the microRNA miR-125b
Abrignani, Sergio, Pagani, Massimiliano, Rossi, Riccardo L, Rossetti, Grazisa, Wenandy, Lynn, Curti, Serena, Ripamonti, Anna, Bonnal, Raoul J P, Birolo, Roberto Sciarretta, Moro, Monica, Crosti, Maria C, Gruarin, Paola, Maglie, Stefano, Marabita, Francesco, Mascheroni, Debora, Parente, Valeria, Comelli, Mario, Trabucchi, Emilio, De Francesco, Raffaele, Geginat, Jens
Published in Nature immunology (01.08.2011)
Published in Nature immunology (01.08.2011)
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Single cell-derived spheroids capture the self-renewing subpopulations of metastatic ovarian cancer
Velletri, Tania, Villa, Carlo Emanuele, Cilli, Domenica, Barzaghi, Bianca, Lo Riso, Pietro, Lupia, Michela, Luongo, Raffaele, López-Tobón, Alejandro, De Simone, Marco, Bonnal, Raoul J. P., Marelli, Luca, Piccolo, Stefano, Colombo, Nicoletta, Pagani, Massimiliano, Cavallaro, Ugo, Minucci, Saverio, Testa, Giuseppe
Published in Cell death and differentiation (01.03.2022)
Published in Cell death and differentiation (01.03.2022)
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OligoMinerApp: a web-server application for the design of genome-scale oligonucleotide in situ hybridization probes through the flexible OligoMiner environment
Passaro, Marco, Martinovic, Martina, Bevilacqua, Valeria, Hershberg, Elliot A, Rossetti, Grazisa, Beliveau, Brian J, Bonnal, Raoul J P, Pagani, Massimiliano
Published in Nucleic acids research (02.07.2020)
Published in Nucleic acids research (02.07.2020)
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