The Ruby UCSC API: accessing the UCSC genome database using Ruby

by Mishima Hiroyuki, Aerts Jan, Katayama Toshiaki, Bonnal Raoul J P, Yoshiura Koh-ichiro
Published 2012-09-01

The Ruby UCSC API: accessing the UCSC genome database using Ruby

by Mishima, Hiroyuki, Aerts, Jan, Katayama, Toshiaki, Bonnal, Raoul J P, Yoshiura, Koh-ichiro
Published 2012

A Simplified Amino Acidic Alphabet to Unveil the T-Cells Receptors Antigens: A Computational Perspective

by Iannuzzi, Raffaele, Rossetti, Grazisa, Spitaleri, Andrea, Bonnal, Raoul J. P., Pagani, Massimiliano, Mollica, Luca
Published in Front Chem (2021)

miRiadne: a web tool for consistent integration of miRNA nomenclature

by Bonnal, Raoul J. P., Rossi, Riccardo L., Carpi, Donatella, Ranzani, Valeria, Abrignani, Sergio, Pagani, Massimiliano
Published in Nucleic Acids Res (2015)

Sharing Programming Resources Between Bio* Projects

by Bonnal, Raoul J. P., Yates, Andrew, Goto, Naohisa, Gautier, Laurent, Willis, Scooter, Fields, Christopher, Katayama, Toshiaki, Prins, Pjotr
Published in Methods Mol Biol (2019)

De novo transcriptome profiling of highly purified human lymphocytes primary cells

by Bonnal, Raoul J.P., Ranzani, Valeria, Arrigoni, Alberto, Curti, Serena, Panzeri, Ilaria, Gruarin, Paola, Abrignani, Sergio, Rossetti, Grazisa, Pagani, Massimiliano
Published in Sci Data (2015)

OligoMinerApp: a web-server application for the design of genome-scale oligonucleotide in situ hybridization probes through the flexible OligoMiner environment

by Passaro, Marco, Martinovic, Martina, Bevilacqua, Valeria, Hershberg, Elliot A, Rossetti, Grazisa, Beliveau, Brian J, Bonnal, Raoul J P, Pagani, Massimiliano
Published in Nucleic Acids Res (2020)

Whole-Genome Pyrosequencing of an Epidemic Multidrug-Resistant Acinetobacter baumannii Strain Belonging to the European Clone II Group

by Iacono, Michele, Villa, Laura, Fortini, Daniela, Bordoni, Roberta, Imperi, Francesco, Bonnal, Raoul J. P., Sicheritz-Ponten, Thomas, De Bellis, Gianluca, Visca, Paolo, Cassone, Antonio, Carattoli, Alessandra
Published 2008

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation

by 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 J Biomed Semantics (2016)

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics

by Bonnal, Raoul J.P., Aerts, Jan, Githinji, George, Goto, Naohisa, MacLean, Dan, Miller, Chase A., Mishima, Hiroyuki, Pagani, Massimiliano, Ramirez-Gonzalez, Ricardo, Smant, Geert, Strozzi, Francesco, Syme, Rob, Vos, Rutger, Wennblom, Trevor J., Woodcroft, Ben J., Katayama, Toshiaki, Prins, Pjotr
Published 2012

Transcriptional Landscape of Human Tissue Lymphocytes Unveils Uniqueness of Tumor-Infiltrating T Regulatory Cells

by 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 (2016)

BioHackathon 2015: Semantics of data for life sciences and reproducible research

by Vos, Rutger A., Katayama, Toshiaki, Mishima, Hiroyuki, Kawano, Shin, Kawashima, Shuichi, Kim, Jin-Dong, Moriya, Yuki, Tokimatsu, Toshiaki, Yamaguchi, Atsuko, Yamamoto, Yasunori, Wu, Hongyan, Amstutz, Peter, Antezana, Erick, Aoki, Nobuyuki P., Arakawa, Kazuharu, Bolleman, Jerven T., Bolton, Evan, Bonnal, Raoul J. P., Bono, Hidemasa, Burger, Kees, Chiba, Hirokazu, Cohen, Kevin B., Deutsch, Eric W., Fernández-Breis, Jesualdo T., Fu, Gang, Fujisawa, Takatomo, Fukushima, Atsushi, García, Alexander, Goto, Naohisa, Groza, Tudor, Hercus, Colin, Hoehndorf, Robert, Itaya, Kotone, Juty, Nick, Kawashima, Takeshi, Kim, Jee-Hyub, Kinjo, Akira R., Kotera, Masaaki, Kozaki, Kouji, Kumagai, Sadahiro, Kushida, Tatsuya, Lütteke, Thomas, Matsubara, Masaaki, Miyamoto, Joe, Mohsen, Attayeb, Mori, Hiroshi, Naito, Yuki, Nakazato, Takeru, Nguyen-Xuan, Jeremy, Nishida, Kozo, Nishida, Naoki, Nishide, Hiroyo, Ogishima, Soichi, Ohta, Tazro, Okuda, Shujiro, Paten, Benedict, Perret, Jean-Luc, Prathipati, Philip, Prins, Pjotr, Queralt-Rosinach, Núria, Shinmachi, Daisuke, Suzuki, Shinya, Tabata, Tsuyosi, Takatsuki, Terue, Taylor, Kieron, Thompson, Mark, Uchiyama, Ikuo, Vieira, Bruno, Wei, Chih-Hsuan, Wilkinson, Mark, Yamada, Issaku, Yamanaka, Ryota, Yoshitake, Kazutoshi, Yoshizawa, Akiyasu C., Dumontier, Michel, Kosaki, Kenjiro, Takagi, Toshihisa
Published in F1000Res (2020)