Data handling strategies for high throughput pyrosequencers. - Gabriele Antonio Trombetti; Raoul Jean Pierre Bonnal; Ermanno Rizzi; Gianluca De Bellis; Luciano Milanesi (BMC Bioinform., 2007)

BioRuby: bioinformatics software for the Ruby programming language. - Naohisa Goto; Pjotr Prins; Mitsuteru Nakao; Raoul Jean Pierre Bonnal; Jan Aerts; Toshiaki Katayama (Bioinform., 2010)

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. - Toshiaki Katayama; Kazuharu Arakawa; Mitsuteru Nakao; Keiichiro Ono; Kiyoko F. Aoki-Kinoshita; Yasunori Yamamoto; Atsuko Yamaguchi; Shuichi Kawashima; Hong-Woo Chun; Jan Aerts; Bruno Aranda; Lord H. Barboza; et al. (J. Biomed. Semant., 2010)

RSSsite: a reference database and prediction tool for the identification of cryptic Recombination Signal Sequences in human and murine genomes. - Ivan Merelli; Alessandro Guffanti; Marco Fabbri; Andrea Cocito; Laura Furia; Ursula Grazini; Raoul Jean Pierre Bonnal; Luciano Milanesi; Fraser McBlane (Nucleic Acids Res., 2010)

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. - Toshiaki Katayama; Mark D. Wilkinson; Rutger A. Vos; Takeshi Kawashima; Shuichi Kawashima; Mitsuteru Nakao; Yasunori Yamamoto; Hong-Woo Chun; Atsuko Yamaguchi; Shin Kawano; Jan Aerts; Kiyoko F. Aoki-Kinoshita; et al. (J. Biomed. Semant., 2011)

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics. - Raoul Jean Pierre Bonnal; Jan Aerts; George Githinji; Naohisa Goto; Daniel MacLean; Chase A. Miller; Hiroyuki Mishima; Massimiliano Pagani; Ricardo Ramirez-Gonzalez; Geert Smant; Francesco Strozzi; Rob Syme; et al. (Bioinform., 2012)

The Ruby UCSC API: accessing the UCSC genome database using Ruby. - Hiroyuki Mishima; Jan Aerts; Toshiaki Katayama; Raoul Jean Pierre Bonnal; Koh-ichiro Yoshiura (BMC Bioinform., 2012)

Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments. - Ricardo Ramirez-Gonzalez; Raoul Jean Pierre Bonnal; Mario Cáccamo; Daniel MacLean (Source Code Biol. Medicine, 2012)

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. - Toshiaki Katayama; Mark D. Wilkinson; Kiyoko F. Aoki-Kinoshita; Shuichi Kawashima; Yasunori Yamamoto; Atsuko Yamaguchi; Shinobu Okamoto; Shin Kawano; Jin-Dong Kim; Yue Wang 040; Hongyan Wu; Yoshinobu Kano; et al. (J. Biomed. Semant., 2014)

Community-driven development for computational biology at Sprints, Hackathons and Codefests. - Steffen Möller; Enis Afgan; Michael Banck; Raoul Jean Pierre Bonnal; Timothy Booth; John Chilton; Peter J. A. Cock; Markus Gumbel; Nomi L. Harris; Richard C. G. Holland; Matús Kalas; László Kaján; et al. (BMC Bioinform., 2014)

miRiadne: a web tool for consistent integration of miRNA nomenclature. - Raoul Jean Pierre Bonnal; Riccardo L. Rossi; Donatella Carpi; Valeria Ranzani; Sergio Abrignani; Massimiliano Pagani (Nucleic Acids Res., 2015)

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation. - Jerven T. Bolleman; Christopher J. Mungall; Francesco Strozzi; Joachim Baran; Michel Dumontier; Raoul Jean Pierre Bonnal; Robert M. Buels; Robert Hoehndorf; Takatomo Fujisawa; Toshiaki Katayama; Peter J. A. Cock (J. Biomed. Semant., 2016)

Pipengine: an ultra light YAML-based pipeline execution engine. - Francesco Strozzi; Raoul Jean Pierre Bonnal (J. Open Source Softw., 2017)

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. - Toshiaki Katayama; Shuichi Kawashima; Gos Micklem; Shin Kawano; Jin-Dong Kim; Simon Kocbek; Shinobu Okamoto; Yue Wang 040; Hongyan Wu; Atsuko Yamaguchi; Yasunori Yamamoto; Erick Antezana; et al. (F1000Research, 2019)

BioHackathon 2015: Semantics of data for life sciences and reproducible research. - Rutger A. Vos; Toshiaki Katayama; Hiroyuki Mishima; Shin Kawano; Shuichi Kawashima; Jin-Dong Kim; Yuki Moriya; Toshiaki Tokimatsu; Atsuko Yamaguchi; Yasunori Yamamoto; Hongyan Wu; Peter Amstutz; et al. (F1000Research, 2020)

OligoMinerApp: a web-server application for the design of genome-scale oligonucleotide in situ hybridization probes through the flexible OligoMiner environment. - Marco Passaro; Martina Martinovic; Valeria Bevilacqua; Elliot A. Hershberg; Grazisa Rossetti; Brian J. Beliveau; Raoul Jean Pierre Bonnal; Massimiliano Pagani (Nucleic Acids Res., 2020)