CoCo: a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data. - Charles Girardot; Oleg Sklyar; Sophie Grosz; Wolfgang Huber; Eileen E. M. Furlong (Bioinform., 2007)

Comparing and Analysing Gene Expression Patterns Across Animal Species Using 4DXpress. - Yannick Haudry; Chuang Kee Ong; Laurence Ettwiller; Hugo Bérubé; Ivica Letunic; Misha Kapushesky; Paul-Daniel Weeber; Xi Wang; Julien Gagneur; Charles Girardot; Detlev Arendt; Peer Bork; et al. (APBC, 2008)

4DXpress: a database for cross-species expression pattern comparisons. - Yannick Haudry; Hugo Bérubé; Ivica Letunic; Paul-Daniel Weeber; Julien Gagneur; Charles Girardot; Misha Kapushesky; Detlev Arendt; Peer Bork; Alvis Brazma; Eileen E. M. Furlong; Joachim Wittbrodt; et al. (Nucleic Acids Res., 2008)

Model-based method for transcription factor target identification with limited data. - Antti Honkela; Charles Girardot; Eleanor Hilary Gustafson; Ya-Hsin Liu; Eileen E. M. Furlong; Neil D. Lawrence; Magnus Rattray (Proc. Natl. Acad. Sci. USA, 2010)

Déchiffrement de l'activité des séquences cis-régulatrices chez la Drosophile basé sur la localisation des facteurs de transcription et la caractérisation de l'état de la chromatine. (Deciphering enhancer activity in Drosophila based on transcription factor occupancy and chromatin state chromatin state characterization). - Charles Girardot (2012)

Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers. - Charles Girardot; Jelle Scholtalbers; Sajoscha Sauer; Shu-Yi Su; Eileen E. M. Furlong (BMC Bioinform., 2016)

Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes. - Abibatou Mbodj; Eleanor Hilary Gustafson; Lucia Ciglar; Guillaume Junion; Aitor González; Charles Girardot; Laurent Perrin; Eileen E. M. Furlong; Denis Thieffry (PLoS Comput. Biol., 2016)

Dynamix: dynamic visualization by automatic selection of informative tracks from hundreds of genomic datasets. - Matthias Monfort; Eileen E. M. Furlong; Charles Girardot (Bioinform., 2017)