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)

easyRNASeq: a bioconductor package for processing RNA-Seq data. - Nicolas Delhomme; Ismaël Padioleau; Eileen E. M. Furlong; Lars M. Steinmetz (Bioinform., 2012)

Predicting Spatial and Temporal Gene Expression Using an Integrative Model of Transcription Factor Occupancy and Chromatin State. - Bartek Wilczynski; Ya-Hsin Liu; Zhen Xuan Yeo; Eileen E. M. Furlong (PLoS Comput. Biol., 2012)

FourCSeq: analysis of 4C sequencing data. - Felix A. Klein; Tibor Pakozdi; Simon Anders; Yad Ghavi-Helm; Eileen E. M. Furlong; Wolfgang Huber (Bioinform., 2015)

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)