A program for prediction of protein secondary structure from nucleotide sequence data: application to histocompatibility antigens. - Jiri Novotny; Charles Auffray (Nucleic Acids Res., 1984)

Issues in Computational Methods for Functional Genomics and Systems Biology. - Magali Roux-Rouquié; Leroy E. Hood; Sandrine Imbeaud; Charles Auffray (CMSB, 2003)

The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms. - Motohiko Tanino; Marie-Anne Debily; Takuro Tamura; Teruyoshi Hishiki; Osamu Ogasawara; Katsuji Murakawa; Shoko Kawamoto; Kouichi Itoh; Shinya Watanabe; Sandro José de Souza; Sandrine Imbeaud; Esther Graudens; et al. (Nucleic Acids Res., 2005)

Computational disease modeling - fact or fiction? - Jesper Tegnér; Albert Compte; Charles Auffray; Gary An; Gunnar Cedersund; Gilles Clermont; Boris S. Gutkin; Zoltán N. Oltvai; Klaas Enno Stephan; Randy Thomas; Pablo Villoslada (BMC Syst. Biol., 2009)

Affinity analysis of differentially expressed genes in hepatocytes expressing HCV core genotype 1b or 3a. - Tommaso Mazza; Stefano Castellana; Angelo Andriulli; Charles Auffray; Manlio Vinciguerra; Valerio Pazienza (Biosyst., 2013)

Representing and querying disease networks using graph databases. - Artem Lysenko; Irina A. Roznovat; Mansoor A. S. Saqi; Alexander Mazein; Christopher J. Rawlings; Charles Auffray (BioData Min., 2016)

STON: exploring biological pathways using the SBGN standard and graph databases. - Vasundra Touré; Alexander Mazein; Dagmar Waltemath; Irina Balaur; Mansoor A. S. Saqi; Ron Henkel; Johann Pellet; Charles Auffray (BMC Bioinform., 2016)

EpiGeNet: A Graph Database of Interdependencies Between Genetic and Epigenetic Events in Colorectal Cancer. - Irina Balaur; Mansoor A. S. Saqi; Ana Barat; Artem Lysenko; Alexander Mazein; Christopher J. Rawlings; Heather J. Ruskin; Charles Auffray (J. Comput. Biol., 2017)

A computational framework for complex disease stratification from multiple large-scale datasets. - Bertrand De Meulder; Diane Lefaudeux; Aruna T. Bansal; Alexander Mazein; Amphun Chaiboonchoe; Hassan Ahmed; Irina Balaur; Mansoor A. S. Saqi; Johann Pellet; Stéphane Ballereau; Nathanaël Lemonnier; Kai Sun 005; et al. (BMC Syst. Biol., 2018)

Community-driven roadmap for integrated disease maps. - Marek Ostaszewski; Stephan Gebel; Inna Kuperstein; Alexander Mazein; Andrei Yu. Zinovyev; Ugur Dogrusoz; Jan Hasenauer; Ronan M. T. Fleming; Nicolas Le Novère; Piotr Gawron; Thomas S. Ligon; Anna Niarakis; et al. (Briefings Bioinform., 2019)

Navigating the disease landscape: knowledge representations for contextualizing molecular signatures. - Mansoor A. S. Saqi; Artem Lysenko; Yike Guo; Tatsuhiko Tsunoda; Charles Auffray (Briefings Bioinform., 2019)

Human-like layout algorithms for signalling hypergraphs: outlining requirements. - Martin Siebenhaller; Sune S. Nielsen; Fintan McGee; Irina Balaur; Charles Auffray; Alexander Mazein (Briefings Bioinform., 2020)

Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps. - Hasan Balci; Metin Can Siper; Nasim Saleh; Ilkin Safarli; Ludovic Roy; Merve Kilicarslan; Rumeysa Ozaydin; Alexander Mazein; Charles Auffray; Özgün Babur; Emek Demir; Ugur Dogrusoz (Bioinform., 2021)

GraphML-SBGN bidirectional converter for metabolic networks. - Irina Balaur; Ludovic Roy; Vasundra Touré; Alexander Mazein; Charles Auffray (J. Integr. Bioinform., 2022)