NORINE: a database of nonribosomal peptides. - Ségolène Caboche; Maude Pupin; Valérie Leclère; Arnaud Fontaine; Philippe Jacques; Gregory Kucherov (Nucleic Acids Res., 2008)

MAGNOLIA: multiple alignment of protein-coding and structural RNA sequences. - Arnaud Fontaine; Antoine de Monte; Hélène Touzet (Nucleic Acids Res., 2008)

Computational identification of protein-coding sequences by comparative analysis. - Arnaud Fontaine; Hélène Touzet (Int. J. Data Min. Bioinform., 2009)

Classification d'ARN codants et d'ARN non-codants. - Arnaud Fontaine (2009)

On-Device Control Flow Verification for Java Programs. - Arnaud Fontaine; Samuel Hym; Isabelle Simplot-Ryl (ESSoS, 2011)

Verifiable Control Flow Policies for Java Bytecode. - Arnaud Fontaine; Samuel Hym; Isabelle Simplot-Ryl (Formal Aspects in Security and Trust, 2011)

A Generic Framework to Develop and Verify Security Mechanisms at the Microarchitectural Level: Application to Control-Flow Integrity. - Matthieu Baty; Pierre Wilke; Guillaume Hiet; Arnaud Fontaine; Alix Trieu (CSF, 2023)