A Fast Algorithm for NA Secondary Structure Prediction Including Pseudoknots. - Fariza Tahi; Stefan Engelen; Mireille Régnier (BIBE, 2003)

An Open Problem in RNA Secondary Structure Prediction by the Comparative Approach. - Stefan Engelen; Fariza Tahi (METMBS, 2004)

P-dcfold or How to Predict all Kinds of Pseudoknots in Rna Secondary Structures. - Fariza Tahi; Stefan Engelen; Mireille Régnier (Int. J. Artif. Intell. Tools, 2005)

Predicting RNA secondary structure by the comparative approach: how to select the homologous sequences. - Stefan Engelen; Fariza Tahi (BMC Bioinform., 2007)

Information Content of Sets of Biological Sequences Revisited. - Alessandra Carbone; Stefan Engelen (Algorithmic Bioprocesses, 2009)

MicroScope: a platform for microbial genome annotation and comparative genomics. - David Vallenet; Stefan Engelen; Damien Mornico; Stéphane Cruveiller; Ludovic Fleury; Aurélie Lajus; Zoé Rouy; David Roche; Gregory Salvignol; Claude Scarpelli; Claudine Médigue (Database J. Biol. Databases Curation, 2009)

Joint Evolutionary Trees: A Large-Scale Method To Predict Protein Interfaces Based on Sequence Sampling. - Stefan Engelen; Ladislas A. Trojan; Sophie Sacquin-Mora; Richard Lavery; Alessandra Carbone (PLoS Comput. Biol., 2009)

MicroScope - an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. - David Vallenet; Eugeni Belda; Alexandra Calteau; Stéphane Cruveiller; Stefan Engelen; Aurélie Lajus; François Le Fèvre; Cyrille Longin; Damien Mornico; David Roche; Zoé Rouy; Gregory Salvignol; et al. (Nucleic Acids Res., 2013)

TE-Tracker: systematic identification of transposition events through whole-genome resequencing. - Arthur Gilly; Mathilde Etcheverry; Mohammed-Amin Madoui; Julie Guy; Leandro Quadrana; Adriana Alberti; Antoine Martin; Tony Heitkam; Stefan Engelen; Karine Labadie; Jeremie Le Pen; Patrick Wincker; et al. (BMC Bioinform., 2014)

BoardION: real-time monitoring of Oxford Nanopore sequencing instruments. - Aimeric Bruno; Jean-Marc Aury; Stefan Engelen (BMC Bioinform., 2021)