Coalescent-Based DNA Barcoding: Multilocus Analysis and Robustness. - Olivier David; Catherine Larédo; Raphaël Leblois; Brigitte Schaeffer; Nicolas Vergne (J. Comput. Biol., 2012)

SMM: An R Package for Estimation and Simulation of Discrete-time semi-Markov Models. - Vlad Stefan Barbu; Caroline Bérard; Dominique Cellier; Mathilde Sautreuil; Nicolas Vergne (R J., 2018)

Improving high-resolution copy number variation analysis from next generation sequencing using unique molecular identifiers. - Pierre-Julien Viailly; Vincent Sater; Mathieu Viennot; Élodie Bohers; Nicolas Vergne; Caroline Bérard; Hélène Dauchel; Thierry Lecroq; Alison Celebi; Philippe Ruminy; Vinciane Marchand; Marie-Delphine Lanic; et al. (BMC Bioinform., 2021)

smmR: A Semi-Markov R package. - Vlad Stefan Barbu; Florian Lecocq; Corentin Lothodé; Nicolas Vergne (J. Open Source Softw., 2023)

dsmmR: Estimation and Simulation of Drifting Semi-Markov Models. - Vlad Stefan Barbu; Ioannis Mavrogiannis; Nicolas Vergne (J. Open Source Softw., 2024)