Models and algorithms for genome rearrangement with positional constraints. - Krister M. Swenson; Pijus Simonaitis; Mathieu Blanchette (Algorithms Mol. Biol., 2016)

(Re)introducing Regular Graph Languages. - Sorcha Gilroy; Adam Lopez; Sebastian Maneth; Pijus Simonaitis (MOL, 2017)

Rearrangement Scenarios Guided by Chromatin Structure. - Sylvain Pulicani; Pijus Simonaitis; Eric Rivals; Krister M. Swenson (RECOMB-CG, 2017)

Finding local genome rearrangements. - Pijus Simonaitis; Krister M. Swenson (Algorithms Mol. Biol., 2018)

A framework for cost-constrained genome rearrangement under Double Cut and Join. - Pijus Simonaitis; Annie Chateau; Krister M. Swenson (CoRR, 2018)

Weighted Minimum-Length Rearrangement Scenarios. - Pijus Simonaitis; Annie Chateau; Krister M. Swenson (WABI, 2019)

A general framework for genome rearrangement with biological constraints. - Pijus Simonaitis; Annie Chateau; Krister M. Swenson (Algorithms Mol. Biol., 2019)

Weighted Genome Rearrangements. (Scénarios évolutifs pondérés de réarrangements génomiques). - Pijus Simonaitis (2020)

A Maximum Parsimony Principle for Multichromosomal Complex Genome Rearrangements. - Pijus Simonaitis; Benjamin J. Raphael (WABI, 2022)