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Catanzaro Daniele, Frohn Martin, Gascuel Olivier, and Pesenti Raffaele. 2022. “A Tutorial on the Balanced Minimum Evolution Problem”. EUROPEAN JOURNAL OF OPERATIONAL RESEARCH 300 (July): 1–19. doi:10.1016/j.ejor.2021.08.004.

Lefort Vincent, Longueville Jean-Emmanuel, and Gascuel Olivier. 2017. “SMS: Smart Model Selection in PhyML”. Molecular Biology and Evolution 34 (September): 2422–2424. doi:10.1093/molbev/msx149.

Cassan Elodie, Arigon-Chifolleau Anne-Muriel, Mesnard Jean-Michel, Gros Antoine, and Gascuel Olivier. 2017. “The Tenth Gene of HIV”. M S-Medecine Sciences 33 (May): 484–485. doi:10.1051/medsci/20173305008.

Saulnier Emma, Gascuel Olivier, and Alizon Samuel. 2017. “Inferring Epidemiological Parameters from Phylogenies Using Regression-ABC: A Comparative Study”. Plos Computational Biology 13 (March): e1005416. doi:10.1371/journal.pcbi.1005416.

Lebre Sophie, and Gascuel Olivier. 2017. “The Combinatorics of Overlapping Genes”. Journal of Theoretical Biology 415 (February): 90–101. doi:10.1016/j.jtbi.2016.09.018.

Villabona-Arenas Christian Julian, Vidal Nicole, Guichet Emilande, Serrano Laetitia, Delaporte Eric, Gascuel Olivier, and Peeters Martine. 2016. “In-Depth Analysis of HIV-1 Drug Resistance Mutations in HIV-Infected Individuals Failing First-Line Regimens in West and Central Africa”. Aids 30 (November): 2577–2589. doi:10.1097/QAD.0000000000001233.

Cassan Elodie, Arigon-Chifolleau Anne-Muriel, Mesnard Jean-Michel, Gross Antoine, and Gascuel Olivier. 2016. “Concomitant Emergence of the Antisense Protein Gene of HIV-1 and of the Pandemic”. Proceedings of the National Academy of Sciences of the United States of America 113 (October): 11537–11542. doi:10.1073/pnas.1605739113.

Gascuel Olivier, and Steel Mike. 2016. “A ’Stochastic Safety Radius’ for Distance-Based Tree Reconstruction”. Algorithmica 74 (April): 1386–1403. doi:10.1007/s00453-015-0005-y.

Binet Manuel, Gascuel Olivier, Scornavacca Celine, Douzery Emmanuel J. P., and Pardi Fabio. 2016. “Fast and Accurate Branch Lengths Estimation for Phylogenomic Trees”. Bmc Bioinformatics 17 (January): 23. doi:10.1186/s12859-015-0821-8.

To Thu-Hien, Jung Matthieu, Lycett Samantha, and Gascuel Olivier. 2016. “Fast Dating Using Least-Squares Criteria and Algorithms”. Systematic Biology 65 (January): 82–97. doi:10.1093/sysbio/syv068.

Lefort Vincent, Desper Richard, and Gascuel Olivier. 2015. “FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program”. Molecular Biology and Evolution 32 (October): 2798–2800. doi:10.1093/molbev/msv150.

Mourad Raphael, Chevennet Francois, Dunn David T., Fearnhill Esther, Delpech Valerie, Asboe David, Gascuel Olivier, and Hue Stephane. 2015. “A Phylotype-Based Analysis Highlights the Role of Drug-Naive HIV-Positive Individuals in the Transmission of Antiretroviral Resistance in the UK”. Aids 29 (September): 1917–1925. doi:10.1097/QAD.0000000000000768.

Gascuel Olivier, and Steel Mike. 2014. “Predicting the Ancestral Character Changes in a Tree Is Typically Easier Than Predicting the Root State”. Systematic Biology 63 (January): 421–435. doi:10.1093/sysbio/syu010.

Schaper Elke, Gascuel Olivier, and Anisimova Maria. 2014. “Deep Conservation of Human Protein Tandem Repeats Within the Eukaryotes”. Molecular Biology and Evolution 31 (January): 1132–1148. doi:10.1093/molbev/msu062.

Chevenet Francois, Jung Matthieu, Peeters Martine, deOliveira Tulio, and Gascuel Olivier. 2013. “Searching for Virus Phylotypes”. Bioinformatics 29 (January): 561–570. doi:10.1093/bioinformatics/btt010.

Pardi Fabio, and Gascuel Olivier. 2012. “Combinatorics of Distance-Based Tree Inference”. Proceedings of the National Academy of Sciences of the United States of America 109 (January): 16443–16448. doi:10.1073/pnas.1118368109.

Le Si Quang, Dang Cuong Cao, and Gascuel Olivier. 2012. “Modeling Protein Evolution With Several Amino Acid Replacement Matrices Depending on Site Rates”. Molecular Biology and Evolution 29 (January): 2921–2936. doi:10.1093/molbev/mss112.

Jung Matthieu, Leye Nafissatou, Vidal Nicole, Fargette Denis, Diop Halimatou, Kane Coumba Toure, Gascuel Olivier, and Peeters Martine. 2012. “The Origin and Evolutionary History of HIV-1 Subtype C in Senegal”. Plos One 7 (January): e33579. doi:10.1371/journal.pone.0033579.

Mooers Arne, Gascuel Olivier, Stadler Tanja, Li Heyang, and Steel Mike. 2012. “Branch Lengths on Birth-Death Trees and the Expected Loss of Phylogenetic Diversity”. Systematic Biology 61 (January): 195–203. doi:10.1093/sysbio/syr090.

Lajoie Mathieu, Gascuel Olivier, Lefort Vincent, and Brehelin Laurent. 2012. “Computational Discovery of Regulatory Elements in a Continuous Expression Space”. Genome Biology 13 (January): R109. doi:10.1186/gb-2012-13-11-r109.