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2026	Trends in substitution models of protein evolution for phylogenetic inference Molecular Phylogenetics and Evolution David Ferreiro, Elena Pazos, Miguel Arenas
2025	Site-Specific Structure and Stability Constrained Substitution Models Improve Phylogenetic Inference Systematic Biology Ivan Lorca-Alonso, Fernando Otero-de-Navascues, Miguel Arenas, Ugo Bastolla
2024	Substitution Models of Protein Evolution with Selection on Enzymatic Activity Molecular Biology and Evolution David Ferreiro, Ruqaiya Khalil, Sergio F Sousa, Miguel Arenas
2024	Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation Bioinformatics David Ferreiro, Catarina Branco, Miguel Arenas
2023	Influence of substitution model selection on protein phylogenetic tree reconstruction Gene Roberto Del Amparo, Miguel Arenas
2023	Consequences of Genetic Recombination on Protein Folding Stability Journal of Molecular Evolution Roberto Del Amparo, Luis Daniel González-Vázquez, Laura Rodríguez-Moure, Ugo Bastolla, Miguel Arenas
2023	Proteome-Wide Structural Computations Provide Insights into Empirical Amino Acid Substitution Matrices International Journal of Molecular Sciences Pablo Aledo, Juan Carlos Aledo
2022	Methods in Molecular Biology Miguel Arenas
2022	Consequences of Substitution Model Selection on Protein Ancestral Sequence Reconstruction Molecular Biology and Evolution Roberto Del Amparo, Miguel Arenas
2021	Analysis of selection in protein-coding sequences accounting for common biases Briefings in Bioinformatics Roberto Del Amparo, Catarina Branco, Jesús Arenas, Alberto Vicens, Miguel Arenas
2021	A thermodynamic model of protein structure evolution explains empirical amino acid substitution matrices Protein Science Christoffer Norn, Ingemar André, Douglas L. Theobald
2020	The influence of heterogeneous codon frequencies along sequences on the estimation of molecular adaptation Bioinformatics Roberto Del Amparo, Alberto Vicens, Miguel Arenas
2020	Protein Evolution in the Flaviviruses Journal of Molecular Evolution Miguel Arenas
2020	ProtASR2: Ancestral reconstruction of protein sequences accounting for folding stability Methods in Ecology and Evolution Miguel Arenas, Ugo Bastolla
2019	mtProtEvol: the resource presenting molecular evolution analysis of proteins involved in the function of Vertebrate mitochondria BMC Evolutionary Biology Anastasia A. Kuzminkova, Anastasia D. Sokol, Kristina E. Ushakova, Konstantin Yu. Popadin, Konstantin V. Gunbin
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