Publications

2025

  • Lorca-Alonso I, Otero-de-Navascues F, Arenas M, Bastolla U. 2025. Site-specific structure and stability constrained substitution models improve phylogenetic inference. Systematic Biology, in press.

2024

  • Ferreiro D, Khalil R, Sousa SF, Arenas M. 2024. Substitution Models of Protein Evolution with Selection on Enzymatic Activity. Molecular Biology and Evolution, 41(2), msae026.
  • Ferreiro D, Branco C, Arenas M. 2024. Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation. Bioinformatics, 40(3), btae096.
  • Uruén C, Fernandez A, Arnal JL, del Pozo M, Amoribieta MC, de Blas I, Jurado P, Calvo JH, Gottschalk M, González-Vázquez LD, Arenas M, Marín CM, Arenas J. 2024. Genomic and phenotypic analysis of invasive Streptococcus suis isolated in Spain reveals genetic diversification and associated virulence traits. Veterinary Research, 55:11.
  • Perez-Losada M, Castro-Nallar E, Arenas M. 2024. Microbial Sequence Typing Strategies for Genetic and Genomic Data. In Genetics and Evolution of Infectious Diseases (Third Edition). Ed, Tibayrenc M. Elsevier. Pp. 427-463.

2023

  • Del Amparo R, González‑Vázquez LD, Rodríguez‑Moure L, Bastolla U, Arenas M. 2023. Consequences of Genetic Recombination on Protein Folding Stability. Journal of Molecular Evolution, 91, 33–45.
  • González-Vázquez LD, Arenas M. 2023. Molecular Evolution of SARS-CoV-2 during the COVID-19 Pandemic. Genes, 14(2), 407.
  • Moreira F, Arenas M, Videira A, Pereira F. 2023. Evolution of TOP1 and TOP1MT Topoisomerases in Chordata. Journal of Molecular Evolution, 91, 192–203.
  • Del Amparo R, Arenas M. 2023. Influence of substitution model selection on protein phylogenetic tree reconstruction. Gene, 865, 147336.

2022

  • Ferreiro D, Khalil R, Gallego MJ, Osorio NS, Arenas M. 2022. The evolution of the HIV-1 protease folding stability. Virus Evolution, 8(2), veac115.
  • Del Amparo R, Arenas M. 2022. Consequences of substitution model selection on protein ancestral sequence reconstruction. Molecular Biology and Evolution, 39(7), msac144.
  • Arenas M. 2022. ProteinEvolverABC: Coestimation of Recombination and Substitution Rates in Protein Sequences by approximate Bayesian computation. Bioinformatics, 38(1), 58–64.
  • Moyano A, Blanch-Lombarte O, Tarancon-Diez L, Pedreño-Lopez N, Arenas M, Alvaro T, Casado C, Olivares I, Vera M, Rodriguez C, del Romero J, López-Galíndez C, Ruiz-Mateos E, Prado JG, Pernas M. 2022. Immunoescape of HIV-1 in Env-EL9 CD8 + T cell response restricted by HLA-B*14:02 in a Non progressor who lost twenty-seven years of HIV-1 control. Retrovirology, 19, 6.
  • Del Amparo R, Arenas M. 2022. HIV Protease and Integrase Empirical Substitution Models of Evolution: Protein-Specific Models Outperform Generalist Models. Genes, 13(1), 61.
  • Branco C, Kanellou M, González-Martín A, Arenas M. 2022. Consequences of the Last Glacial Period on the Genetic Diversity of Southeast Asians. Genes, 13(2), 384.
  • Moreira F, Arenas M, Videira A, Pereira F. 2022. Evolutionary history of TOPIIA topoisomerases in animals. Journal of Molecular Evolution, 90, 149–165.
  • Arenas M. 2022. Methodologies for Microbial Ancestral Sequence Reconstruction. In Environmental Microbial Evolution: Methods and Protocols. Ed, Luo, H. Springer. Pp. 283–303.
  • Baselga A, Gómez-Rodríguez C, Araújo MB, Castro-Insua A, Arenas M, Posada D, Vogler AP. 2022. Joint analysis of species and genetic variation to quantify the role of dispersal limitation and environmental constraint in community turnover. Ecography, e05808.

2021

  • Del Amparo R, Branco C, Arenas J, Vicens A, Arenas M. 2021. Analysis of selection in protein-coding sequences accounting for common biases. Briefings in Bioinformatics, 22(5), bbaa431.
  • Monteiro B, Arenas M, Prata MJ, Amorim A. 2021. Evolutionary dynamics of the human pseudoautosomal regions. PLoS Genetics, 17(4): e1009532.
  • Ferreiro D, Núñez-Estévez B, Canedo M, Branco C, Arenas M. 2021. Evaluating causes of current genetic gradients of modern humans of the Iberian Peninsula. Genome Biology and Evolution, 13(4), evab071.
  • Macedo A, Gómez C, Rebelo MÂ, Poza J, Gomes I, Martins S, Maturana-Candelas A, Pablo VG, Durães L, Sousa P, Figueruelo M, Rodriguez M, Pita C, Arenas M, Alvarez L, Hornero R, Lopes AM, Pinto N. 2021. Risk Variants in Three Alzheimer’s Disease Genes Show Association with EEG Endophenotypes. Journal of Alzheimer’s Disease, 80: 209–223.
  • Moreira F, Arenas M, Videira A, Pereira F. 2021. Molecular Evolution of DNA Topoisomerase III Beta (TOP3B) in Metazoa. Journal of Molecular Evolution, 89: 384–395.
  • Arenas M. 2021. General considerations for online teaching practices in bioinformatics in the time of COVID-19. Biochemistry and Molecular Biology Education, 49: 683–684.
  • Arenas M. 2021. Computational Analysis of Recombination in Viral Nucleotide Sequences. In Encyclopedia of Virology 4th Edition. Eds, Bamford D, Zuckerman M. Elsevier. Pp. 108–115.

2020

  • Arenas M. 2020. Protein Evolution in the Flaviviruses. Journal of Molecular Evolution, 88: 473–476.
  • Branco C, Ray N, Currat M, Arenas M. 2020. Influence of Paleolithic Range Contraction, Admixture and Long-Distance Dispersal on Genetic Gradients of Modern Humans in Asia. Molecular Ecology, 29: 2150–2159.
  • Del Amparo R, Vicens A, Arenas M. 2020. The Influence of Heterogeneous Codon Frequencies along Sequences on the Estimation of Molecular Adaptation. Bioinformatics, 36(2): 430–436.
  • Arenas M, Bastolla U. 2020. ProtASR2: Ancestral Reconstruction of Protein Sequences accounting for Folding Stability. Methods in Ecology and Evolution, 11: 248–257.
  • Arenas M, Gorostiza A, Baquero JM, Campoy E, Branco C, Rangel-Villalobos H, Gonzalez-Martin A. 2020. The Early Peopling of the Philippines based on mtDNA. Scientific Reports, 10:4901.
  • Perez-Losada M, Arenas M, Galan JC, Alma Bracho M, Hillung J, Garcia-Gonzalez N, Gonzalez-Candelas F. 2020. High-Throughput Sequencing (HTS) for the analysis of viral populations. Infection, Genetics and Evolution, 80:104208.
  • Lago-Docampo M, Tenorio J, Hernández-González I, Pérez-Olivares C, Escribano-Subías P, Pousada G, Baloira A, Arenas M, Lapunzina P, Valverde D. 2020. Characterization of rare ABCC8 variants identified in Spanish pulmonary arterial hypertension patients. Scientific Reports, 10:15135.
  • Rebelo MÂ, Gómez C, Gomes I, Poza J, Martins S, Maturana-Candelas A, Ruiz-Gómez SJ, Durães L, Sousa P, Figueruelo M, Rodríguez M, Pita C, Arenas M, Álvarez L, Hornero R, Pinto N, Lopes AM. 2020. Genome-Wide Scan for Five Brain Oscillatory Phenotypes Identifies a New QTL Associated with Theta EEG Band. Brain Sciences, 10(11):870.

2019

  • Pascual-Garcia A, Arenas M, Bastolla U. 2019. The molecular clock in the evolution of protein structures. Systematic Biology, 68(6): 987–1002.
  • Arenas M. 2019. Applications of the Coalescent for the Evolutionary Analysis of Genetic Data. In Encyclopedia of Bioinformatics and Computational Biology. Eds, Ranganathan S, Gribskov M, Nakai K, Schönbach C. Elsevier. Pp. 746–758.
  • Bastolla U, Arenas M. 2019. The Influence of Protein Stability on Sequence Evolution: Applications to Phylogenetic Inference. In Computational Methods in Protein Evolution. Ed, Sikosek T. Springer. Pp. 215–231.
  • Oliveira M, Arenas M, Pinto N, Amorim, A. 2019. Genética forense no humana. In Genetica Forense. Del laboratorio a los Tribunales. Eds, Crespillo MC, Barrio PA. Ediciones Diaz de Santos. Pp. 291-318.
  • Vicens A, Vinuesa P, Arenas M, Treviño CL. 2019. Analyzing the functional divergence of Slo1 and Slo3 channel subfamilies. Molecular Phylogenetics and Evolution, 133: 33–41.
  • Pimenta J, Lopes AM, Carracedo A, Arenas M, Amorim A, Comas D. 2019. Spatially explicit analysis reveals complex human genetic gradients in the Iberian Peninsula. Scientific Reports, 9:7825.
  • Negredo A, Habela MA, Ramírez de Arellano E, Diez F, Lasala F, López P, Sarria A, Labiod N, Calero-Bernal R, Arenas M, Tenorio A, Estrada A, Sánchez-Seco MP. 2019. Survey of Crimean-Congo Hemorrhagic Fever Enzootic Focus, Spain, 2011–2015. Emerging Infectious Diseases, 25(6): 1177-1184.
  • Illera JC, Arenas M, López-Sánchez CA, Obeso JR, Laiolo P. 2019. Gradual Distance Dispersal Shapes the Genetic Structure in an Alpine Grasshopper. Genes, 10(8):590.
  • Currat M, Arenas M, Quilodran CS, Excoffier L, Ray N. 2019. SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal. Bioinformatics, 35(21): 4480–4483.

2018

  • Branco C, Velasco M, Benguigui M, Currat M, Ray N, Arenas M. 2018. Consequences of Diverse Evolutionary Processes on American Genetic Gradients of Modern Humans. Heredity, 121(6): 548–556.
  • Branco C, Arenas M. 2018. Selecting among Alternative Scenarios of Human Evolution by Simulated Genetic Gradients. Genes, 9(10), 506.
  • Jimenez-Santos MJ, Arenas M, Bastolla U. 2018. Influence of mutation bias and hydrophobicity on the substitution rates and sequence entropies of protein evolution. PeerJ, 6:e5549.
  • Oliveira M, Arenas M, Lage O, Cunha M, Amorim MI. 2018. Epiphytic fungal community in Vitis vinifera of the Portuguese wine regions. Letters in Applied Microbiology, 66:93–102.
  • Ramirez-Amaro S, Picornell A, Arenas M, Castro JA, Massutí E, Ramon MM, Terrasa B. 2018. Contrasting evolutionary patterns in populations of demersal sharks throughout the western Mediterranean. Marine Biology. 165:3.
  • Jimenez MJ, Arenas M, Bastolla U. 2018. Substitution rates predicted by stability-constrained models of protein evolution are not consistent with empirical data. Molecular Biology and Evolution, 35(3):743–755.
  • Oliveira M, Arenas M, Amorim, A. 2018. New Trends in Microbial Epidemiology: Can An Old Dog Learn New Tricks?. Annals of Microbiology and Immunology, 1(1):1004.
  • Perez-Losada M, Arenas M, Castro-Nallar E. 2018. Microbial sequence typing in the genomic era. Infection, Genetics and Evolution, 63:346-359.
  • Arenas M, Araujo NM, Branco C, Castelhano N, Castro-Nallar E, Perez-Losada M. 2018. Mutation and recombination in pathogen evolution: Relevance, methods and controversies. Infection, Genetics and Evolution, 63:295-306.

2017

  • Arenas M, Weber CC, Liberles D, Bastolla U. 2017. ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability. Systematic Biology, 66(6):1054–1064.
  • Castelhano N, Araujo NM, Arenas M. 2017. Heterogeneous recombination among Hepatitis B virus genotypes. Infection, Genetics and Evolution. 54:486–490.
  • Arenas M, Pereira F, Oliveira M, Pinto N, Lopes AM, Gomes V, Carracedo A, Amorim A. 2017. Forensic genetics and genomics: Much more than just a human affair. PLoS Genetics. 13(9): e1006960.
  • Pimenta J, Lopes AM, Comas D, Amorim A, Arenas M. 2017. Evaluating the Neolithic Expansion at Both Shores of the Mediterranean Sea. Molecular Biology and Evolution, 34(12):3232–3242.