| Year |
Citation |
Score |
| 2024 |
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. Genomic and phenotypic analysis of invasive Streptococcus suis isolated in Spain reveals genetic diversification and associated virulence traits. Veterinary Research. 55: 11. PMID 38268053 DOI: 10.1186/s13567-024-01267-0 |
0.388 |
|
| 2023 |
Del Amparo R, Arenas M. Influence of substitution model selection on protein phylogenetic tree reconstruction. Gene. 865: 147336. PMID 36871672 DOI: 10.1016/j.gene.2023.147336 |
0.395 |
|
| 2023 |
González-Vázquez LD, Arenas M. Molecular Evolution of SARS-CoV-2 during the COVID-19 Pandemic. Genes. 14. PMID 36833334 DOI: 10.3390/genes14020407 |
0.404 |
|
| 2023 |
Moreira F, Arenas M, Videira A, Pereira F. Evolution of TOP1 and TOP1MT Topoisomerases in Chordata. Journal of Molecular Evolution. 91: 192-203. PMID 36651963 DOI: 10.1007/s00239-022-10091-z |
0.356 |
|
| 2023 |
Arenas M. ProteinEvolverABC: coestimation of recombination and substitution rates in protein sequences by approximate Bayesian computation. Bioinformatics (Oxford, England). 38: 58-64. PMID 34450622 DOI: 10.1093/bioinformatics/btab617 |
0.378 |
|
| 2022 |
Ferreiro D, Khalil R, Gallego MJ, Osorio NS, Arenas M. The evolution of the HIV-1 protease folding stability. Virus Evolution. 8: veac115. PMID 36601299 DOI: 10.1093/ve/veac115 |
0.722 |
|
| 2022 |
Del Amparo R, González-Vázquez LD, Rodríguez-Moure L, Bastolla U, Arenas M. Consequences of Genetic Recombination on Protein Folding Stability. Journal of Molecular Evolution. 91: 33-45. PMID 36463317 DOI: 10.1007/s00239-022-10080-2 |
0.679 |
|
| 2022 |
Arenas M. Methodologies for Microbial Ancestral Sequence Reconstruction. Methods in Molecular Biology (Clifton, N.J.). 2569: 283-303. PMID 36083454 DOI: 10.1007/978-1-0716-2691-7_14 |
0.393 |
|
| 2022 |
Del Amparo R, Arenas M. Consequences of Substitution Model Selection on Protein Ancestral Sequence Reconstruction. Molecular Biology and Evolution. 39. PMID 35789388 DOI: 10.1093/molbev/msac144 |
0.387 |
|
| 2022 |
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. 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. PMID 35346235 DOI: 10.1186/s12977-022-00591-7 |
0.226 |
|
| 2022 |
Branco C, Kanellou M, González-Martín A, Arenas M. Consequences of the Last Glacial Period on the Genetic Diversity of Southeast Asians. Genes. 13. PMID 35205429 DOI: 10.3390/genes13020384 |
0.802 |
|
| 2022 |
Moreira F, Arenas M, Videira A, Pereira F. Evolutionary History of TOPIIA Topoisomerases in Animals. Journal of Molecular Evolution. 90: 149-165. PMID 35165762 DOI: 10.1007/s00239-022-10048-2 |
0.375 |
|
| 2022 |
Ferreiro D, Núñez-Estévez B, Canedo M, Branco C, Arenas M. Evaluating Causes of Current Genetic Gradients of Modern Humans of the Iberian Peninsula. Genome Biology and Evolution. 13. PMID 33837782 DOI: 10.1093/gbe/evab071 |
0.801 |
|
| 2021 |
Del Amparo R, Arenas M. HIV Protease and Integrase Empirical Substitution Models of Evolution: Protein-Specific Models Outperform Generalist Models. Genes. 13. PMID 35052404 DOI: 10.3390/genes13010061 |
0.367 |
|
| 2021 |
Arenas M. General considerations for online teaching practices in bioinformatics in the time of COVID-19. Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology. 49: 683-684. PMID 34231941 DOI: 10.1002/bmb.21558 |
0.191 |
|
| 2021 |
Moreira F, Arenas M, Videira A, Pereira F. Molecular Evolution of DNA Topoisomerase III Beta (TOP3B) in Metazoa. Journal of Molecular Evolution. PMID 33999213 DOI: 10.1007/s00239-021-10011-7 |
0.353 |
|
| 2021 |
Monteiro B, Arenas M, Prata MJ, Amorim A. Evolutionary dynamics of the human pseudoautosomal regions. Plos Genetics. 17: e1009532. PMID 33872316 DOI: 10.1371/journal.pgen.1009532 |
0.586 |
|
| 2021 |
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, et al. Risk Variants in Three Alzheimer's Disease Genes Show Association with EEG Endophenotypes. Journal of Alzheimer's Disease : Jad. PMID 33522999 DOI: 10.3233/JAD-200963 |
0.204 |
|
| 2021 |
Del Amparo R, Branco C, Arenas J, Vicens A, Arenas M. Analysis of selection in protein-coding sequences accounting for common biases. Briefings in Bioinformatics. 22. PMID 33479739 DOI: 10.1093/bib/bbaa431 |
0.747 |
|
| 2020 |
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, et al. Genome-Wide Scan for Five Brain Oscillatory Phenotypes Identifies a New QTL Associated with Theta EEG Band. Brain Sciences. 10. PMID 33218114 DOI: 10.3390/brainsci10110870 |
0.275 |
|
| 2020 |
Lago-Docampo M, Tenorio J, Hernández-González I, Pérez-Olivares C, Escribano-Subías P, Pousada G, Baloira A, Arenas M, Lapunzina P, Valverde D. Characterization of rare ABCC8 variants identified in Spanish pulmonary arterial hypertension patients. Scientific Reports. 10: 15135. PMID 32934261 DOI: 10.1038/s41598-020-72089-1 |
0.234 |
|
| 2020 |
Arenas M. Protein Evolution in the Flaviviruses. Journal of Molecular Evolution. 88: 473-476. PMID 32451560 DOI: 10.1007/s00239-020-09953-1 |
0.347 |
|
| 2020 |
Branco C, Ray N, Currat M, Arenas M. Influence of Paleolithic Range Contraction, Admixture and Long-Distance Dispersal on Genetic Gradients of Modern Humans in Asia. Molecular Ecology. PMID 32436243 DOI: 10.1111/Mec.15479 |
0.805 |
|
| 2020 |
Arenas M, Gorostiza A, Baquero JM, Campoy E, Branco C, Rangel-Villalobos H, González-Martín A. The Early Peopling of the Philippines based on mtDNA. Scientific Reports. 10: 4901. PMID 32184451 DOI: 10.1038/s41598-020-61793-7 |
0.774 |
|
| 2020 |
Pérez-Losada M, Arenas M, Galán JC, Bracho MA, Hillung J, García-González N, González-Candelas F. High-throughput sequencing (HTS) for the analysis of viral populations. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 104208. PMID 32001386 DOI: 10.1016/J.Meegid.2020.104208 |
0.348 |
|
| 2020 |
Del Amparo R, Vicens A, Arenas M. The influence of heterogeneous codon frequencies along sequences on the estimation of molecular adaptation. Bioinformatics (Oxford, England). 36: 430-436. PMID 31304972 DOI: 10.1093/bioinformatics/btz558 |
0.329 |
|
| 2019 |
Illera JC, Arenas M, López-Sánchez CA, Obeso JR, Laiolo P. Gradual Distance Dispersal Shapes the Genetic Structure in an Alpine Grasshopper. Genes. 10. PMID 31387238 DOI: 10.3390/genes10080590 |
0.494 |
|
| 2019 |
Pimenta J, Lopes AM, Carracedo A, Arenas M, Amorim A, Comas D. Spatially explicit analysis reveals complex human genetic gradients in the Iberian Peninsula. Scientific Reports. 9: 7825. PMID 31127131 DOI: 10.1038/s41598-019-44121-6 |
0.8 |
|
| 2019 |
Pascual-García A, Arenas M, Bastolla U. The Molecular Clock in the Evolution of Protein Structures. Systematic Biology. PMID 31111152 DOI: 10.1093/sysbio/syz022 |
0.681 |
|
| 2019 |
Negredo A, Habela MÁ, Ramírez de Arellano E, Diez F, Lasala F, López P, Sarriá A, Labiod N, Calero-Bernal R, Arenas M, Tenorio A, Estrada-Peña A, Sánchez-Seco MP. Survey of Crimean-Congo Hemorrhagic Fever Enzootic Focus, Spain, 2011-2015. Emerging Infectious Diseases. 25: 1177-1184. PMID 31107219 DOI: 10.3201/eid2506.180877 |
0.34 |
|
| 2019 |
Currat M, Arenas M, Quilodran CS, Excoffier L, Ray N. SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal. Bioinformatics (Oxford, England). PMID 31077292 DOI: 10.1093/Bioinformatics/Btz311 |
0.798 |
|
| 2019 |
Bastolla U, Arenas M. The Influence of Protein Stability on Sequence Evolution: Applications to Phylogenetic Inference. Methods in Molecular Biology (Clifton, N.J.). 1851: 215-231. PMID 30298399 DOI: 10.1007/978-1-4939-8736-8_11 |
0.687 |
|
| 2018 |
Vicens A, Vinuesa P, Arenas M, Treviño CL. Analyzing the functional divergence of Slo1 and Slo3 channel subfamilies. Molecular Phylogenetics and Evolution. 133: 33-41. PMID 30586650 DOI: 10.1016/j.ympev.2018.12.026 |
0.255 |
|
| 2018 |
Branco C, Arenas M. Selecting among Alternative Scenarios of Human Evolution by Simulated Genetic Gradients. Genes. 9. PMID 30340387 DOI: 10.3390/genes9100506 |
0.806 |
|
| 2018 |
Jiménez-Santos MJ, Arenas M, Bastolla U. Influence of mutation bias and hydrophobicity on the substitution rates and sequence entropies of protein evolution. Peerj. 6: e5549. PMID 30310736 DOI: 10.7717/peerj.5549 |
0.67 |
|
| 2018 |
Branco C, Velasco M, Benguigui M, Currat M, Ray N, Arenas M. Consequences of diverse evolutionary processes on american genetic gradients of modern humans. Heredity. PMID 30022169 DOI: 10.1038/S41437-018-0122-X |
0.801 |
|
| 2017 |
Jimenez MJ, Arenas M, Bastolla U. Substitution rates predicted by stability-constrained models of protein evolution are not consistent with empirical data. Molecular Biology and Evolution. PMID 29294047 DOI: 10.1093/molbev/msx327 |
0.673 |
|
| 2017 |
Pimenta J, Lopes AM, Comas D, Amorim A, Arenas M. Evaluating the Neolithic Expansion at Both Shores of the Mediterranean Sea. Molecular Biology and Evolution. 34: 3232-3242. PMID 29029191 DOI: 10.1093/molbev/msx256 |
0.79 |
|
| 2017 |
Arenas M, Araujo NM, Branco C, Castelhano N, Castro-Nallar E, Pérez-Losada M. Mutation and recombination in pathogen evolution: Relevance, methods and controversies. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. PMID 28951202 DOI: 10.1016/j.meegid.2017.09.029 |
0.749 |
|
| 2017 |
Pérez-Losada M, Arenas M, Castro-Nallar E. Microbial sequence typing in the genomic era. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. PMID 28943406 DOI: 10.1016/j.meegid.2017.09.022 |
0.316 |
|
| 2017 |
Arenas M, Pereira F, Oliveira M, Pinto N, Lopes AM, Gomes V, Carracedo A, Amorim A. Forensic genetics and genomics: Much more than just a human affair. Plos Genetics. 13: e1006960. PMID 28934201 DOI: 10.1371/journal.pgen.1006960 |
0.631 |
|
| 2017 |
Castelhano N, Araujo NM, Arenas M. Heterogeneous recombination among Hepatitis B virus genotypes. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. PMID 28827173 DOI: 10.1016/j.meegid.2017.08.015 |
0.346 |
|
| 2017 |
Arenas M, Weber CC, Liberles DA, Bastolla U. ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability. Systematic Biology. PMID 28057858 DOI: 10.1093/Sysbio/Syw121 |
0.689 |
|
| 2016 |
Arenas M, Lorenzo-Redondo R, Lopez-Galindez C. Influence of mutation and recombination on HIV-1 in vitro fitness recovery. Molecular Phylogenetics and Evolution. 94: 264-70. PMID 26358613 DOI: 10.1016/j.ympev.2015.09.001 |
0.273 |
|
| 2015 |
Alves I, Arenas M, Currat M, Hanulova AS, Sousa VC, Ray N, Excoffier L. Long distance dispersal shaped patterns of human genetic diversity in Eurasia. Molecular Biology and Evolution. PMID 26637555 DOI: 10.1093/Molbev/Msv332 |
0.793 |
|
| 2015 |
Arenas M. Trends in substitution models of molecular evolution. Frontiers in Genetics. 6: 319. PMID 26579193 DOI: 10.3389/fgene.2015.00319 |
0.373 |
|
| 2015 |
Arenas M. Genetic Consequences of Antiviral Therapy on HIV-1. Computational and Mathematical Methods in Medicine. 2015: 395826. PMID 26170895 DOI: 10.1155/2015/395826 |
0.383 |
|
| 2015 |
Arenas M, Sánchez-Cobos A, Bastolla U. Maximum-Likelihood Phylogenetic Inference with Selection on Protein Folding Stability. Molecular Biology and Evolution. 32: 2195-207. PMID 25837579 DOI: 10.1093/molbev/msv085 |
0.659 |
|
| 2015 |
Arenas M. Advances in computer simulation of genome evolution: toward more realistic evolutionary genomics analysis by approximate bayesian computation. Journal of Molecular Evolution. 80: 189-92. PMID 25808249 DOI: 10.1007/s00239-015-9673-0 |
0.308 |
|
| 2015 |
Arenas M, Lopes JS, Beaumont MA, Posada D. CodABC: a computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate Bayesian computation. Molecular Biology and Evolution. 32: 1109-12. PMID 25577191 DOI: 10.1093/Molbev/Msu411 |
0.563 |
|
| 2015 |
Pérez-Losada M, Arenas M, Galán JC, Palero F, González-Candelas F. Recombination in viruses: mechanisms, methods of study, and evolutionary consequences. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 30: 296-307. PMID 25541518 DOI: 10.1016/J.Meegid.2014.12.022 |
0.373 |
|
| 2014 |
Benguigui M, Arenas M. Spatial and temporal simulation of human evolution. Methods, frameworks and applications. Current Genomics. 15: 245-55. PMID 25132795 DOI: 10.2174/1389202915666140506223639 |
0.47 |
|
| 2014 |
Arenas M, Posada D. Simulation of genome-wide evolution under heterogeneous substitution models and complex multispecies coalescent histories. Molecular Biology and Evolution. 31: 1295-301. PMID 24557445 DOI: 10.1093/Molbev/Msu078 |
0.599 |
|
| 2013 |
Arenas M. The importance and application of the ancestral recombination graph. Frontiers in Genetics. 4: 206. PMID 24133504 DOI: 10.3389/fgene.2013.00206 |
0.213 |
|
| 2013 |
Arenas M, Dos Santos HG, Posada D, Bastolla U. Protein evolution along phylogenetic histories under structurally constrained substitution models. Bioinformatics (Oxford, England). 29: 3020-8. PMID 24037213 DOI: 10.1093/Bioinformatics/Btt530 |
0.749 |
|
| 2013 |
Arenas M. Computer programs and methodologies for the simulation of DNA sequence data with recombination. Frontiers in Genetics. 4: 9. PMID 23378848 DOI: 10.3389/fgene.2013.00009 |
0.356 |
|
| 2013 |
Arenas M, François O, Currat M, Ray N, Excoffier L. Influence of admixture and paleolithic range contractions on current European diversity gradients. Molecular Biology and Evolution. 30: 57-61. PMID 22923464 DOI: 10.1093/Molbev/Mss203 |
0.814 |
|
| 2012 |
Arenas M. Simulation of molecular data under diverse evolutionary scenarios. Plos Computational Biology. 8: e1002495. PMID 22693434 DOI: 10.1371/journal.pcbi.1002495 |
0.347 |
|
| 2012 |
Arenas M, Ray N, Currat M, Excoffier L. Consequences of range contractions and range shifts on molecular diversity. Molecular Biology and Evolution. 29: 207-18. PMID 21778191 DOI: 10.1093/Molbev/Msr187 |
0.788 |
|
| 2011 |
Pérez-Losada M, Jobes DV, Sinangil F, Crandall KA, Arenas M, Posada D, Berman PW. Phylodynamics of HIV-1 from a phase III AIDS vaccine trial in Bangkok, Thailand. Plos One. 6: e16902. PMID 21423744 DOI: 10.1371/Journal.Pone.0016902 |
0.649 |
|
| 2010 |
Arenas M, Posada D. Computational design of centralized HIV-1 genes. Current Hiv Research. 8: 613-21. PMID 21054255 DOI: 10.2174/157016210794088263 |
0.566 |
|
| 2010 |
Arenas M, Patricio M, Posada D, Valiente G. Characterization of phylogenetic networks with NetTest. Bmc Bioinformatics. 11: 268. PMID 20487540 DOI: 10.1186/1471-2105-11-268 |
0.537 |
|
| 2010 |
Arenas M, Posada D. The effect of recombination on the reconstruction of ancestral sequences. Genetics. 184: 1133-9. PMID 20124027 DOI: 10.1534/Genetics.109.113423 |
0.59 |
|
| 2010 |
Arenas M, Posada D. Coalescent simulation of intracodon recombination. Genetics. 184: 429-37. PMID 19933876 DOI: 10.1534/Genetics.109.109736 |
0.608 |
|
| 2009 |
Pérez-Losada M, Posada D, Arenas M, Jobes DV, Sinangil F, Berman PW, Crandall KA. Ethnic differences in the adaptation rate of HIV gp120 from a vaccine trial. Retrovirology. 6: 67. PMID 19604405 DOI: 10.1186/1742-4690-6-67 |
0.621 |
|
| 2009 |
Arenas M, Villaverde MC, Sussman F. Prediction and analysis of binding affinities for chemically diverse HIV-1 PR inhibitors by the modified SAFE_p approach. Journal of Computational Chemistry. 30: 1229-40. PMID 18988271 DOI: 10.1002/jcc.21147 |
0.241 |
|
| 2008 |
Arenas M, Valiente G, Posada D. Characterization of reticulate networks based on the coalescent with recombination. Molecular Biology and Evolution. 25: 2517-20. PMID 18927089 DOI: 10.1093/Molbev/Msn219 |
0.531 |
|
| 2007 |
Arenas M, Posada D. Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography. Bmc Bioinformatics. 8: 458. PMID 18028540 DOI: 10.1186/1471-2105-8-458 |
0.611 |
|
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