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PUBLICATIONS
86. 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. pdf
85. 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. pdf
84. 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. pdf
83. Del Amparo R, Arenas M. 2023. Influence of substitution model selection on protein phylogenetic tree reconstruction. Gene, 865, 147336. pdf
82. Moreira F, Arenas M, Videira A, Pereira F. 2023. Evolution of TOP1 and TOP1MT Topoisomerases in Chordata. Journal of Molecular Evolution, 91, 192-203. pdf
81. González-Vázquez LD, Arenas M. 2023. Molecular Evolution of SARS-CoV-2 during the COVID-19 Pandemic. Genes, 14(2), 407. pdf
80. 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. pdf
79. 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. pdf
78. Del Amparo R, Arenas M. 2022. Consequences of substitution model selection on protein ancestral sequence reconstruction. Molecular Biology and Evolution, 39(7), msac144. pdf
77. Arenas M. 2022. Methodologies for Microbial Ancestral Sequence Reconstruction. In "Environmental Microbial Evolution: Methods and Protocols". Ed, Luo, H. Springer. Pp. 283-303. pdf
76. 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. pdf
75. Moreira F, Arenas M, Videira A, Pereira F. 2022. Evolutionary history of TOPIIA topoisomerases in animals. Journal of Molecular Evolution, 90, 149–165. pdf
74. 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. pdf
73. 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. pdf
72. 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. pdf
71. Arenas M. 2022. ProteinEvolverABC: Coestimation of Recombination and Substitution Rates in Protein Sequences by approximate Bayesian computation. Bioinformatics, 38(1), 58–64. pdf
70. 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. pdf
69. 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. pdf
68. 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. pdf
67. Monteiro B, Arenas M, Prata MJ, Amorim A. 2021. Evolutionary dynamics of the human pseudoautosomal regions. PLoS Genetics, 17(4): e1009532. pdf
66. 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. pdf
65. 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. pdf
64. 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.
63. 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. pdf
62. Arenas M. 2020. Protein Evolution in the Flaviviruses. Journal of Molecular Evolution, 88:473–476. pdf
61. 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.
60. 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. pdf
59. Arenas M, Bastolla U. 2020. ProtASR2: Ancestral Reconstruction of Protein Sequences accounting for Folding Stability. Methods in Ecology and Evolution, 11: 248–257. pdf
58. 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. pdf
57. 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. pdf
56. 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.
55. 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. pdf
54. 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. pdf
53. Pascual-Garcia A, Arenas M, Bastolla U. 2019. The molecular clock in the evolution of protein structures. Systematic Biology, 68(6): 987–1002. pdf
52. 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. pdf
51. 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. pdf
50. 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. pdf
49. Oliveira M, Arenas M, Pinto N, Amorim A. 2019. Genética forense no humana [Non-human forensic genetics]. In "Genetica forense: Del laboratorio a los tribunales" ["Forensic genetics: From the laboratory to the court"]. Ed. Crepillo MC, Barrio PA. Ediciones Diaz de Santos. Pp. 291-318. pdf
48. 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. pdf
47. 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. pdf
46. 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. pdf
45. Branco C, Arenas M. 2018. Selecting among Alternative Scenarios of Human Evolution by Simulated Genetic Gradients. Genes, 9(10), 506. pdf
44. 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. pdf
43. 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. pdf
42. 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. pdf
41. 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. pdf
40. 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(1):93-102. pdf
39. 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. pdf
38. Perez-Losada M, Arenas M, Castro-Nallar E. 2018. Microbial sequence typing in the genomic era. Infection, Genetics and Evolution, 63:346-359. pdf
37. 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. pdf
36. 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. pdf
35. Castelhano N, Araujo NM, Arenas M. 2017. Heterogeneous recombination among Hepatitis B virus genotypes. Infection, Genetics and Evolution, 54:486-490. pdf
34. 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. pdf
33. Perez-Losada M, Arenas M, Castro-Nallar E. 2017. Multilocus Sequence Typing of Pathogens: Methods, Analyses, and Applications. In "Genetics and Evolution of Infectious Diseases (Second Edition)". Ed., Tibayrenc, M. Elsevier. Pp. 383-404. pdf pdf
32. Alves I, Arenas M, Currat M, Sramkova Hanulova A, Sousa VC, Ray N, Excoffier L. 2016. Long-Distance Dispersal Shaped Patterns of Human Genetic Diversity in Eurasia. Molecular Biology and Evolution, 33(4):946-958. pdf
31. Arenas M, Lorenzo-Redondo R, Lopez-Galindez, C. 2016. Influence of mutation and recombination on HIV-1 in vitro fitness recovery. Molecular Phylogenetics and Evolution, 94:264–270. pdf
30. Mallo D, Sanchez-Cobos A, Arenas M. 2016. Diverse Considerations for Successful Phylogenetic Tree Reconstruction: Impacts from Model Misspecification, Recombination, Homoplasy and Pattern Recognition. In "Pattern Recognition in Computational Molecular Biology: Techniques and Approaches". Eds., Elloumi M, Iliopoulos CS, Wang JTL, Zomaya AY. John Wiley & Sons. Pp. 439-456. pdf
29. Arenas M. 2015. Trends in Substitution Models of Molecular Evolution. Frontiers in Genetics, 6:319. pdf
28. Lopez-Bueno A, Rastrojo A, Peiro R, Arenas M, Alcami A. 2015. Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake. Molecular Ecology, 24(19):4812–4825. "From the Cover" article. pdf
27. Arenas M. 2015. Genetic Consequences of Antiviral Therapy on HIV-1. Computational and Mathematical Methods in Medicine, 2015: 1-9. pdf
26. Arenas M, Sanchez-Cobos A, Bastolla U. 2015. Maximum-Likelihood Phylogenetic Inference with Selection on Protein Folding Stability. Molecular Biology and Evolution, 32(8):2195-2207. pdf
25. Arenas M. 2015. Advances in Computer Simulation of Genome Evolution: Toward more Realistic Evolutionary Genomics Analysis by Approximate Bayesian Computation. Journal of Molecular Evolution, 80(3-4):189-192. pdf
24. Arenas M, Lopes JS, Beaumont MA, Posada D. 2015. CodABC: A Computational Framework to Coestimate Recombination, Substitution and Molecular Adaptation Rates by Approximate Bayesian Computation. Molecular Biology and Evolution, 32(4):1109-1112. pdf
23. Perez-Losada M, Arenas M, Galan JC, Palero F, Gonzalez-Candelas F. 2015. Recombination in viruses: Mechanisms, methods of study, and evolutionary consequences. Infection, Genetics and Evolution, 30:296-307. pdf
22. Arenas M, Posada D. 2014. The influence of recombination on the estimation of selection from coding sequence alignments. In "Natural Selection: Methods and Applications". Ed., Fares MA. CRC Press/Taylor & Francis. Pp. 112-125. pdf
21. Arenas M, Mona S, Trochet A, Sramkova Hanulova A, Currat M, Ray N, Chikhi L, Rasteiro R, Schmeller DS, Excoffier L. 2014. The scaling of genetic diversity in a changing and fragmented world. In "Scaling in Ecology and Biodiversity Conservation" . Eds., Henle K, Potts SG, Kunin WE, Matsinos YG, Similä J, Pantis JD, Grobelnik V, Penev L, Settele J. Pensoft Publishers, Sofia. Pp. 55-60. pdf
20. Benguigui M, Arenas M. 2014. Spatial and Temporal Simulation of Human Evolution. Methods, Frameworks and Applications. Current Genomics, 15(4):245-255. Editor's Choice. pdf
19. Arenas M, Posada D. 2014. Simulation of Genome-Wide Evolution under Heterogeneous Substitution Models and Complex Multispecies Coalescent Histories. Molecular Biology and Evolution, 31(5):1295-1301. pdf
18. Lopes JS, Arenas M, Posada D, Beaumont MA. 2014. Coestimation of Recombination, Substitution and Molecular Adaptation rates by approximate Bayesian computation. Heredity, 112:255-264. pdf
17. Mona S, Ray N, Arenas M, Excoffier L. 2014. Genetic consequences of habitat fragmentation during a range expansion. Heredity, 112: 291-299. pdf
16. Arenas M, Dos Santos HG, Posada D, Bastolla U. 2013. Protein Evolution along Phylogenetic Histories under Structurally Constrained Substitution Models. Bioinformatics, 29(23):3020-3028. pdf
15. Arenas M. 2013. The Importance and Application of the Ancestral Recombination Graph. Frontiers in Genetics, 4:206. pdf
14. Arenas M. 2013. Computer programs and methodologies for the simulation of DNA sequence data with recombination. Frontiers in Genetics, 4:9. pdf
13. Arenas M, François O, Currat M, Ray N, Excoffier L. 2013. Influence of Admixture and Paleolithic Range Contractions on Current European Diversity Gradients. Molecular Biology and Evolution, 30(1):57-61. pdf
12. Arenas M. 2012. Simulation of Molecular Data under Diverse Evolutionary Scenarios. PLoS Computational Biology, 8(5): e1002495. pdf
11. Arenas M, Ray N, Currat M, Excoffier L. 2012. Consequences of Range Contractions and Range Shifts on Molecular Diversity. Molecular Biology and Evolution, 29(1):207-218. pdf
10. Arenas M, Posada D. 2012. Simulation of Coding Sequence Evolution. In "Codon Evolution: Mechanisms and Models". Eds., Cannarozzi GM, Schneider A. Oxford University Press. Pp. 126-132. pdf
9. Perez-Losada M, Jobes DV, Sinangil F, Crandall KA, Arenas M, Posada D, Berman PW. 2011. Phylodynamics of HIV-1 from a Phase III AIDS Vaccine Trial in Bangkok, Thailand. PLoS ONE, 6(3): e16902. pdf
8. Arenas M, Posada D. 2010. Computational Design of Centralized HIV-1 Genes. Current HIV Research, 8(8):613-621. pdf
7. Arenas M, Patricio M, Posada D, Valiente G. 2010. Characterization of Phylogenetic Networks with NetTest. BMC Bioinformatics, 11:268. pdf
6. Arenas M, Posada D. 2010. The effect of recombination on the reconstruction of ancestral sequences. Genetics, 184(4):1133-1139. Issue highlights. pdf
5. Arenas M, Posada D. 2010. Coalescent simulation of intracodon recombination. Genetics, 184(2):429-437. pdf
4. Perez-Losada M, Posada D, Arenas M, Jobes DV, Sinangil F, Berman PW, Crandall KA. 2009. Ethnic differences in the adaptation rate of HIV gp120 from a vaccine trial. Retrovirology, 6:67. pdf
3. Arenas M, Villaverde MC, Sussman F. 2009. Prediction and Analysis of Binding Affinities for Chemically Diverse HIV-1 PR Inhibitors by the Modified SAFE_p Approach. Journal of Computational Chemistry, 30(8):1229-1240. pdf
2. Arenas M, Valiente G, Posada D. 2008. Characterization of Reticulate Networks based on the Coalescent with Recombination. Molecular Biology and Evolution, 25(12):2517-2520. pdf
1. Arenas M, Posada D. 2007. Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography. BMC Bioinformatics, 8:458. Highly accessed. pdf
PLACES
2023-Present. Professor TU. University of Vigo (Spain). Computational Molecular Evolution (CME) Team.
2022-2023. Professor PCD. University of Vigo (Spain). Computational Molecular Evolution (CME) Team.
2017-2022. Principal Investigator (Ramón y Cajal). University of Vigo (Spain). Computational Molecular Evolution (CME) Team.
2015-2017. Principal Investigator. IPATIMUP / i3S, University of Porto (Portugal). Antonio Amorim Lab (Population Genetics & Evolution).
2014. Visiting Scientist. University of Wyoming, Laramie (USA). David Liberles Lab.
2012-2015. PostDoc at the Centre for Molecular Biology "Severo Ochoa", CSIC (Spain). Ugo Bastolla Lab (Bioinformatics Unit).
2010-2012. PostDoc at the University of Bern (Switzerland). Laurent Excoffier Lab (CMPG Lab).
2010. PostDoc at the University of Vigo (Spain). David Posada Lab (Phylogenomics Lab).
2009. Visiting Scientist. University of Reading, Reading (UK). Mark Beaumont Lab.
2008. Visiting Scientist. Brigham Young University, Utah (USA). Keith A. Crandall Lab.
2007. Visiting Scientist. Instituto de Salud Carlos III (ISCIII), Madrid (Spain). Cecilio Lopez Galindez Lab.
2005-2010. PhD Thesis in Genetics. University of Vigo (Spain). Cum Laude (highest score). Supervised by Prof David Posada (Phylogenomics Lab). 26/02/2010. Thesis Award (best Thesis of the University of Vigo in 2010).
SEMINARS UPON INVITATION
2020. Ancestral reconstruction of protein sequences accounting for fitness based on structural constraints. July, 10. Invited by Claudia Bank Lab. Instituto Gulbenkian de Ciência (IGC). Lisbon (Portugal).
2018. Investigating the evolution of Paleolithic and Neolithic populations of North Africa and Philippines. October, 31. Invited by Mathias Currat Lab. University of Geneve. Geneve (Switzerland).
2018. The coalescent and its applications for the evolutionary analysis of genetic data. October, 30. Invited by Tanja Stadler Lab. Swiss Federal Institute of Technology Zurich (ETH). Basel (Switzerland).
2018. Deciphering migration routes with approximate Bayesian computation based on spatially-explicit computer simulations. October, 29. Invited by Laurent Excoffier Lab. University of Bern. Bern (Switzerland).
2018. Applying spatially explicit computer simulations to study human evolution. June, 1 & 8. Invited by Lab seminars of Genetics Area. University of Vigo. Vigo (Spain).
2018. The Influence of Protein Stability on Sequence Evolution: Applications to Phylogenetic Inference. March, 9 & April, 13. Invited by Lab seminars of Genetics Area. University of Vigo. Vigo (Spain).
2016. Human Evolutionary Analysis based on Computer Simulations of Genetic Data. February, 15. Invited by Juan Carlos Illera. University of Oviedo. Oviedo (Spain).
2015. Bioinformatics for DNA and Protein Evolutionary Analysis. Introduction to Cancer Molecular Evolution. September, 30. Invited by IPATIMUP. IPATIMUP. Porto (Portugal).
2015. Computer Simulations for the Evolutionary Analysis. May, 12. Invited by Alfonso Valencia. CNIO. Madrid (Spain).
2015. Applying Computer Simulations to the Evolutionary Analysis of Genetic Data. February, 13. Invited by Antonio Gonzalez. University Complutense de Madrid. Madrid (Spain).
2013. Computer Simulations of Molecular Evolution. Methods and Applications. May, 30. Invited by Cecilio López-Galíndez. Institute of Health Carlos III (ISCIII), Madrid (Spain).
2013. Evolutionary and phylogenetic analysis of DNA and amino acid sequences. March, 1. Invited by the Department of Cell Biology and Immunology. Centre for Molecular Biology "Severo Ochoa", CSIC. Madrid (Spain).
2012. Computer programs for the simulation of molecular data under diverse evolutionary scenarios. November, 5. Invited by David Posada. University of Vigo, Vigo (Spain).
2012. Simulation of molecular data by the coalescent with recombination, migration and demographics. February, 22. Invited by Maria Anisimova. Swiss Federal Institute of Technology (ETH), Zurich (Switzerland).
2011. Consequences of Range Contractions and Range Shifts on Molecular Diversity. February, 10. Invited by Olivier François. University of Grenoble (France).
2010. Applications of the coalescent with recombination in molecular evolution. October, 4. Invited by Laurent Excoffier. University of Bern (Switzerland).
CONGRESS/SYMPOSIUM COMMUNICATIONS
2023. VI Annual Meeting of the CINBIO. Vigo (Spain). July, 28-29.
- A database of substitution models of evolution for protein drug targets.
- A substitution model of evolution for the HIV-1 protease based on molecular activity.
- Testing recombination along the SARS-CoV-2 genome.
2022. Meeting of the Society for Molecular Biology and Evolution (SMBEeverywhere). Online along 2022.
- Forecasting protein folding stability along the ancestral recombination graph.
- Evaluating recombination events along the evolutionary history of the SARS-CoV-2.
- Evolutionary constraints in the HIV-1 protease folding stability.
- Evaluating molecular adaptation of SARS-CoV-2 in Galicia.
2022. VIII Biennial Congress of the Spanish Society for Evolutionary Biology. Vigo (Spain). February, 2-4.
- Estimating recombination and substitution rates in protein sequences with ProteinEvolverABC.
2022. 19th Meeting Portugaliae Genetica. Porto (Portugal). March, 24-25.
- Evolutionary fluctuations of the HIV-1 protease folding stability
- Identifying the best-fitting substitution model of protein evolution accounting for structural constraints.
- Approximate Bayesian Computation modeling of the successful out-of-Africa migration of modern humans.
- Substitution model selection affects ancestral sequence reconstruction. Consequences on the prediction of ancestral HIV-1 epitopes.
- Developing a new substitution model of HIV-1 protease evolution that accounts for functional constraints
2022. V Annual Meeting CINBIO. Vigo (Spain). July, 28-29.
- Temporal fluctuations of the HIV-1 protease stability under diverse evolutionary scenarios.
- A new HIV-1 Protease Substitution Model based on Functional Constraints.
- Molecular evolution of SARS-CoV-2 in Galicia.
2021. II International Meeting of the Portuguese Society of Genetics. Online. July, 1-2.
- Influence of the sea level variation on the genetic diversity of Southeast Asian populations.
2021. Meeting of the Society for Molecular Biology and Evolution (SMBE2021). Online. July, 4-8.
- Influence of the Last Glacial Period on the genetic diversity of current Southeast Asians.
- Novel empirical substitution models for specific HIV-1 proteins.
- Evolution of the HIV-1 protease folding stability.
2020. XVI National Meeting of Evolutionary Biology. 16-17 December. Virtual event.
- Empirical substitution models of protein evolution traditionally used in phylogenetics and recombination bias protein folding stability
- Evaluating the causes of current genetic gradients of modern humans of the Iberian Peninsula with spatially explicit computer simulations
- Genetic consequences of the Last Glacial Period on modern humans from Southeast Asia
2020. EMBL From Functional Genomics To Systems Biology. 16-19 November. Virtual event.
- Evaluating the causes of current genetic gradients of modern humans of the Iberian Peninsula with spatially explicit computer simulations
2020. ISCB-Latin America SoIBio BioNetMX Symposium on Bioinformatics 2020. 28-29 October. Virtual event.
- Influence of empirical substitution models of evolution and recombination on the protein folding stability.
- Identifying the causes of current genetic gradients of modern humans of the Iberian Peninsula.
- Consequences of diverse past evolutionary processes on the genetic gradients of current Asians.
2020. IX Bioinformatics Open Days. 19-21 February. Braga, Portugal.
- Computational analyses of the influence of evolutionary processes on the spatial genetic variation of Asian Modern Humans.
2019. 23rd Annual Meeting of the Portuguese Society of Human Genetics. Coimbra (Portugal). November, 14-16.
- Genome-wide characterization of a cohort of Alzheimer's patients from Iberia: a focus on rare variants.
- APOE allele frequency in late onset Alzheimer's disease patients from Iberia.
2019. XV National Meeting of Evolutionary Biology. Matosinhos (Portugal). November, 14-15.
- Influence of environmental and evolutionary processes on the genetic gradients of current Asians.
- The estimation of dN/dS is biased when ignoring the variation of codon frequencies among sites.
2019. Meeting of the Society for Molecular Biology and Evolution (SMBE2019). Manchester (UK). July, 21-25.
- Ignored heterogeneous codon frequencies among sites biases the estimation of molecular adaptation through dN/dS.
- Reconstruction of ancestral protein sequences accounting for protein folding stability with ProtASR.
- Consequences of the last glacial period on genetic gradients of current Asians.
2019. European Human Genetics Conference 2019. Gothenburg (Sweden). June, 15-18.
- Rare ABCC8 variants identified in Spanish pulmonary arterial hypertension patients.
2019. XI Genetics and Biotechnology Conference. Vila Real (Portugal). March, 13-15.
- Consequences of the last glacial period and population admixture on current Asian genetic gradients.
2019. 3rd Annual Meeting CINBIO. Vigo (Spain). July, 1-2.
- Estimating molecular adaptation in protein-coding sequences accounting for heterogeneous codon frequencies among sites.
- Influence of the last glacial period and admixture on genetic gradients of current Asians.
2018. Annual Meeting 2018 of the Portuguese Society of Genetics. Porto (Portugal). June, 14-15.
- Influence of Diverse Evolutionary Processes on Genetic Gradients of American Modern Humans.
2018. 18th Meeting Portugaliæ Genetica. Porto (Portugal). March, 22-23.
- Accounting for protein stability in sequence evolution: Applications to Phylogenetics.
- Influence of admixture and last Ice Age on genetic diversity gradients of the Americans.
- Contrasting molecular adaption in Slo1 and Slo3 channel subfamilies.
- Identification of genetic variants contributing to late-onset Alzheimer’s disease risk and correlation with cerebral activity of patients.
2017. Alzheimer's Global Summit. Lisbon (Portugal). September, 20-22.
- Analysis and correlation between the genome and cerebral activity of late-onset Alzheimer's disease patients.
2017. 2017 Congress of the European Society for Evolutionary Biology (ESEB2017). Groningen (Netherlands). August, 20-25.
- Population history of an endemic flightless grasshopper: expansion, demography and migration rates in Cantabrian Mountains.
2017. XLI Jornadas Portuguesas de Genética. Aveiro (Portugal). June, 8-9.
- Principal Component Analyses of American Modern Humans.
2017. IX Jornadas de Genetica e Biotecnologia. Vila Real (Portugal). March, 8-10.
- Consequences of admixture and Last Glacial Maximum on current American genetic diversity gradients.
2016. XIII Symposium on Bioinformatics. Valencia (Spain). May, 10-13.
- Ancestral Protein Reconstruction with Selection on Structural Stability with ProtASR.
2016. 17th Meeting Portugaliæ Genetica. Porto (Portugal). March, 17-18.
- Mutation and recombination drive HIV-1 in vitro fitness recovery.
2015. 13th Spanish National Congress of Virology. Madrid (Spain). June, 7-10.
- Ecological connectivity shapes quasispecies structure of RNA viruses in an antarctic lake.
2015. 2015 Aquatic Sciences Meeting. Granada (Spain). February, 22-25.
- Ecological connectivity shapes viral assemblages and variability in freshwater antarctic environments.
2014. XII Symposium on Bioinformatics. Sevilla (Spain). September, 21-24.
- Maximum likelihood phylogenetic computations with selection on protein folding stability.
2014. Cell Symposium: Evolution of Modern Humans - From Bones to Genomes. Sitges (Spain). March, 16-18.
- Testing alternative scenarios of the human worldwide colonization using spatially explicit simulations.
2013. Meeting of Computational Biology Groups at the Autonomous University of Madrid (COMP-BIOL). Madrid (Spain). June, 5.
- Simulation of molecular evolution. Methods and applications. (oral)
2012. SCALES Meeting- Securing the conservation of biodiversity across administrative levels and spatial, temporal, and ecological scales (SCALES2012). Nicosia (Cyprus). March, 19-23.
- sWP 2.2: Genetic Diversity Scaling. (oral)
2012. Swiss Institute of Bioinformatics Meeting (SIB2012). Biel/Bienne (Switzerland). January, 30-31.
- Principal component analysis of European human range expansion and contraction.
2011. Evolution 2011. Norman, Oklahoma (USA). June, 17-21.
- Evolutionary Patterns in Population History of Marine Bacteria.
2011. SCALES Meeting- Securing the conservation of biodiversity across administrative levels and spatial, temporal, and ecological scales (SCALES2011). Sofia (Bulgaria). April, 12-15.
- sWP 2.2: Genetic Diversity Scaling. (oral)
2011. Swiss Institute of Bioinformatics Meeting (SIB2011). Biel/Bienne (Switzerland). January, 31 - February, 1.
- Implications of Range Contractions and Range Shifts on Molecular Diversity.
2010. Evolutionary and ecological genomics of adaptation. Fribourg (Switzerland). September, 2-3.
2010. Annual Meeting of the Society of Molecular Biology and Evolution (SMBE). Lyon (France). July, 4-8.
- Coestimation of recombination, adaptation and substitution rates using approximate Bayesian computation.
2010. XVIII Seminario de Genética de Poblaciones y evolución. (XVIII Meeting of Population Genetics and Evolution). Guitiriz (Spain). May, 5-7.
- Inference of ancestral sequences, recombination and adaptation from recombining sequences.
2009. II Xornada Galega de Bioinformatica. (Second Galician Meeting on Bioinformatics). Santiago de Compostela (Spain). December, 4.
- Coalescent simulation of coding sequences with recombination and other evolutionary processes.
- The Impact of Recombination on the Reconstruction of Ancestral Sequences.
2009. Jornadas de Bioinformática "JB2009", Lisbon, (Portugal). November, 3-6.
- Coalescent simulation of coding sequences with recombination, migration, selection, demographics and longitudinal sampling. (oral)
- Recombination biases the reconstruction of ancestral DNA and protein sequences.
2009. Understanding emergence of infectious diseases: focus on new experimental and theoretical approaches to virus evolution. Jacques Monod Conferences. Roscoff (France). September, 26-30.
- Ancestral sequence reconstruction in the presence of recombination: Implications for HIV-1.
2009. 16th International HIV Dynamics and Evolution. University of Oxford, Oxford (UK). April, 4-7.
- Accuracy of ancestral sequence reconstruction in the presence of recombination: Implications for HIV-1.
2009. International Workshop in Memoriam of Angel Ramirez Ortiz. Structural Bioinformatics and Beyond. Madrid (Spain). January, 26-28.
- Simulation of coding sequences in the ancestral recombination graph.
2008. Cesga-Finis Terrae Computational Science Conference. Santiago de Compostela (Spain). June, 12.
2008. Annual Meeting of the Society of Molecular Biology and Evolution (SMBE). Barcelona (Spain). June, 5-8.
- A new coalescence algorithm to simulate DNA sequences with intra-codon recombination.
2008. I Xornada Galega de Bioinformatica. (First Galician Meeting on Bioinformatics). University of A Coruña. A Coruña (Spain). April, 4.
2008. VIII Jornadas de Bioinformatica. (VIII Meeting on Bioinformatics). Centro de Investigacion Principe Felipe. Valencia (Spain). February, 13-15.
2008. 52nd Biophysical Society Annual Meeting 2008. Long Beach, CA (USA). February, 2-6.
- Predicting inhibitor binding affinities: the SAFE_p approach.
2007. XXXVI Congreso de la Real Sociedad Española de Genetica. (XXXVI Symposium of the Spanish Real Society of Genetics). Leon (Spain). September, 18-21.
- Nuevo software para la simulacion de secuencias de ADN mediante coalescencia con recombinacion, migracion, demografia y modelos de codones
(A new software for the simulation of DNA sequences by coalescent with recombination, migration, demographics and codon models).
2007. Current Challenges and Problems in Phylogenetics. Isaac Newton Institute for Mathematical Sciences, Cambrige (UK). September, 3-7.
- Coalescent simulations with complex models.
2005. XXX Reunion Bienal de la Real Sociedad Española de Quimica (RSEQ). (XXX Symposium of the Spanish Real Society of Chemistry). Lugo (Spain). September, 19-23.
- Desarrollo de un nuevo metodo de prediccion de afinidad de inhibidores de la proteasa del VIH-1. (Development of a new method to affinity prediction of HIV-1 protease inhibitors).
2004. 5th Spanish-Italian Symposium on Organic Chemistry (SISOC-5). Santiago de Compostela (Spain). September, 10-13.
- Intramolecular Metal Catalyzed Cyclization of Cyclopropenes and Alkenes.
- Synthesis of Triphenylene Derivatives by Palladium-Catalyzed Cyclotrimerization of Arynes.
EVENTS ORGANIZATION
2022. VIII Bienal Congress of the Spanish Society for Evolutionary Biology. Vigo (Spain). February, 2-4.
2019. 3rd Annual Meeting CINBIO. Vigo (Spain). July, 1-2.
2016. 17th Meeting Portugaliæ Genetica. Porto (Portugal). March, 17-18.
FELLOWSHIPS
- "Ramon y Cajal" Grant from the Spanish Government (2017-currently). At the University of Vigo, Vigo (Spain).
- FCT Starting Grant from the Portuguese Government (2 years). At the Institute of Molecular Pathology and Immunology at the University of Porto -IPATIMUP-, Porto (Portugal).
- PostDoctoral Fellowship "Sara Borrell" from the Instituto de Salud Carlos III -ISCIII-. At the ISCIII. Madrid (Spain).
- EMBO Fellowship (European Molecular Biology Organization). Stay in the David Liberles Lab (University of Wyoming, WY, USA), 3 months in 2014.
- PostDoctoral Fellowship "Juan de la Cierva" from the Spanish Government (3 years). At the Bioinformatics Unit, Centre for Molecular Biology "Severo Ochoa". CSIC - University Autonoma of Madrid (Spain).
- PreDoctoral Fellowship from Spanish Government (FPI, 4 years). At the Department of Biochemistry, Genetics and Immunology. University of Vigo.
- Several Fellowships from The Ministry of Education and Science of Spain for visiting labs in USA, UK and Spain. Also Fellowships from The University of Vigo for traveling to diverse Meetings.
AGENCIES FUNDING MY RESEARCH PROJECTS
Ministerio de Economía y Competitividad
Xunta de Galicia
Fundación BBVA
The Foundation for Science and Technology
European Molecular Biology Organization
EU FP7, H2020
TEACHING ACTIVITIES
Since 2022 this is not updated. Contact Miguel Arenas for more recent information.
2017-Present. Teaching activities at the Department of Biochemistry, Genetics and Immunology, University of Vigo (Spain).
BSc degree: Biology (coordinator), Genetics II. Master in Advanced Biotechnology: Bioinformatics. Master in Genetics and Genomics (organization member at UVigo): Introduction to programming and bioinformatic analysis of data. PhD program: Molecular ecology and population genetics.
2020. Teacher of Course. Advances in Genome and Protein Evolution. University of Zaragoza / CSIC. Jaca, Spain. 28-29/02/2020.
2018. Speaker. Phylogenetics: theoretical concepts, in Cycle of Workshops in Forensic Genetics. University of Porto. Porto (Portugal).
2015-17. Teacher of Master: Forensic Genetics, Non-human Forensic Applications. University of Porto. Porto (Portugal).
2015-17. Teacher of Master: GABBA: Graduate Program in Areas of Basic and Applied Biology. University of Porto. Porto (Portugal).
2015. Teacher of Master: Physical Anthropology: Human Evolution and Biodiversity. University Complutense de Madrid. Madrid (Spain).
2014-15. Teacher of Master: Physics of Condensed Matter and Biological Systems. Autonomous University of Madrid. Madrid (Spain).
2013-14. Teacher of Master: Biophysics. Autonomous University of Madrid. Madrid (Spain).
2011. Teacher of Course. Introduction to Coalescent Theory. Section: Coalescent Simulation of Coding Data. Doctoral program in populaiton genetics. September, 5-8. University of Lausanne, University of Geneve, University of Bern (Switzerland).
2006-09. Teacher of General Genetics for Biology degree. Department of Biochemistry, Genetics and Immunology, University of Vigo (Spain).
2004-05. Teacher of Practical Lessons for Chemistry degree. Laboratory of Organic Chemistry Department, University of Santiago de Compostela (Spain).
2004-05. Personal Assistant of Computational Service at University of Santiago de Compostela (Spain). Computational Net Rooms (RAI) in the Faculty of Chemistry.
2004. Teacher for primary and high school level at the Private School Ana Maria Parada in Villagarcia de Arosa (Spain).
SUPERVISION OF RESEARCH
Undergraduate students (Project for end of Grade, TFG)
- María J Gallego (Chemistry; University of Vigo; 2021).
- Luis D González (Biology; University of Vigo; 2021).
- Beatriz Fernández (Biology; University of Vigo; 2021).
- Marina Kanellou (Biology, Erasmus+; University of Vigo; 2020).
- Bernabé Núñez (Biology; University of Vigo; 2019).
- Laura Rodriguez (Biology; University of Vigo; 2018).
Graduate students (Project for end of Master, TFM).
- Javier A Cabaleiro (Genetics; University of Vigo; 2023).
- Luis D González (Genetics; University of Vigo; 2022).
- Alberto Martínez (Genetics; University of Vigo; 2021).
- Pablo M Canedo (Genetics; University of Vigo; 2019).
- Catarina Branco (Human evolution; University of Tras-Os-Montes e Alto Douro; 2017).
- Miguel Velasco (Human evolution; Autonomous University of Madrid, Complutense University of Madrid, University of Alcalá; 2015).
- Juan Miguel Baquero (Evolutionary biology; Complutense University of Madrid; 2015).
- Macarena Benguigui (Human evolution; Autonomous University of Madrid, Complutense University of Madrid, University of Alcalá; 2014).
- Agustín Sánchez (Biophysics; Autonomous University of Madrid; 2014).
PhD students (finished and ongoing)
- Joao Pimenta (University of Porto & University of Vigo; 2018).
- Roberto Del Amparo (University of Vigo; 2021).
- Catarina Branco (University of Vigo; 2022).
- David Ferreiro (University of Vigo; Ongoing).
- Luis D González (University of Vigo; Ongoing).
Visitors & Postdocs
- Dr Valeria Zoni (University of Vigo; 2024-).
- Dr Roberto Del Amparo (University of Vigo; 2021-).
- Dr Ruqaiya Khalil (University of Vigo; 2021-2023).
- Sergio Ramírez (Biology; Universitat de les Illes Balears, visiting IPATIMUP; 2015).
OTHER INFORMATION
Associate Editor of Journals
Genes; Frontiers in Ecology and Evolution; Frontiers in Genetics; Frontiers in Plant Science.
Reviewer of Journals
Bioinformatics; Biology; Biomedical and Environmental Sciences; BioMed Research International; BMC Bioinformatics; BMC Evolutionary Biology; BMC Ecology and Evolution; Briefings in Bioinformatics; Computational and Structural Biotechnology Journal; Conservation Genetics Resources; Diversity and Distributions; eLife ;Enzyme Engineering; Evolution; Frontiers in Ecology and Evolution; Frontiers In Fungal Biology; Frontiers in Genetics; Frontiers in Microbiology; Frontiers in Public Health; Gene; Gene Reports; Genes; G3: Genes, Genomes, Genetics; Heredity; Human Heredity; Infection, Genetics and Evolution; International Journal of Biodiversity and Conservation; International Journal of Molecular Sciences; International Journal of Virology and AIDS; Journal of Advanced Techniques in Biology and Medicine; Journal of Bioinformatics and Computational Biology; Journal of General Virology; Journal of Medical Microbiology; Journal of Molecular Evolution; Journal of Theoretical Biology; Methods in Ecology and Evolution; Microbial Drug Resistance; Microbial Genomics; Molecular Biology and Evolution; Molecular Ecology; Molecular Ecology Resources; Molecular Phylogenetics and Evolution; Molecules; Nature Communications; PeerJ; PLoS Computational Biology; PLoS ONE; Proceedings of the Royal Society B; Research & Reviews in BioSciences; Scientific Reports; Statistical Applications in Genetics and Molecular Biology; Systematic Biology; The Scientific World Journal; Virus Evolution; Virus Research; among others.
Reviewer for Research Agencies
- Research Foundation Flanders’ (FWO), European Science Foundation. Belgium.
- The Biotechnology and Biological Sciences Research Council (BBSRC). UK.
- National Agency of Scientific Evaluation of Spain [Agencia Nacional de Evaluación y Prospectiva (ANEP)]. Government of Spain. Spain.
- The French National Research Agency (ANR). Government of France. France.
- National Science Centre of Poland. Government of Poland. Poland.
- BiodivERsA "The network programming and funding research on biodiversity and ecosystem services across European countries and territories". ERA-NET Co-fund, funded under the EU’s - Horizon 2020 Framework Programme for Research and Innovation. EU.
- DC CFAR "Public Research Body for AIDS Research". Washington, DC, USA.
- The Univeristy of The Americas (UDLA). Ecuador.
Membership and networks
- Spanish society of Bioinformatics and Computational Biology (Sociedad Española de Bioinformática y Biología Computacional), 2021.
- Swiss Institute of Bioinformatics, 2010.
- Society for Molecular Biology and Evolution (SMBE), 2008.
- Young membership of Real Spanish Society of Chemistry, from 2005.
- BIOCOMP. Computational biology network, from 2013.
- SCALES. Securing the Conservation of biodiversity across Administrative Levels and spatial, temporal, and Ecological Scales, from 2010.
- Red Española de Diversidad, Evolución y Sistemática, from 2009.
- Red Gallega de Bioinformática, from 2008.
- Official College of Chemistry of Galicia, 2009.
PRIZES AND DIVULGATION
Group Leader Junior of the Group “Computational Molecular Evolution” of the CINBIO. 2021. Accepted after evaluation by a scientific committee.
Interview for “Faro de Vigo” newspaper. 2019. html pdf
Group Leader of the Group “Computational Genetics and Genomics” of the IPATIMUP/I3S. Accepted after evaluation by an external scientific committee.
Interview for “Television de Galicia”. 2017. Video
Article in "La Nueva España" newspaper. 2016. pdf
Interview for “Faro de Vigo” newspaper. 2015. pdf
Thesis Award. Best Thesis of the University of Vigo in 2010.
ATTENDED RELEVANT COURSES AND WORKSHOPS
2009. Bioinformática estructural: Modelización y Simulación de Moléculas Biológicas. (Structural Bioinformatics: Modellization and Simulation of Biological Molecules). University of Santiago de Compostela. November, 30 - December, 3. Santiago de Compostela (Spain).
2009. Optimizacion del uso de la jerarquia de memoria. (Optimization of the use of memory hierarchy). GHPC (Galician network of high-performance computing) and University of La Coruña. October, 13-15. Santiago de Compostela (Spain).
2008. Workshop on Molecular Evolution. MBL - Marine Biological Laboratory. July, 27 - August, 8. Woods Hole, Boston (MA), (USA).
2008. Matematica computacional. (Computational mathematics). i-MATH (Ingenio Mathematica) and CESGA (Superior center of supercomputation of Galicia). June, 30 - July, 4. Santiago de Compostela (Spain).
2008. Molecular Markers and Population Genetics. Gulbenkian Institute of Science. June, 23-27. Oeiras, Lisbon (Portugal).
2008. Seminario de Tecnologias del Instituto Nacional de Bioinformatica. (Seminar on Technologies of the Bioinformatics National Institute). May, 29. Santiago de Compostela, (Spain).
2007. Chrom Forum VWR. Institute of Health Carlos III - ISCIII. October, 2. Majadahonda, Madrid, (Spain).
2007. Elementary Bioinformatic Skills. Gulbenkian Institute of Science. May, 20-25. Oeiras, Lisbon (Portugal).
2006. Workshop on Coalescent Theory. Gulbenkian Institute of Science. June, 21-24. Oeiras, Lisbon (Portugal).
2006. Phylogenetics and Genealogies of DNA: Reconstruction and Applications. Certfem, University of Barcelona. July, 4-14. Barcelona (Spain).
2005. The challenge of energy sources in the XXI century. University of Santiago de Compostela and Xunta de Galicia.
2005. The radioactive isotopes. University of Santiago de Compostela and Xunta de Galicia.
2005. Sustainable development and clean production. University of Santiago de Compostela, Consello Social and Xunta de Galicia.
2004. Pc: Operating and Components. University of Santiago de Compostela.
2003-04. Pedagogic Aptitude Certificate (CAP). ICE, Institute of education science. University of Santiago de Compostela.
2003. Bioactive compounds obtained from residues of food and agriculture industry and forest industry. Chemistry Faculty, University of Santiago de Compostela.
2003. Initiation to the operation in chemical plants. Santiago de Compostela (Spain). Participation of Repsol YPF, ISE and University of Santiago de Compostela.
2003. Microsoft Access. University of Santiago de Compostela.
2003. DreamWeaver. University of Santiago de Compostela.
2003. First aids. Red Cross, Villagarica de Arosa, Pontevedra (Spain).
2002. Visual Programming: Visual Basic. University of Santiago de Compostela.
2002. Making a web site with FrontPage. University of Santiago de Compostela.
COMPUTING SKILLS
OS & Programs
Windows, Macintosh, Basic, MS-DOS, UNIX and Linux.
Supercomputers, Clusters.
USER. Bioinformatics software: MrBayes, OmegaMap, Beast, PAML, Hyphy, phyml, PAUP, SplitsTree, TCS, BLAST, ClustalX/W, MacClade, BioEdit, OmegaMap, TreeView, FigTree, etc. Others: ChemOffice, Mestre C, InsightII, Charmm, SAFE_p, Scifinder, Xcode, Codewarrior, etc
Programming Languages
C, Perl, R, Java, HTML.
Others: Basic, Matlab, DreamWeaver, Visual Programming: Visual Basic. Starting: C++.
Developer of Recodon, software (BMC Bioinformatics, 2007, 8:458) available at http://code.google.com/p/recodon/.Written in C.
Developer of NetRecodon, software (Genetics, 2010, 184(2):429-437) available at http://code.google.com/p/netrecodon/. Written in C.
Developer of NetTest, perl scripts software (BMC Bioinformatics, 2010, 11:268) available at http://darwin.uvigo.es/software/nettest. Written in Perl.
Developer of ProteinEvolver (Bioinformatics, 2013, 29(23):3020-3028), available from http://code.google.com/p/proteinevolver/. Written in C.
Developer of CoalEvol, available from http://code.google.com/p/coalevol/. Written in C.
Developer of SGWE (Molecular Biology and Evolution, 2014, 31(5):1295-1301), available from http://code.google.com/p/sgwe-project/. Written in C, Java, R and Perl.
Developer of CodABC (Molecular Biology and Evolution, 2015, 32(4):1109-1112), available from https://code.google.com/p/codabc/. Written in C, Java, R and Perl.
Developer of ProtASR and ProtASR2 (Systematic Biology, 2017, 66(6):1054-1064, Methods in Ecology and Evolution, 2020, 11:248–257), available from https://github.com/MiguelArenas/protasr. Written in C and Perl.
Contributor to the development of SPLATCHE3 (Bioinformatics, 2019, 35(21): 4480–4483), available from http://www.splatche.com/splatche3. Written in C++.
Developer of ProteinEvolverABC (Bioinformatics, 38(1), 58–64), available from https://github.com/MiguelArenas/ProteinEvolverABC. Written in C, Java, R and Perl.
INDUSTRY JOBS
2005. Professional training at Ence S.A. Laboratory Section.
2003. Professional training at Brenntag Q S.A. Laboratory Section.
2002. Professional training at Metalgrafica Gallega S.A. Department of Quality Control.