Publications

last 5 years

In press

  • Lago-Docampo M, Tenorio J, González-Hernández 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, in press.

 

2020

  • Posada D. 2020. CellCoal: coalescent simulation of single-cell sequencing samples. Molecular Biology and Evolution 37: 1535–1542.
  • da Fonseca R, Couto A, Machado A et al (including Rocha S). 2020. A draft genome sequence of the elusive giant squid, Architeuthis dux. GigaScience 9, 11-12.
  • Suarez-Bregua P, Pérez-Figueroa A, Hernández-Urcera J, Morán P, Rotllant J. 2020 Temperature-independent genome-wide DNA methylation profile in turbot post-embryonic development. Journal of Thermal Biology 88, 102483.
  • Darriba D, Posada D, Kozlov AM, Stamatakis A, Morel B, Flouri T. 2020. ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models. Molecular Biology and Evolution 37:291–294.
  • Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Demeulemeester J, Ju YS, Zamora J, Detering H, Li Y, Contino G, Dentro SC, Bruzos AL et al. Pan-cancer analysis of whole genomes reveals driver rearrangements promoted by LINE-1 retrotransposition in human tumours. Nature Genetics 52: 306–319.
  • 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.
  • 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.
  • Arenas M. 2020. Protein Evolution in the Flaviviruses. Journal of Molecular Evolution 88: 473–476.
  • Liberles A, Chang B, Geiler-Samerotte K, Goldman A, Hey J, Kacar B, Meyer M, Murphy W, Posada D, Storfer A. 2020. Emerging Frontiers in the Study of Molecular Evolution. Journal of Molecular Evolution 88: 211–226.

 

2019

  • Alves JMPrado-Lopez S, Cameselle-Teijeiro JM, Posada D. 2019. Rapid evolution and biogeographic spread in a colorectal cancer. Nature Communications 10: 5139.
  • Soliman T, Fernandez-Silva I, Kise H, Kurihara H, Reimer JD. 2019. Population differentiation across small distances in a coral reef-associated vermetid (Ceraesignum maximum) in Palau. Coral Reefs 38: 1159-1172.
  • Chávez JC, Vicens A, Wrighton DC, Andrade-López K, Beltrán C, Gutiérrez RM, Lippiat JD, Treviño CL. A cytoplasmic Slo3 isoform is expressed in somatic tissues. Molecular Biology Reports 46 (5): 5561–5567.
  • Ren M, Feng X, Huang Y, Wang H, Huh Z, Clingenpeel S, Swan B, Fonseca M, Posada D, Stepanauskas R, Hollibaugh J, Foster PG, Woyke T, Luo H. 2019. Phylogenomics Suggests Oxygen Availability as a Driving Force in Thaumarchaeota Evolution. ISMEJ 13: 2150-2161.
  • Romero MR, Pérez-Figueroa A, Carrera M, Swanson WJ, Skibinski DO, Diz AP. 2019. RNA-seq coupled to proteomic analysis reveals high sperm proteome variation between two closely related marine mussel species. Journal of Proteomics 192:169-187.
  • 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. 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.
  • Blom MPK, Matzke NJ, Bragg JG Arida E, Austin CC, Backlin AR, Carretero MA, Fisher, RN, Glaw F, Hathaway S, Iskandar DT, McGuire JA, Karin BR, Reilly SB, Rittmeyer EN, Rocha S, Sanchez M, Stubbs AL, Vences M, Moritz C. Habitat preference modulates trans-oceanic dispersal in a terrestrial vertebrate. Proc. R. Soc. B 286: 20182575.
  • Ribeiro AM, Canchaya C, Penaloza F, Galindo J, Fonseca R. 2019. Population genomic footprints of environmental pollution pressure in natural populations of the Mediterranean mussel. Marine Genomics 45:11-15
  • López-Cortegano E, Pérez-Figueroa A, Caballero A. 2019. Metapop2: re‐implementation of software for the analysis and management of subdivided populations using gene and allelic diversity. Molecular Ecology Resources 19, 1095-1100.
  • Dueñas M, Pérez-Figueroa A, Oliveira C, Suárez-Cabrera C, Souza A, Oliveira P, Villacampa F, Paramio JM, Martínez-Fernández M. 2019. Gene Expression Analyses in Non Muscle Invasive Bladder Cancer Reveals a Role for Alternative Splicing and Tp53 Status. Scientific Reports 9:10362.
  • López-Cortegano E, Pouso R, Labrador A, Pérez-Figueroa A, Fernández J, Caballero A. 2019. Optimal management of genetic diversity in subdivided populations. Frontiers in Genetics 10:843.
  • Lázaro S, Pérez-Crespo M, Lorz C, Bernardini A, Oteo M, Enguita AB, Romero E, Hernández P, Tomás L, Morcillo MA, Paramio JM, and Santos M. 2019. Differential development of large-cell neuroendocrine or small-cell lung carcinoma upon inactivation of 4 tumor suppressor genes. PNAS 116 (44) 22300-22306. 1

 

2018

  • Takama O, Fernandez-Silva I, López C, Reimer JD. 2018. Molecular phylogeny demonstrates need for taxonomic reconsideration of species diversity of the hydrocoral genus Millepora (Cnidaria: Hydrozoa) in the Pacific. Zoological Science 35 (2), 123-133.
  • Fernandez-Silva I, Henderson JB, Rocha LA, Simison WB. 2018. Whole-genome assembly of the coral reef Pearlscale Pygmy Angelfish (Centropyge vrolikii). Scientific Reports 8 (1), 1498.
  • Watson RGA, Baldanzi S, Pérez-Figueroa A, Gouws G, Porri F. 2018. Morphological and epigenetic variation in mussels from contrasting environments. Marine Biology 165:50. https://doi.org/10.1007/s00227-018-3310-6
  • Oliveira M, Arenas M, Lage O, Cunha M, Amorim AM. 2018. Epiphytic fungal community in Vitis vinifera of the Portuguese wine regions. Letters in Applied Microbiology, 66(1):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.
  • 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.
  • Branco C, Arenas M. 2018. Selecting among Alternative Scenarios of Human Evolution by Simulated Genetic Gradients. Genes, 9(10), 506.
  • 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.
  • Alves JA, Posada D. 2018. Sensitivity to sequencing depth in single-cell cancer genomics. Genome Medicine 10:29.
  • Escalona M, Rocha S, Posada D. (2018) NGSphy: phylogenomic simulation of next-generation sequencing data. Bioinformatics, 34(14): 2506-2507
  • Diz AP, Romero MR, Pérez-Figueroa A, Swanson WJ, Skibinski DO. 2018. RNA-seq data from mature male gonads of marine mussels Mytilus edulis and M. galloprovincialis. Data in Brief, 21:167-175.
  • Rivas MJ, Saura M, Pérez-Figueroa A, Panova M, Johansson T, André C, Caballero A, Rolán-Alvarez E, Johannesson K, Quesada H. 2018. Population genomics of parallel evolution in gene expression and gene sequence during ecological adaptation. Scientific Reports 8:16147.
  • Duchemin W, Guillaume G, Arigon AM, Arvestad L, Bansal MS, Berry V, Boussau B, Chevenet F, Comte N, Davín A, Dessimoz C, Dylus D, Hasic D, Mallo D, Planel R, Posada D, Scornavacca C, Szöllosi G, Zhang L, Tannier E, Daubin V. 2018. RecPhyloXML – a format for reconciled gene trees. Bioinformatics 34: 3646-3652.
  • Vicens A, Treviño CL. 2018. Positive selection in the evolution of mammalian CRISPs. Journal of Molecular Evolution 86 (19), 635-645.
  • Vicens A, Posada D. 2018. Selective pressures on human cancer genes along the evolution of mammals. Genes 9:582.
  • Tourón N, Fernández-Silva I, Rodríguez-Castro J, González N, Catoira JL, Rey-Méndez M. 2018. Genetic Characterization of Paracentrotus lividus (Lamarck, 1816) Populations from NW Spain and the Canary Islands. Journal of Shellfish Research 37 (3): 651-658

 

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.
  • Alves JA, Prieto T, Posada D. 2017. Multiregional tumor trees are not phylogenies. Trends in Cancer: Cancer 3: 546-550.
  • Maley C, Aktipis A, Graham T, Sottoriva A, Boddy A, Janiszewska M, Silva A, Gerlinger M, Yuan Y, Pienta K, Anderson K, Gatenby R, Swanton C, Posada D, Wu C-I, Schiffman J, Hwang S, Polyak K, Anderson A, Brown J, Greaves M, Shibata D. 2017. Classifying the Evolutionary and Ecological Features of Neoplasms. Nature Reviews Cancer 17: 605-619.
  • Martins LO, Posada D. 2017. Species Tree Estimation from Genome-wide Data with Guenomu. In Bioinformatics Vol I. 2º ed. Keith JM ed. Methods in Molecular Biology 1525: 461-478. Springer. ISBN 978-1-4939-6620-2; doi:10.1007/978-1-4939-6622-6; ISBN 978-1-4939-6622-6 (eBook).

2016

  • Soliman T, Takama O, Fernandez-Silva I, Reimer JD. 2016. Extremely low genetic variability within and among locations of the greenfish holothurian Stichopus chloronotus Brandt, 1835 in Okinawa, Japan. PeerJ 4:e2410.
  • Escalona M, Rocha S, Posada D. 2016. A comparison of tools for the simulation of genomic NGS data. Nature Reviews Genetics 17: 459-469.
  • Mallo D, Posada D. 2016. Multilocus inference of species trees and DNA barcoding. Philosophical Transactions of the Royal Society B 371: 20150335.
  • Rocha S, Perera A, Silva A, Posada D, Harris J. 2016. Evolutionary history of Trachylepis skinks from the Seychelles islands: introgressive hybridization, morphological evolution and geographic structure. Biological Journal of the Linnean Society 119: 15-36.
  • Posada D. 2016. Phylogenomics for Systematic Biology. Systematic Biology 65: 353-356.
  • Martins LO, Mallo D, Posada D. 2016. A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction. Systematic Biology 65: 397-416.
  • Martins LO, Posada D. 2016. Infinitely Long Branches and an Informal Test of Common Ancestry. Biology Direct 11: 19.
  • Murgarella M, Puiu D, Novoa B, Figueras A, Posada DCanchaya C. 2016. A first insight into the genome of the filter-feeder mussel Mytilus galloprovincialisPLoS ONE 11(3): e0151561. doi:10.1371/journal.pone.0151561
  • Gulia Nuss et al (includes Jose Tubio). 2016. Genomic insights into the Ixodes scapularis tick vector of Lyme disease. Nature communications 7:10507.
  • Mallo D, Martins LO, Posada D. 2016. SimPhy: Phylogenomic Simulation of Gene, Locus and Species Trees. Systematic Biology 65: 334-344.
  • Rodríguez-Pascual M, Kanellopoulos C, Rubio-Montero AJ, Darriba D, Prnjat O, Posada D, Mayo-García R. 2016. Adapting Reproducible Research Capabilities to Resilient Distributed Calculations. International Journal of Grid and High Performance Computing 8: 58-69.
  • Prieto T, Alves JM, Posada D. 2016. NGS analysis of somatic mutations in cancer genomes. In Big Data Analytics in Genomics. Ed Wong KC. Pp 357-372.Springer. ISBN 978-3-319-41278-8
DOI 10.1007/978-3-319-41279-5.

2015

  • Posada D. Cancer molecular evolution. 2015. Journal of Molecular Evolution 81: 81-83.
  • Moreira R, Pereiro P, Canchaya CPosada D, Figueras A, Novoa B. 2015. RNA-Seq in Mytilus galloprovincialis: Comparative transcriptomics and expression profiles among different tissues. BMC Genomics 16:728..
  • 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: 1109-1112.
  • Palopoli MF, Fergus DJ, Minot S, Pei DT, Simison WB, Fernandez-Silva I, Thoemmes MS, Dunn RR, Trautwein M. 2015. Global divergence of the human follicle mite Demodex folliculorum: Persistent associations between host ancestry and mite lineages. Proceedings of the National Academy of Sciences 112: 15958-15963.

For older please publications look at the personal web pages.