Publications

last 5 years

In press

  • Martins LO, Posada D. In press. Species Tree Estimation from Genome-wide Data with Guenomu. In Bioinformatics Vol I. 2º ed. Keith JM ed. Methods in Molecular Biology. Springer.
  • Fernandez-Silva I, Randall JE, Coleman RR, DiBattista JD, Rocha LA, Reimer JD, Meyer C., Bowen BW. In press. Yellow tails in a Red Sea: Phylogeography of the Indo-Pacific goatfish Mulloidichthys flavolineatus reveals isolation in peripheral biogeographical provinces and a cryptic evolutionary lineage in the Red Sea that persisted through glacial cycles. Journal of Biogeography.
  • Prieto T, Alves JM, Posada D. In press. “NGS analysis of somatic mutations in cancer genomes” In Big Data Analytics in Genomics. Ed Wong KC. Springer.
  • Arenas M, Weber CC, Liberles D, Bastolla U. In press. ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability. Systematic Biology.

 

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.

 

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.

 

2014

  • Arenas M and Posada D. 2014. The influence of recombination on the estimation of selection from coding sequence alignments. In “Natural Selection: Methods and Applications” (Fares MA, ed.). CRC Press/Taylor & Francis. Pp. 112-125.
  • Mallo D, Martins LO, Posada D. 2014. Estimation of Species Trees. In Encyclopedia of Life Sciences 2014, John Wiley & Sons, Ltd: Chichester. http://www.els.net.
  • Mallo D, Martins LO, Posada D. 2014. Unsorted Homology within Locus and Species Trees. Systematic Biology 63: 988-992.
  • Fonseca MM, Harris DJ, Posada D. 2014. The inversion of the control region in three mitogenomes provides further evidence for an asymmetric model of vertebrate mtDNA replication. PLoS ONE: e106654.
  • Faria NR, Rambaut A, Suchard MA, Baele G, Bedford T, Ward MJ, Tatem AJ, Sousa JD, Arinaminpathy JP, Pépin J, Posada D, Peeters M, Pybus OG, Lemey P. 2014. The early spread and epidemic ignition of HIV-1 in human populations. Science 364: 56-61.
  • Martins LO, Posada D. 2014. Testing for Universal Common Ancestry. Systematic Biology 63: 838-842.
  • Forn-Cuní G, Reis ES, Dios S, Posada D, Lambris JD, Figueras A, Novoa B. 2014. The Evolution and Appearance of C3 Duplications in Fish Originate an Exclusive Teleost c3Gene Form with Anti-Inflammatory Activity. PLoS ONE 9(6): e99673.
  • Arenas MPosada D. 2014. Simulation of Genome-wide Evolution under Heterogeneous Substitution models and Complex Multispecies Coalescent Histories. Molecular Biology and Evolution 31: 1295-1301.
  • 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.
  • Darriba D, Taboada GL, Doallo R, Posada D. 2014. HPC Selection of Models of DNA Substitution for Multicore Clusters. International Journal of High Performance Computing 28: 112-125.
  • Santorum JM, Taboada GL, Darriba D, Posada D. 2014. jmodeltest.org: selection of nucleotide substitution models on the cloud. Bioinformatics 30: 1312-1313.
  • Fonseca MM, Harris DJ, Posada D. 2014. Origin and length distribution of unidirectional prokaryotic overlapping genes. G3: Genes, Genomes, Genetics 4: 19-27

 

2013

  • Rocha S, Posada D, Harris DJ. 2013. Phylogeography and diversification history of the day-gecko genus Phelsuma in the Seychelles islands. BMC Evolutionary Biology 13: 3. doi:10.1186/1471-2148-13-3
  • Martins LO, Mallo D, Posada D. 2013. Phylogenetic Likelihood. In Encyclopedia of Life Sciences 2013, John Wiley & Sons, Ltd: Chichester. doi:10.1002/9780470015902.a0005141 http://www.els.net.
  • Bizinoto MC, Yabe S, Leal E, Kishino H, Martins LO, Lima ML, Morais ER, Diaz RS, Janini LM. 2013. Codon pairs of the HIV-1 vif gene correlate with CD4+ T cell count. BMC Infectious Diseases 13:173. doi:10.1186/1471-2334-13-173.
  • Lima A, Harris D.J., Rocha S., Miralles A, Glaw F, Vences M. 2013. Phylogenetic relationships of Trachylepis skink species from Madagascar and the Seychelles (Scincidae: Lygosominae). Molecular Phylogenetics and Evolution 67: 615-629. doi: 10.1016/j.ympev.2013.02.001.
  • Posada D. 2013. Phylogenetic Models of Molecular Evolution: Next-Generation Data, Fit, and Performance. Journal of Molecular Evolution 76: 351-352. doi: 10.1007/s00239-013-9566-z
  • Arenas M, Dos Santos HG, Posada D, Bastolla U. 2013. Protein Evolution along Phylogenetic Histories under Structurally Constrained Substitution Models. Bioinformatics 29: 3020-3028. doi:10.1093/bioinformatics/btt530.

 

2012

  • Moreira R, Balseiro P, Romero A, Dios S, Posada D, Novoa B, Figueras A. 2012. Gene expression analysis of clams Ruditapes philippinarum and Ruditapes decussatus following bacterial infection yields molecular insights into pathogen resistance and immunity. Developmental and Comparative Immunology 36: 140-149.
  • Abascal F, Posada D, Zardoya R. 2012. The evolution of the mitochondrial genetic code in arthropods revisited. mtDNA 23: 84-91.
  • Martins LO, Posada D. 2012.Proving universal common ancestry with similar sequences. Trends in Evolutionary Biology 4:e5.
  • Fonseca MM, Rocha S, Posada D. 2012. Base-pairing versatility determines wobble sites in tRNA anticodons of vertebrate mitogenomes. PLoS One 7: e36605.
  • Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9: 772.
  • Coulthart MB, Andonov A, Crandall KA, Pérez-Losada M, Posada D, Padmore R, Giulivi A, Oger JJ, Peters AA, Dekaban GA. 2012. Insights into origins of Human T-cell Lymphotropic Virus Type 1 based on new strains from aboriginal people of Canada. Infection, Genetics and Evolution 8:1822-1830.
  • Arenas M and Posada D. 2012. Simulation of Coding Sequence Evolution. In “Codon Evolution: Mechanisms and Models”. (Cannarozzi GM and Schneider A., eds.). Oxford University Press. 978-0-19-960116-5.
  • Posada D. 2012. Selection of Phylogenetic Models of Molecular Evolution. In Encyclopedia of Life Sciences 2012, John Wiley & Sons, Ltd: Chichester. http://www.els.net. DOI: 10.1002/9780470015902.a0022845.
  • Posada D. 2012. Reconstrucción de árboles filogenéticos. En “El árbol de la vida: sistemática y evolución de los seres vivos” (Vargas P, Zardoya R, eds.). Madrid, 617 pp.

 

For older please publications look at the personal web pages.