A new multitest correction (SGoF) that increases its statistical power when increasing the number of tests
BMC Bioinformatics 10:209 [PDF]
Publications
Unifying quantification methods for sexual selection and assortative mating using information theory.
Theoretical Population Biology 158: 206-215. Doi: 10.1016/j.tpb.2024.06.007. Mathematical Appendix and Supplementary tables and figures available HERE
QInfoMating: Sexual selection and assortative mating estimation.
bioRxiv. Doi: 10.1101/2023.09.06.556585
1LocusSim a mobile-friendly simulator for teaching population genetics.
Bioinformatics Advances 3(1):vbad087. Doi: 10.1093/bioadv/vbad087
Detecting Local Adaptation between North and South European Atlantic Salmon Populations.
Biology 11: 933. Doi: 10.3390/biology11060933
A simulation study of the ecological speciation conditions in the Galician marine snail Littorina saxatilis.
Frontiers in Genetics 13: 680792. Doi: 10.3389/fgene.2022.680792
Bioinformatics of Correction of Multiple Testing: An Introduction for Life Scientists.
in Bioinformatics and Human Genomics Research. CRC Press. Doi: 10.1201/9781003005926-17 [PDF].
An integrated approach to infer the mechanisms of mate choice for size.
Animal Behaviour 175: 33-43. Doi: 10.1016/j.anbehav.2021.02.020.
Mate choice contributes to the maintenance of shell color polymorphism in a marine snail via frequency-dependent sexual selection.
Front. Mar. Sc 14. Doi: 10.3389/fmars.2020.614237.
Evaluation of Existing Methods for High-Order Epistasis Detection.
IEEE/ACM Transactions on Computational Biology and Bioinformatics . Doi: 10.1109/TCBB.2020.3030312.
Toxo: a library for calculating penetrance tables of high-order epistasis models.
BMC Bioinformatics 21: 138. Doi: 10.1186/s12859-020-3456-3.
Mate choice based on body size similarity in sexually dimorphic populations causes strong sexual selection.
Animal Behaviour 160: 69-78. Doi: 10.1016/j.anbehav.2019.12.005.
Multi-model inference of non-random mating from an information theoretic approach.
Theoretical Population Biology 131: 38-53. Doi: 10.1016/j.tpb.2019.11.002. Peer-reviewed and recommended by PCI Evolutionary Biology. [PDF].
Data and models from multi-model inference of non-random mating from an information theoretic approach.
Data in Brief 28: 104969. Doi: 10.1016/j.dib.2019.104969.
Geographic and Temporal Variation of Distinct Intracellular Endosymbiont Strains of Wolbachia sp. in the Grasshopper Chorthippus parallelus: a Frequency-Dependent Mechanism?
Microbial Ecology 77: 1-12. Doi: 10.1007/s00248-019-01338-2.
A generalization of the informational view of non-random mating: Models with variable population frequencies.
Theoretical Population Biology. 125: 67-74. Doi: 10.1016/j.tpb.2018.12.004.
A novel method to estimate the spatial scale of mate choice in the wild.
Behavioral Ecology and Sociobiology 72: 195. Doi: 10.1007/s00265-018-2622-3.
MateSim: Monte Carlo simulation for the generation of mating tables.
BioSystems 171: 26-30 Doi: 10.1016/j.biosystems.2018.07.001. (biorxiv preprint) doi:10.1101/239178
Non-random mating and information theory.
Theoretical Population Biology 120: 103-113. Doi: 10.1016/j.tpb.2018.01.003. Preprint (bioRxiv)
Myriads: p-value-based multiple testing correction.
Bioinformatics 34 (6): 1043-1045. Doi: 10.1093/bioinformatics/btx746
Testing the role of mating preference in a case of incomplete ecological speciation with gene flow.
Biological Journal of the Linnean Society 122 (3): 549-557. Doi: 10.1093/biolinnean/blx107
HacDivSel: Two new methods (haplotype-based and outlier-based) for the detection of divergent selection in pairs of populations.
PLOS ONE 12(4): e0175944. Doi: 10.1371/journal.pone.0175944
A novel method for estimating the strength of positive mating preference by similarity in the wild.
Ecol Evol. 7:1-11. Doi: 10.1002/ece3.2835
Incorporación de la programación informática en el currículum de Biología.
Magister. Vol. 27, pp. 76-82. Doi: 10.1016/j.magis.2015.12.002
The scale-of-choice effect and how estimates of assortative mating in the wild can be biased due to heterogeneous samples.
Evolution. Vol. 67, pp. 1845-1857. Doi: 10.1111/evo.12691
Detecting the Genomic Signature of Divergent Selection in Presence of Gene Flow.
Current Genomics. Vol. 16, pp. 203-212. Doi: 10.2174/1389202916666150313230943
A comparative study of Gaussian mating preference functions: a key element of sympatric speciation models.
Biological Journal of the Linnean Society. Vol. 113, pp. 642-657. Doi: [Journal Link]
Impact of deep coalescence and recombination on the estimation of phylogenetic relationships among species using AFLP markers
Molecular Phylogenetics and Evolution. Vol. 76, pp. 102-109 [Journal Link]
Teaching the fluctuation test in silico by using Mutate: A program to distinguish between the adaptive and spontaneous mutation hypotheses
Biochemistry and Molecular Biology Education. Vol. 40, No. 4, pp. 277–283. [Journal Link]
AFLPMax: a user-friendly application for computing the optimal number of amplified fragment length polymorphism markers needed in phylogenetic reconstruction
Molecular Ecology Resources. 12 (3): 566-569. Doi: 10.1111/j.1755-0998.2011.03113.x
Assessing significance in high-throughput experiments by sequential goodness of fit and q-value estimation
PLoS ONE. 6 (9): e24700. [Journal Link]
A Simulation Study on the Impact of Strong Dependence in High-Dimensional Multiple-Testing I: The Case without Effects
PACBB. Advances in Intelligent and Soft Computing 93: 241-246. Doi: [10.1007/978-3-642-19914-1_32]
Multiple hypothesis testing in proteomics: A strategy for experimental work
Molecular & Cellular Proteomics 10: M110.004374. Doi: 10.1074/mcp.M110.004374
SGoFicance Trace: Assessing Significance in High Dimensional Testing Problems
PLoS ONE. 5 (12):e15930. Doi: 10.1371/journal.pone.0015930
Simulation of Genes and Genomes Forward in Time.
Current Genomics 11 (1): 58-61.
A new multitest correction (SGoF) that increases its statistical power when increasing the number of tests
BMC Bioinformatics 10:209 [PDF]
Population Extinction in Genetic Algorithms: Application in Evolutionary Studies
LNCS (IWANN 2009) 5518: 1028-1034
Detecting recombination and diversifying selection in human alpha-papillomavirus
Infection, Genetics and Evolution 8: 689-692 [PDF] (see also Figure 1 corrigendum)
GENOMEPOP: A program to simulate genomes in populations
BMC Bioinformatics 9: 223 [PDF]
Simulation of genomes: A review.
Current Genomics 9 (3): 155-159.
The role of recombination in the post-genomic era: Challenges and Perspectives.
in Genetic Recombination Research Progress pp. 205-227. Ed. Jacob H. Schulz. Nova Science Publishers, Inc. New York.
Disease progression and evolution of the HIV-1 C2V3C3 env gene region from 24 infected infants
Infection, Genetics and Evolution 8: 110-120. Doi: 10.1016/j.meegid.2007.10.009
Simulating Genomes and Populations in the Mutation Space: An example with the evolution of HIV drug resistance.
Evidence of recombination within human Alpha-Papillomavirus.
Virology Journal 4 :33. Doi: 10.1186/1743-422X-4-33]
Recombination favors the evolution of drug resistance in HIV-1 during antiretroviral therapy
Infection, Genetics and Evolution 7: 476-483. Doi: 10.1016/j.meegid.2007.02.001
The importance of bio-computational tools for predicting HIV drug resistance
Recent Patents on DNA & Gene Sequences.Volume 1, Number 1: 63-68 [PDF]
Lack of temporal structure in the short term HIV-1 evolution within asymptomatic naïve patients.
Virology 362: 294-303. Doi: 10.1016/j.virol.2006.11.039
Genetic variation for shell traits in a direct-developing marine snail involved in a putative sympatric ecological speciation process
Evolutionary Ecology 21: 635-650. Doi: 10.1007/s10682-006-9142-8
FamSphere: A computer program for parental allocation from known genotypic pools.
Molecular Ecology Notes. 7: 213-216. Doi: 10.1111/j.1471-8286.2006.01599.x
An example of application of the geometric morphometric tools to the morphological diagnosis of two sibling species in Nassarius (Mollusca, Prosobranchia).
Iberus 24 (2): 81-88 [PDF]
JMATING: a software for the analysis of sexual selection and sexual isolation effects from mating frequency data.
Recombination Estimation under Complex Evolutionary Models with the Coalescent Composite Likelihood Method.
Molecular Biology and Evolution 23(4): 817-827. Doi: 10.1093/molbev/msj102.
Caracterización y modelado computacional de la recombinación en secuencias de ADN en el virus del SIDA (VIH-1).
Biojournal.net 2 [PDF].
Application of relative warp analysis to the evaluation of two-dimensional gels in proteomics: Studying isoelectric point and relative molecular mass variation
Journal of Proteome Research. Volume 4 (4): 1318 - 1323.
Decomposing shell form into size and shape by geometric-morphometric methods in two sympatric ecotypes of Littorina saxatilis.
Journal of Molluscan Studies 71: 313-318 PDF
Quantitative variation as a tool for detecting human-induced impacts on genetic diversity
Biological Conservation. 124: 1-13 PDF
MODICOS: Morphometric and Distance Computation Software for evolutionary studies.
Online Journal of Bioinformatics 6 : 34-40 Abstract
The evolutionary forces maintaining a wild polymorphism of Littorina saxatilis: model selection by computer simulations
Journal of Evolutionary Biology 18: 191-202.
GASP: A new Genetic Algorithm (based on) Surviving Probability
Online Journal of Bioinformatics 5:23-31.[PDF]
A system of complementary Genes in hybrids between D. koepferae and D. buzzatii: A Markov chain model allows to make inferences about their number and relationships.
Genes and Genetic Systems 76:345-353. Doi: 10.1266/ggs.76.345
Developmental disruption in hybrids between D. koepferae and D. buzzatii
Int. Journ. of Dev. Biol. Suplement: 93s-94s [PDF].
A three-locus system of interspecific incompatibility underlies male inviability in hybrids between Drosophila buzzatii and D.koepferae
Genetica 98:1-19 [PDF].