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Publications:  Dr Mario Dos Reis Barros

McGowen MR, Tsagkogeorga G, Álvarez-Carretero S, Dos Reis M, Struebig M, Deaville R, Jepson PD, Jarman S et al.(2019). Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture. Systematic Biology
Kawahara AY, Plotkin D, Espeland M, Meusemann K, Toussaint EFA, Donath A, Gimnich F, Frandsen PB et al.(2019). Phylogenomics reveals the evolutionary timing and pattern of butterflies and moths. Proceedings of the National Academy of Sciences201907847-201907847.
Dos Reis M, Yang Z(2019). Bayesian Molecular Clock Dating Using Genome-Scale Datasets. Methods Mol Biol vol. 1910, 309-330.
Halliday TJD, dos Reis M, Tamuri AU, Ferguson-Gow H, Yang Z, Goswami A(2019). Rapid morphological evolution in placental mammals post-dates the origin of the crown group. Proceedings of the Royal Society B: Biological Sciences
Álvarez-Carretero S, Goswami A, Yang Z, dos Reis M(2019). Bayesian estimation of species divergence times using correlated quantitative characters. Systematic Biology
dos Reis M(2018). Fossil-free dating. Nature Ecology and Evolution
Barba-Montoya J, dos Reis M, Schneider H, Donoghue P, Yang Z(2018). Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution. New Phytologist
dos Reis M, Gunnell GF, Barba-Montoya J, Wilkins A, Yang Z, Yoder AD(2018). Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case. Systematic Biology
Nascimento FF, dos Reis M, Yang Z(2017). A biologist’s guide to Bayesian phylogenetic analysis. Nature Ecology and Evolution vol. 1, 1446-1454.
Barba-Montoya J, Dos Reis M, Yang Z(2017). Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating. Mol Phylogenet Evol vol. 114, 386-400.
Angelis K, Álvarez-Carretero S, dos Reis M, Yang Z(2017). An evaluation of different partitioning strategies for Bayesian estimation of species divergence times. Systematic Biology
Lozano-Fernandez J, dos Reis M, Donoghue PCJ, Pisani D(2017). RelTime rates collapse to a strict clock when estimating the timeline of animal diversification. Genome Biol Evol
Thiltgen G, dos Reis M, Goldstein RA(2016). Finding direction in the search for selection. Journal of Molecular Evolution
Yoder AD, Campbell CR, Blanco MB, Dos Reis M, Ganzhorn JU, Goodman SM, Hunnicutt KE, Larsen PA et al.(2016). Geogenetic patterns in mouse lemurs (genus Microcebus) reveal the ghosts of Madagascar's forests past. Proc Natl Acad Sci U S A vol. 113, (29) 8049-8056.
dos Reis M(2016). Notes on the birth-death prior with fossil calibrations for Bayesian estimation of species divergence times. Philosophical Transactions of the Royal Society of London: Biological Sciences
Dos Reis M, Donoghue PCJ, Yang Z(2016). Bayesian molecular clock dating of species divergences in the genomics era. Nature Reviews Genetics vol. 17, (2) 71-80.
Tarver JE, Dos Reis M, Mirarab S, Moran RJ, Parker S, O'Reilly JE, King BL, O'Connell MJ et al.(2016). The interrelationships of placental mammals and the limits of phylogenetic inference. Genome Biology and Evolution vol. 8, (2) 330-344.
Dos Reis M, Thawornwattana Y, Angelis K, Telford MJ, Donoghue PCJ, Yang Z(2015). Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales. Current Biology vol. 25, (22) 2939-2950.
Dos Reis M(2015). How to calculate the non-synonymous to synonymous rate ratio of protein-coding genes under the fisher-wright mutation-selection framework. Biology Letters vol. 11, (4)
Zhu T, Dos Reis M, Yang Z(2015). Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci. Syst Biol vol. 64, (2) 267-280.
Jeffares DC, Tomiczek B, Sojo V, dos Reis M(2015). A beginners guide to estimating the non-synonymous to synonymous rate ratio of all protein-coding genes in a genome. Methods in Molecular Biology vol. 1201, 65-90.
O'Reilly JE, dos Reis M, Donoghue PCJ(2015). Dating Tips for Divergence-Time Estimation. Trends in Genetics vol. 31, (11) 637-650.
Angelis K, Dos Reis M(2015). The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times. Current Zoology vol. 61, (5) 874-885.
Tamuri AU, Goldman N, dos Reis M(2014). A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data. Genetics vol. 197, (1) 257-271.
Angelis K, Dos Reis M, Yang Z(2014). Bayesian estimation of nonsynonymous/synonymous rate ratios for pairwise sequence comparisons. Molecular Biology and Evolution vol. 31, (7) 1902-1913.
Yoder AD, Chan LM, Dos Reis M, Larsen PA, Campbell CR, Rasoloarison R, Barrett M, Roos C et al.(2014). Molecular evolutionary characterization of a V1R subfamily unique to strepsirrhine primates. Genome Biology and Evolution vol. 6, (1) 213-227.
Dos Reis M, Donoghue PCJ, Yang Z(2014). Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals. Biology Letters vol. 10, (1)
Dos Reis M, Zhu T, Yang Z(2014). The impact of the rate prior on bayesian estimation of divergence times with multiple loci. Systematic Biology vol. 63, (4) 555-565.
dos Reis M (2013). Population genetics and substitution models of adaptive evolution. Abstract: java.sql.Clob org.hibernate.engine.jdbc.WrappedClob , Notes: 24 pages, 4 figures and 1 table. Manuscript written between January and April 2010,
dos Reis M, Yang Z(2013). Why do more divergent sequences produce smaller nonsynonymous/synonymous rate ratios in pairwise sequence comparisons?. Genetics vol. 195, (1) 195-204.
Dos Reis M, Yang Z(2013). The unbearable uncertainty of Bayesian divergence time estimation. Journal of Systematics and Evolution vol. 51, (1) 30-43.
Tamuri AU, dos Reis M, Goldstein RA(2012). Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models. Genetics vol. 190, (3) 1101-1115.
dos Reis M, Inoue J, Hasegawa M, Asher RJ, Donoghue PCJ, Yang Z(2012). Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proceedings of the Royal Society B: Biological Sciences vol. 279, (1742) 3491-3500.
Hofinger BJ, Russell JR, Bass CG, Baldwin T, Dos Reis M, Hedley PE, Li Y, MacAulay M et al.(2011). An exceptionally high nucleotide and haplotype diversity and a signature of positive selection for the eIF4E resistance gene in barley are revealed by allele mining and phylogenetic analyses of natural populations. Molecular Ecology vol. 20, (17) 3653-3668.
Reis MD, Yang Z(2011). Approximate likelihood calculation on a phylogeny for Bayesian Estimation of Divergence Times. Molecular Biology and Evolution vol. 28, (7) 2161-2172.
Dos Reis M, Tamuri AU, Hay AJ, Goldstein RA(2011). Charting the host adaptation of influenza viruses. Molecular Biology and Evolution vol. 28, (6) 1755-1767.
Yang Z, Dos Reis M(2011). Statistical properties of the branch-site test of positive selection. Molecular Biology and Evolution vol. 28, (3) 1217-1228.
Noël ES, Dos Reis M, Arain Z, Ober EA(2010). Analysis of the Albumin/α-Fetoprotein/Afamin/Group specific component gene family in the context of zebrafish liver differentiation. Gene Expression Patterns vol. 10, (6) 237-243.
Tamuri AU, Dos Reis M, Hay AJ, Goldstein RA(2009). Identifying changes in selective constraints: Host shifts in influenza. PLoS Computational Biology vol. 5, (11)
Dos Reis M, Hay AJ, Goldstein RA(2009). Using non-homogeneous models of nucleotide substitution to identify host shift events: Application to the origin of the 1918 'spanish' influenza pandemic virus. Journal of Molecular Evolution vol. 69, (4) 333-345.
Dos Reis M, Wernisch L(2009). Estimating translational selection in eukaryotic genomes. Molecular Biology and Evolution vol. 26, (2) 451-461.
Withers M, Wernisch L, Dos Reis M(2006). Archaeology and evolution of transfer RNA genes in the Escherichia coli genome. RNA vol. 12, (6) 933-942.
dos Reis M, Savva R, Wernisch L(2004). Solving the riddle of codon usage preferences: A test for translational selection. Nucleic Acids Research vol. 32, (17) 5036-5044.
dos Reis M, Wernisch L, Savva R(2003). Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome. Nucleic Acids Research vol. 31, (23) 6976-6985.
Sheng G, Dos Reis M, Stern CD(2003). Churchill, a Zinc Finger Transcriptional Activator, Regulates the Transition between Gastrulation and Neurulation. Cell vol. 115, (5) 603-613.
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