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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
10.1093/sysbio/syz068
https://qmro.qmul.ac.uk/xmlui/handle/123456789/61154
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.
10.1073/pnas.1907847116
https://qmro.qmul.ac.uk/xmlui/handle/123456789/61085
Dos Reis M, Yang Z(2019). Bayesian Molecular Clock Dating Using Genome-Scale Datasets. Methods Mol Biol vol. 1910, 309-330.
10.1007/978-1-4939-9074-0_10
https://qmro.qmul.ac.uk/xmlui/handle/123456789/59223
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
10.1098/rspb.2018.2418
https://qmro.qmul.ac.uk/xmlui/handle/123456789/56314
Álvarez-Carretero S, Goswami A, Yang Z, dos Reis M(2019). Bayesian estimation of species divergence times using correlated quantitative characters. Systematic Biology
10.1093/sysbio/syz015
https://qmro.qmul.ac.uk/xmlui/handle/123456789/56154
dos Reis M(2018). Fossil-free dating. Nature Ecology and Evolution
10.1038/s41559-018-0532-4
https://qmro.qmul.ac.uk/xmlui/handle/123456789/36276
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
10.1111/nph.15011
https://qmro.qmul.ac.uk/xmlui/handle/123456789/33063
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
10.1093/sysbio/syy001
https://qmro.qmul.ac.uk/xmlui/handle/123456789/31933
Nascimento FF, dos Reis M, Yang Z(2017). A biologist’s guide to Bayesian phylogenetic analysis. Nature Ecology and Evolution vol. 1, 1446-1454.
10.1038/s41559-017-0280-x
https://qmro.qmul.ac.uk/xmlui/handle/123456789/25287
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.
10.1016/j.ympev.2017.07.005
https://qmro.qmul.ac.uk/xmlui/handle/123456789/25020
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
10.1093/sysbio/syx061
https://qmro.qmul.ac.uk/xmlui/handle/123456789/25248
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
10.1093/gbe/evx079
https://qmro.qmul.ac.uk/xmlui/handle/123456789/25018
Thiltgen G, dos Reis M, Goldstein RA(2016). Finding direction in the search for selection. Journal of Molecular Evolution
10.1007/s00239-016-9765-5
https://qmro.qmul.ac.uk/xmlui/handle/123456789/18416
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.
10.1073/pnas.1601081113
https://qmro.qmul.ac.uk/xmlui/handle/123456789/33931
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
10.1098/rstb.2015.0128
https://qmro.qmul.ac.uk/xmlui/handle/123456789/12480
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.
10.1038/nrg.2015.8
https://qmro.qmul.ac.uk/xmlui/handle/123456789/12727
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.
10.1093/gbe/evv261
https://qmro.qmul.ac.uk/xmlui/handle/123456789/12154
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.
10.1016/j.cub.2015.09.066
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)
10.1098/rsbl.2014.1031
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.
10.1093/sysbio/syu109
https://qmro.qmul.ac.uk/xmlui/handle/123456789/15695
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.
10.1007/978-1-4939-1438-8_4
O'Reilly JE, dos Reis M, Donoghue PCJ(2015). Dating Tips for Divergence-Time Estimation. Trends in Genetics vol. 31, (11) 637-650.
10.1016/j.tig.2015.08.001
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.
10.1093/czoolo/61.5.874
https://qmro.qmul.ac.uk/xmlui/handle/123456789/13193
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.
10.1534/genetics.114.162263
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.
10.1093/molbev/msu142
https://qmro.qmul.ac.uk/xmlui/handle/123456789/12250
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.
10.1093/gbe/evu006
https://qmro.qmul.ac.uk/xmlui/handle/123456789/12307
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)
10.1098/rsbl.2013.1003
https://qmro.qmul.ac.uk/xmlui/handle/123456789/13900
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.
10.1093/sysbio/syu020
https://qmro.qmul.ac.uk/xmlui/handle/123456789/14882
dos Reis M (2013). Population genetics and substitution models of adaptive evolution. Abstract: java.sql.Clob org.hibernate.engine.jdbc.WrappedClob java.io.Serializable , Notes: 24 pages, 4 figures and 1 table. Manuscript written between January and April 2010,
https://qmro.qmul.ac.uk/xmlui/handle/123456789/23890
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.
10.1534/genetics.113.152025
Dos Reis M, Yang Z(2013). The unbearable uncertainty of Bayesian divergence time estimation. Journal of Systematics and Evolution vol. 51, (1) 30-43.
10.1111/j.1759-6831.2012.00236.x
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.
10.1534/genetics.111.136432
https://qmro.qmul.ac.uk/xmlui/handle/123456789/14968
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.
10.1098/rspb.2012.0683
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.
10.1111/j.1365-294X.2011.05201.x
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.
10.1093/molbev/msr045
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.
10.1093/molbev/msq317
https://qmro.qmul.ac.uk/xmlui/handle/123456789/14886
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.
10.1093/molbev/msq303
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.
10.1016/j.gep.2010.05.002
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)
10.1371/journal.pcbi.1000564
https://qmro.qmul.ac.uk/xmlui/handle/123456789/14070
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.
10.1007/s00239-009-9282-x
https://qmro.qmul.ac.uk/xmlui/handle/123456789/14885
Dos Reis M, Wernisch L(2009). Estimating translational selection in eukaryotic genomes. Molecular Biology and Evolution vol. 26, (2) 451-461.
10.1093/molbev/msn272
https://qmro.qmul.ac.uk/xmlui/handle/123456789/14883
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.
10.1261/rna.2272306
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.
10.1093/nar/gkh834
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.
10.1093/nar/gkg897
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.
10.1016/S0092-8674(03)00927-9
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