Google Scholar profile: scholar.google.co.uk/citations?user=zy5V3qMAAAAJ&hl

2019

(42) Bayesian estimation of species divergence times using correlated quantitative characters
Álvarez-Carretero S, Goswami A, Yang Z, and dos Reis M. (2018) Systematic Biology (in press)
DOI: 10.1093/sysbio/syz015

(41) Rapid morphological evolution in placental mammals post-dates the origin of the crown group
Halliday T, dos Reis M, Tamuri A, Ferguson-Grow H Yang Z, and Goswami A. Proceedings of the Royal Society B (in press)
DOI: 10.1098/rspb.2018.2418

(40) Bayesian molecular clock dating using genome-scale datasets
dos Reis M and Yang Z. (2019) In: Anisimova M (ed.) Evolutionary Genomics: Statistical and Computational Methods, Springer (in press)
Chapter and code: github.com/mariodosreis/divtime

2018

(39) Fossil-free dating
dos Reis M (2018) Nature Ecology and Evolution, 2: 771–772.
DOI: 10.1038/s41559-018-0532-4

(38) Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution
Barba-Montaya J, dos Reis M, Schneider H, Donoghue PJD and Yang Z. (2018) New Phytologist, 218: 819–834.
DOI: 10.1111/nph.15011

(37) Using phylogenomic data to explore the effects of relaxed clocks and calibration strategies on divergence time estimation: Primates as a test case
dos Reis M, Gunnell GF, Barba-Montoya J, Wilkins A, Yang Z and Yoder AD. (2018) Systematic Biology, 67: 594–615.
DOI: 10.1093/sysbio/syy001

(36) An evaluation of different partitioning strategies for Bayesian estimation of species divergence times
Angelis K, Álvarez-Carretero A, dos Reis M and Yang Z. (2018) Systematic Biology, 67: 61–77.
DOI: 10.1093/sysbio/syx061

2017

(35) A biologist’s guide to Bayesian phylogenetic analysis
Nascimento FF, dos Reis M, and Yang Z. (2017) Nature Ecology and Evolution, 1: 1446–1454.
DOI: 10.1038/s41559-017-0280-x

(34) Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating
Barba-Montaya J, dos Reis M and Yang Z. (2017) Molecular Phylogenetics and Evolution, 114: 386–400.
DOI: 10.1016/j.ympev.2017.07.005

(33) RelTime rates collapse to a strict clock when estimating the timeline of animal diversification
Lozano Fernandez J, dos Reis M, Donoghue PCJ and Pisani D. (2017) Genome Biology and Evolution, 9: 1320–1328.
DOI: 10.1093/gbe/evx079

(32) Finding direction in the search for selection
Thiltgen G, dos Reis M and Goldstein RA. (2017) Journal of Molecular Evolution, 84: 39–50.
DOI: 10.1007/s00239-016-9765-5 Data: DOI: 10.6084/m9.figshare.4284380.v1

2016

(31) Geogenetic patterns in mouse lemurs (genus Microcebus) reveal the ghosts of Madagascar’s forests past
Yoder AD, Campbell CR, Blanco MB, dos Reis M, Ganzhorn JU, Goodman SM, Hunnicutt KE, Larsen PA, Kappeler PM, Rasoloarison RM, Ralison JM, Swofford DL and Weisrock DW. (2016) Proceedings of the National Academy of Sciences, 113: 8049–8056. Comments in The Washington Post, and National Geographic
DOI: 10.1073/pnas.1601081113

(30) Notes on the birth-death prior with fossil calibrations for Bayesian estimation of species divergence times
dos Reis M. (2016) Philosophical Transactions of the Royal Society B, 371: 20150128.
DOI: 10.1098/rstb.2015.0128

(29) The Interrelationships of placental mammals and the limits of phylogenetic inference
Tarver JE, dos Reis M, Mirarab S, Moran RJ, Parker S, O’Reilly JE, King BL, O’Connell MJ, Asher RJ, Warnow T, Peterson KJ, Donoghue PCJ and Pisani D. (2016) Genome Biology and Evolution, 8: 330–344.
DOI: 10.1093/gbe/evv261

(28) Bayesian molecular clock dating of species divergences in the genomics era
dos Reis M, Donoghue PCJ and Yang Z. (2016) Nature Reviews Genetics, 17: 71–80.
DOI: 10.1038/nrg.2015.8

2015

(27) Uncertainty in the timing of origin of animals and the limits of precision in molecular timescales
dos Reis M, Thawornwattana Y, Angelis K, Telford M, Donoghue PCJ and Yang Z. (2015) Current Biology, 25: 2939–2950. Featured article
DOI: 10.1016/j.cub.2015.09.066 Data: DOI: 10.6084/m9.figshare.1525089

(26) Dating tips for divergence time estimation
O’Reilly J, dos Reis M and Donoghue PCJ. (2015) Trends in Genetics, 31: 637–650.
DOI: 10.1016/j.tig.2015.08.001

(25) The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times
Angelis K and dos Reis M. (2015) Current Zoology, 61: 874–885.
DOI: 10.1093/czoolo/61.5.874

(24) How to calculate the non-synonymous to synonymous rate ratio of protein-coding coding genes under the Fisher-Wright mutation-selection framework
dos Reis M. (2015) Biology Letters, 11: 20141031.
DOI: 10.1098/rsbl.2014.1031 Data: DOI: 10.5061/dryad.3r3q4 R code and examples: DOI: 10.6084/m9.figshare.4282835.v1

(23) Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci
Zhu T, dos Reis M and Yang Z. (2015) Systematic Biology, 64: 267–280.
DOI: 10.1093/sysbio/syu109

(22) A beginner’s guide to estimating the non-synonymous to synonymous rate ratio of all protein-coding genes in a genome
Jeffares DC, Tomiczek B, Sojo V and dos Reis M. (2015) Parasite Genomics Protocols, Methods in Molecular Biology, 1201: 65–90.
DOI: 10.1007/978-1-4939-1438-8_4

2014

(21) Bayesian estimation of nonsynonymous/synonymous rate ratios for pairwise sequence comparisons
Angelis, K. dos Reis M and Yang Z. (2014) Molecular Biology and Evolution, 31: 1902–1913.
DOI: 10.1093/molbev/msu142

(20) The impact of the rate prior on Bayesian estimation of divergence times with multiple loci
dos Reis M, Zhu T and Yang Z. (2014) Systematic Biology, 63: 555–565.
DOI: 10.1093/sysbio/syu020

(19) A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data
Tamuri AU, Goldman N and dos Reis M. (2014) Genetics, 197: 257–271. Highlighted article
DOI: 10.1534/genetics.114.162263

(18) Molecular evolutionary characterization of a V1R subfamily unique to strepsirrhine Primates
Yoder AD, Chan LM, dos Reis M, Larsen PA, Campbell CR, Rasolarison R, Barrett M, Roos C, Kappeler P, Bielawski JP and Yang Z. (2014) Genome Biology and Evolution, 6: 213–227.
DOI: 10.1093/gbe/evu006

(17) Neither phylogenomic nor palaeontological data support a Paleogene origin of placental mammals
dos Reis M, Donoghue PCJ and Yang Z. (2014) Biology Letters, 10: 20131003. Comments in Nature, The Scientist, and Phys.org - F1000 review
DOI: 10.1098/rsbl.2013.1003

2013

(16) Why do more divergent sequences produce smaller nonsynonymous/synonymous rate ratios in pairwise sequence comparisons?
dos Reis M and Yang Z. (2013) Genetics, 195: 195–204.
DOI: 10.1534/genetics.113.152025

(15) The unbearable uncertainty of Bayesian divergence time estimation
dos Reis M and Yang Z. (2013) Journal of Systematics and Evolution, 51: 30–43.
DOI: 10.1111/j.1759-6831.2012.00236.x

2012

(14) Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny
dos Reis M, Inoue J, Hasegawa M, Asher RJ, Donoghue PCJ and Yang Z. (2012) Proceedings of the Royal Society B., 279: 3491–3500. Timetrees (nexus) - 274 species timetree (pdf) - Data - F1000 review
DOI: 10.1098/rspb.2012.0683

(13) Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models
Tamuri AU, dos Reis M and Goldstein RA. (2012) Genetics, 190: 1101–1115.
DOI: 10.1534/genetics.111.136432

2011

(12) 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
Hofinger BJ, Russell JR, Bass CG, Baldwin T, dos Reis M, Hedley PE, Li Y, Macaulay M, Waugh R, Hammond-Kosack KE and Kanyuka K. (2011) Molecular Ecology, 20: 3653–3668.
DOI: 10.1111/j.1365-294X.2011.05201.x

(11) Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times
dos Reis M and Yang Z. (2011) Molecular Biology and Evolution, 28: 2161–2172. R code
DOI: 10.1093/molbev/msr045

(10) Charting the host adaptation of influenza viruses
dos Reis M, Tamuri AU, Hay AJ and Goldstein RA. (2011) Molecular Biology and Evolution, 28: 1755–1767. Featured in Evolutionary Analysis
DOI: 10.1093/molbev/msq317

(9) Statistical properties of the branch-site test of positive selection
Yang Z and dos Reis M. (2011) Molecular Biology and Evolution, 28: 1217–1228.
DOI: 10.1093/molbev/msq303

2010

(8) Analysis of the Albumin/alpha-Fetoprotein/Afamin/Group specific component gene family in the context of zebrafish liver differentation
Noël ES, dos Reis M, Arain Z and Ober EA. (2010) Gene Expression Patterns, 10: 237–243.
DOI: 10.1016/j.gep.2010.05.002

2009

(7) Identifying changes in selective constraints: host shifts in influenza
Tamuri AU, dos Reis M, Hay AJ and Goldstein RA. (2009) PLoS Computational Biology, 5: e1000564.
DOI: 10.1371/journal.pcbi.1000564

(6) Using non-homogeneous models to identify host shift events: application to the origin of the 1918 ‘Spanish’ influenza virus
dos Reis M, Hay AJ and Goldstein RA. (2009) Journal of Molecular Evolution, 69: 333–345. Additional data - Featured in Evolutionary Analysis
DOI: 10.1007/s00239-009-9282-x

(5) Estimating translational selection in eukaryotic genomes
dos Reis M and Wernisch L. (2009) Molecular Biology and Evolution, 26: 451–461. Supporting material
DOI: 10.1093/molbev/msn272

2006

(4) Archaeology and evolution of transfer RNA genes in the Escherichia coli genome
Withers M, Wernisch L, and dos Reis M. (2006) RNA, 12: 933–942. Supporting material
DOI: 10.1261/rna.2272306

2004

(3) Solving the riddle of codon usage preferences: a test for translational selection
dos Reis M, Savva R and Wernisch L. (2004) Nucleic Acids Research, 32: 5036–5044. Software
DOI: 10.1093/nar/gkh834

2003

(2) Churchill, a zinc finger transcriptional activator, regulates the transition between gastrulation and neurulation
Sheng G, dos Reis M, and Stern CD. (2003) Cell, 115: 603–613. Supporting material - F1000 review
DOI: 10.1016/S0092-8674(03)00927-9

(1) Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome
dos Reis M, Wernisch L, and Savva R. (2003) Nucleic Acids Research, 31: 6976–6985.
DOI: 10.1093/nar/gkg897

Preprints

(3) Bayesian estimation of species divergence times using correlated quantitative characters
Álvarez-Carretero S, Goswami A, Yang Z, and dos Reis M. (2018) bioRxiv, 441105.
DOI: 10.1101/441105

(2) Using phylogenomic data to explore the effects of relaxed clocks and calibration strategies on divergence time estimation: Primates as a test case
dos Reis M, Gunnell GF, Barba-Montoya J, Wilkins A, Yang Z, and Yoder A. (2017) bioRxiv, 201327.
DOI: 10.1101/201327

(1) Population genetics and substitution models of adaptive evolution
dos Reis M. (2013) arXiv, 1311.6682.
arXiv: 1311.6682

Peer-review

Reviewer for Algorithms for Molecular Biology, Animal Genetics, Bioinformatics, Biology Letters, BioSystems, BMC Evolutionary Biology, Cladistics, Current Biology, F1000Research, FEBS letters, Gene Expression Patterns, Genome Biology and Evolution, Geobiology, Infection Genetics and Evolution, Journal of Molecular Evolution, Journal of Theoretical Biology, Mechanisms of Development, Molecular Biology and Evolution, Molecular Ecology Resources, Molecular Genetics and Genomics, Molecular Phylogenetics and Evolution, Nature Ecology and Evolution, Nature Methods, Nucleic Acids Research, PeerJ, Palaeontology, Plant Cell Reports, Philosophical Transactions of the Royal Society B, PLoS Computational Biology, PLoS Genetics, PLoS One, Proceedings of the National Academy of Sciences, Proceedings of the Royal Society B, Science Advances, Scientific Reports, Systematic Biology, Trends in Ecology and Evolution, and Virus Evolution. Grant reviewer for The Austrian Science Fund (FWF), The Biotechnology and Biological Sciences Research Council (BBSRC, UK) The French National Research Agency (ANR), The Ministry of Health of Singapore, and the Wellcome Trust UK.