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Mario dos Reis - Publications

Affiliations: 
2015- School of Biological and Chemical Sciences Queen Mary University of London, London, England, United Kingdom 
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43 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Dos Reis M. Dating Microbial Evolution with MCMCtree. Methods in Molecular Biology (Clifton, N.J.). 2569: 3-22. PMID 36083441 DOI: 10.1007/978-1-0716-2691-7_1  0.334
2021 Álvarez-Carretero S, Tamuri AU, Battini M, Nascimento FF, Carlisle E, Asher RJ, Yang Z, Donoghue PCJ, Dos Reis M. A Species-Level Timeline of Mammal Evolution Integrating Phylogenomic Data. Nature. PMID 34937052 DOI: 10.1038/s41586-021-04341-1  0.739
2021 Tamuri AU, Dos Reis M. A mutation-selection model of protein evolution under persistent positive selection. Molecular Biology and Evolution. PMID 34694387 DOI: 10.1093/molbev/msab309  0.765
2021 Potter JHT, Davies KTJ, Yohe LR, Sanchez MKR, Rengifo EM, Struebig M, Warren K, Tsagkogeorga G, Lim BK, Dos Reis M, Dávalos LM, Rossiter SJ. Dietary Diversification and Specialization in Neotropical Bats Facilitated by Early Molecular Evolution. Molecular Biology and Evolution. 38: 3864-3883. PMID 34426843 DOI: 10.1093/molbev/msab028  0.303
2021 Campbell CR, Tiley GP, Poelstra JW, Hunnicutt KE, Larsen PA, Lee HJ, Thorne JL, Dos Reis M, Yoder AD. Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur. Heredity. PMID 34272504 DOI: 10.1038/s41437-021-00446-5  0.308
2021 Potter JHT, Davies KTJ, Yohe LR, Sanchez MKR, Rengifo EM, Struebig M, Warren K, Tsagkogeorga G, Lim BK, Dos Reis M, Dávalos LM, Rossiter SJ. Dietary Diversification and Specialisation in New World Bats Facilitated by Early Molecular Evolution. Molecular Biology and Evolution. PMID 33585899 DOI: 10.1093/molbev/msab028  0.309
2021 Perri AR, Mitchell KJ, Mouton A, Álvarez-Carretero S, Hulme-Beaman A, Haile J, Jamieson A, Meachen J, Lin AT, Schubert BW, Ameen C, Antipina EE, Bover P, Brace S, Carmagnini A, ... ... Dos Reis M, et al. Dire wolves were the last of an ancient New World canid lineage. Nature. PMID 33442059 DOI: 10.1038/s41586-020-03082-x  0.792
2020 Tiley GP, Poelstra JW, Dos Reis M, Yang Z, Yoder AD. Molecular Clocks without Rocks: New Solutions for Old Problems. Trends in Genetics : Tig. PMID 32709458 DOI: 10.1016/J.Tig.2020.06.002  0.612
2019 Kawahara AY, Plotkin D, Espeland M, Meusemann K, Toussaint EFA, Donath A, Gimnich F, Frandsen PB, Zwick A, Dos Reis M, Barber JR, Peters RS, Liu S, Zhou X, Mayer C, et al. Phylogenomics reveals the evolutionary timing and pattern of butterflies and moths. Proceedings of the National Academy of Sciences of the United States of America. PMID 31636187 DOI: 10.1073/Pnas.1907847116  0.317
2019 McGowen MR, Tsagkogeorga G, Álvarez-Carretero S, Dos Reis M, Struebig M, Deaville R, Jepson PD, Jarman S, Polanowski A, Morin PA, Rossiter SJ. Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture. Systematic Biology. PMID 31633766 DOI: 10.1093/Sysbio/Syz068  0.803
2019 Dos Reis M, Yang Z. Bayesian Molecular Clock Dating Using Genome-Scale Datasets. Methods in Molecular Biology (Clifton, N.J.). 1910: 309-330. PMID 31278669 DOI: 10.1007/978-1-4939-9074-0_10  0.618
2019 Halliday TJD, Dos Reis M, Tamuri AU, Ferguson-Gow H, Yang Z, Goswami A. Rapid morphological evolution in placental mammals post-dates the origin of the crown group. Proceedings. Biological Sciences. 286: 20182418. PMID 30836875 DOI: 10.1098/Rspb.2018.2418  0.771
2019 Álvarez-Carretero S, Goswami A, Yang Z, Dos Reis M. Bayesian Estimation of Species Divergence Times Using Correlated Quantitative Characters. Systematic Biology. PMID 30816937 DOI: 10.1093/Sysbio/Syz015  0.794
2018 Barba-Montoya J, Dos Reis M, Schneider H, Donoghue PCJ, Yang Z. Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution. The New Phytologist. PMID 29399804 DOI: 10.1111/Nph.15011  0.615
2017 Angelis K, Álvarez-Carretero S, Dos Reis M, Yang Z. An Evaluation of Different Partitioning Strategies for Bayesian Estimation of Species Divergence Times. Systematic Biology. PMID 29029343 DOI: 10.1093/Sysbio/Syx061  0.801
2017 Barba-Montoya J, Dos Reis M, Yang Z. Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating. Molecular Phylogenetics and Evolution. PMID 28709986 DOI: 10.1016/J.Ympev.2017.07.005  0.554
2017 Lozano-Fernandez J, Dos Reis M, Donoghue PCJ, Pisani D. RelTime rates collapses to a strict clock when estimating the timeline of animal diversification. Genome Biology and Evolution. PMID 28449025 DOI: 10.1093/Gbe/Evx079  0.304
2016 Thiltgen G, Dos Reis M, Goldstein RA. Finding Direction in the Search for Selection. Journal of Molecular Evolution. PMID 27913840 DOI: 10.1007/S00239-016-9765-5  0.477
2016 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 PC, Pisani D. The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference. Genome Biology and Evolution. PMID 26733575 DOI: 10.1093/Gbe/Evv261  0.322
2015 Dos Reis M, Donoghue PC, Yang Z. Bayesian molecular clock dating of species divergences in the genomics era. Nature Reviews. Genetics. PMID 26688196 DOI: 10.1038/Nrg.2015.8  0.64
2015 Dos Reis M, Thawornwattana Y, Angelis K, Telford MJ, Donoghue PC, Yang Z. Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales. Current Biology : Cb. PMID 26603774 DOI: 10.1016/J.Cub.2015.09.066  0.608
2015 O'Reilly JE, Dos Reis M, Donoghue PC. Dating Tips for Divergence-Time Estimation. Trends in Genetics : Tig. 31: 637-50. PMID 26439502 DOI: 10.1016/j.tig.2015.08.001  0.386
2015 Zhu T, Dos Reis M, Yang Z. Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci. Systematic Biology. 64: 267-80. PMID 25503979 DOI: 10.1093/Sysbio/Syu109  0.652
2015 Jeffares DC, Tomiczek B, Sojo V, dos Reis M. A beginners guide to estimating the non-synonymous to synonymous rate ratio of all protein-coding genes in a genome Methods in Molecular Biology. 1201: 65-90. PMID 25388108 DOI: 10.1007/978-1-4939-1438-8_4  0.356
2015 Angelis K, Dos Reis M. The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times Current Zoology. 61: 874-885.  0.33
2014 Angelis K, Dos Reis M, Yang Z. Bayesian estimation of nonsynonymous/synonymous rate ratios for pairwise sequence comparisons Molecular Biology and Evolution. 31: 1902-1913. PMID 24748652 DOI: 10.1093/Molbev/Msu142  0.609
2014 Dos Reis M, Zhu T, Yang Z. The impact of the rate prior on Bayesian estimation of divergence times with multiple Loci. Systematic Biology. 63: 555-65. PMID 24658316 DOI: 10.1093/Sysbio/Syu020  0.621
2014 Tamuri AU, Goldman N, dos Reis M. A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data. Genetics. 197: 257-71. PMID 24532780 DOI: 10.1534/Genetics.114.162263  0.781
2014 dos Reis M, Donoghue PC, Yang Z. Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals. Biology Letters. 10: 20131003. PMID 24429684 DOI: 10.1098/Rsbl.2013.1003  0.499
2014 Yoder AD, Chan LM, dos Reis M, Larsen PA, Campbell CR, Rasoloarison R, Barrett M, Roos C, Kappeler P, Bielawski J, Yang Z. Molecular evolutionary characterization of a V1R subfamily unique to strepsirrhine primates. Genome Biology and Evolution. 6: 213-27. PMID 24398377 DOI: 10.1093/Gbe/Evu006  0.581
2013 Dos Reis M, Yang Z. Why do more divergent sequences produce smaller nonsynonymous/synonymous rate ratios in pairwise sequence comparisons? Genetics. 195: 195-204. PMID 23792953 DOI: 10.1534/Genetics.113.152025  0.591
2013 Dos Reis M, Yang Z. The unbearable uncertainty of Bayesian divergence time estimation Journal of Systematics and Evolution. 51: 30-43. DOI: 10.1111/J.1759-6831.2012.00236.X  0.614
2012 dos Reis M, Inoue J, Hasegawa M, Asher RJ, Donoghue PC, Yang Z. Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proceedings. Biological Sciences / the Royal Society. 279: 3491-500. PMID 22628470 DOI: 10.1098/Rspb.2012.0683  0.618
2012 Tamuri AU, dos Reis M, Goldstein RA. Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models Genetics. 190: 1101-1115. PMID 22209901 DOI: 10.1534/Genetics.111.136432  0.767
2011 dos Reis M, Yang Z. Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times. Molecular Biology and Evolution. 28: 2161-72. PMID 21310946 DOI: 10.1093/Molbev/Msr045  0.615
2011 dos Reis M, Tamuri AU, Hay AJ, Goldstein RA. Charting the host adaptation of influenza viruses. Molecular Biology and Evolution. 28: 1755-67. PMID 21109586 DOI: 10.1093/Molbev/Msq317  0.741
2011 Yang Z, dos Reis M. Statistical properties of the branch-site test of positive selection. Molecular Biology and Evolution. 28: 1217-28. PMID 21087944 DOI: 10.1093/Molbev/Msq303  0.527
2009 Tamuri AU, Dos Reis M, Hay AJ, Goldstein RA. Identifying changes in selective constraints: host shifts in influenza. Plos Computational Biology. 5: e1000564. PMID 19911053 DOI: 10.1371/Journal.Pcbi.1000564  0.759
2009 dos Reis M, Hay AJ, Goldstein RA. 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. 69: 333-45. PMID 19787384 DOI: 10.1007/S00239-009-9282-X  0.493
2009 dos Reis M, Wernisch L. Estimating translational selection in eukaryotic genomes. Molecular Biology and Evolution. 26: 451-61. PMID 19033257 DOI: 10.1093/Molbev/Msn272  0.677
2006 Withers M, Wernisch L, dos Reis M. Archaeology and evolution of transfer RNA genes in the Escherichia coli genome. Rna (New York, N.Y.). 12: 933-42. PMID 16618964 DOI: 10.1261/Rna.2272306  0.64
2004 dos Reis M, Savva R, Wernisch L. Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Research. 32: 5036-44. PMID 15448185 DOI: 10.1093/Nar/Gkh834  0.656
2003 dos Reis M, Wernisch L, Savva R. Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome. Nucleic Acids Research. 31: 6976-85. PMID 14627830 DOI: 10.1093/Nar/Gkg897  0.599
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