Mario dos Reis

发表

Archaeology and evolution of transfer RNA genes in the Escherichia coli genome.

L. Wernisch, M. dos Reis, Mike Withers, 2006, RNA.

Estimating the Distribution of Selection Coefficients from Phylogenetic Data Using Sitewise Mutation-Selection Models

Richard A. Goldstein, Asif U. Tamuri, R. Goldstein, 2012, Genetics.

The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference

Raymond J. Moran, T. Warnow, S. Mirarab, 2016, Genome biology and evolution.

The Impact of the Rate Prior on Bayesian Estimation of Divergence Times with Multiple Loci

Ziheng Yang, M. dos Reis, Tianqi Zhu, 2014, Systematic biology.

Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

Masami Hasegawa, Robert J Asher, Philip C J Donoghue, 2012, Proceedings of the Royal Society B: Biological Sciences.

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

K. Hammond-Kosack, P. Hedley, R. Waugh, 2011, Molecular ecology.

Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case

Ziheng Yang, A. Yoder, M. dos Reis, 2017, bioRxiv.

Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times.

Ziheng Yang, M. dos Reis, Mario dos Reis, 2011, Molecular biology and evolution.

A species-level timeline of mammal evolution integrating phylogenomic data

Asif U. Tamuri, Ziheng Yang, M. dos Reis, 2021, Nature.

Bayesian Estimation of Species Divergence Times Using Correlated Quantitative Characters

Anjali Goswami, Mario Dos Reis, Ziheng Yang, 2018, bioRxiv.

Dire wolves were the last of an ancient New World canid lineage

A. Ozga, R. Wayne, B. Shapiro, 2021, Nature.

Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales

Angelis, Ziheng Yang, M. dos Reis, 2015, Current Biology.

Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome.

Lorenz Wernisch, Renos Savva, L. Wernisch, 2003, Nucleic Acids Research.

Estimating Translational Selection in Eukaryotic Genomes

Lorenz Wernisch, L. Wernisch, M. dos Reis, 2008, Molecular biology and evolution.

Solving the riddle of codon usage preferences: a test for translational selection.

L. Wernisch, M. dos Reis, R. Savva, 2004, Nucleic acids research.

Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome.

L. Wernisch, R. Savva, Mario dos Reis, 2003, Nucleic acids research.

Dietary Diversification and Specialization in Neotropical Bats Facilitated by Early Molecular Evolution

S. Rossiter, M. dos Reis, K. Warren, 2021, Molecular biology and evolution.

A Mutation–Selection Model of Protein Evolution under Persistent Positive Selection

Asif U. Tamuri, M. dos Reis, Mario dos Reis, 2021, bioRxiv.

Phylogenomics reveals the evolutionary timing and pattern of butterflies and moths

Emmanuel F. A. Toussaint, J. Yack, B. Misof, 2019, Proceedings of the National Academy of Sciences.

Rapid morphological evolution in placental mammals post-dates the origin of the crown group

Asif U. Tamuri, Ziheng Yang, M. dos Reis, 2019, Proceedings of the Royal Society B.

Molecular Clocks without Rocks: New Solutions for Old Problems.

Ziheng Yang, A. Yoder, M. dos Reis, 2020, Trends in genetics : TIG.

Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution

Ziheng Yang, M. dos Reis, H. Schneider, 2018, The New phytologist.

Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating

Ziheng Yang, M. dos Reis, Jose Barba-Montoya, 2017, Molecular phylogenetics and evolution.

RelTime Rates Collapse to a Strict Clock When Estimating the Timeline of Animal Diversification

M. dos Reis, P. Donoghue, D. Pisani, 2017, Genome biology and evolution.

Dating Tips for Divergence-Time Estimation.

P. Donoghue, Joseph E. O’Reilly, Mario dos Reis, 2015, Trends in genetics : TIG.

Characterization of the Uncertainty of Divergence Time Estimation under Relaxed Molecular Clock Models Using Multiple Loci

Ziheng Yang, M. dos Reis, Tianqi Zhu, 2014, Systematic biology.

Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals

Ziheng Yang, M. dos Reis, P. Donoghue, 2014, Biology Letters.

The unbearable uncertainty of Bayesian divergence time estimation

Mario dos Reis, Ziheng Yang, 2012 .

Bayesian Molecular Clock Dating Using Genome-Scale Datasets.

Ziheng Yang, Mario Dos Reis, Ziheng Yang, 2019, Methods in molecular biology.

Notes on the birth–death prior with fossil calibrations for Bayesian estimation of species divergence times

Mario dos Reis, 2016, Philosophical Transactions of the Royal Society B: Biological Sciences.

Molecular Evolutionary Characterization of a V1R Subfamily Unique to Strepsirrhine Primates

Ziheng Yang, A. Yoder, P. Kappeler, 2014, Genome biology and evolution.

Statistical properties of the branch-site test of positive selection.

Ziheng Yang, Ziheng Yang, M. dos Reis, 2011, Molecular biology and evolution.

A beginners guide to estimating the non-synonymous to synonymous rate ratio of all protein-coding genes in a genome.

Daniel C. Jeffares, M. dos Reis, B. Tomiczek, 2015, Methods in molecular biology.

Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur

J. Thorne, A. Yoder, M. dos Reis, 2021, Heredity.

Geogenetic patterns in mouse lemurs (genus Microcebus) reveal the ghosts of Madagascar's forests past

A. Yoder, D. Swofford, P. Kappeler, 2016, Proceedings of the National Academy of Sciences.

Pedigree-based measurement of the de novo mutation rate in the gray mouse lemur reveals a high mutation rate, few mutations in CpG sites, and a weak sex bias

J. Thorne, A. Yoder, M. dos Reis, 2019, bioRxiv.

How to calculate the non-synonymous to synonymous rate ratio of protein-coding genes under the Fisher–Wright mutation–selection framework

M. dos Reis, Mario dos Reis, 2015, Biology Letters.

Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture

A. Polanowski, S. Rossiter, P. Jepson, 2019, Systematic biology.

Bayesian Estimation of Nonsynonymous/Synonymous Rate Ratios for Pairwise Sequence Comparisons

Konstantinos Angelis, Ziheng Yang, Ziheng Yang, 2014, Molecular biology and evolution.

Finding Direction in the Search for Selection

R. Goldstein, M. dos Reis, G. Thiltgen, 2016, Journal of Molecular Evolution.