Mario dos Reis

Interests

Bioinformatics, phylogenetics, molecular evolution and genomics.

Research

I am now working on Bayesian estimation of divergence times using soft-bound fossil calibrations, with particular emphasis on mammals. We work with mitochondrial and nuclear genome data for various mammal species and we use extensive fossil calibrations that encompass the breath of mammalian phylogeny. The fossil record shows the sudden appearance of a large diversity of placental mammals 65 My ago, just after the mass extinction event (the K-Pg event when dinosaurs disappeared). However, several molecular studies have suggested that many placental mammal groups started to diversified before this date, despite the absence of placental fossils older than 65 My. This has caused heated debate between the paleontological and molecular phylogenetic communities. We are trying to solve the controversy using unprecedented amounts of genomic data and fossil information.

We are also developing and improving methods of divergence time estimation. Recently we improved the approximate likelihood method for Bayesian estimation of divergence times, and we are now looking into novel ways to incorporate fossil information in the construction of the time prior in the Bayesian estimation problem.

I have also worked on the evolution of influenza viruses (NIMR), studying patterns of codon usage bias in Eukaryotic and Prokaryotic genomes (Birkbeck) and chick embryology (Anatomy, UCL).

Short CV

2010-:

Research Associate, Department of Genetics, Evolution and Environment, UCL, London. UK.

2007-2010:

Research Fellow, Division of Mathematical Biology, NIMR, London. UK.

2004 -2007:

PhD Structural Molecular Biology, Birkbeck College, London. UK.

2001-2003:

MSc Bioinformatics, Birkbeck College, London. UK.
Research Technician, Department of Anatomy and Developmental Biology, University College, London. UK.

1995-2000:

Lic. Biología, Universidad Simon Bolívar, Caracas. Venezuela.

Have reviewed papers for Molecular Biology and Evolution, PLoS Genetics, PLoS Computational Biology, Nucleic Acids Research, Molecular Phylogenetics and Evolution, BMC Evolutionary Biology, FEBS letters, Mechanisms of Development, Gene Expression Patterns, BioSystems, and Plant Cell Reports. Have reviewed a chapter for a book on evolutionary genomics (Springer). Have reviewed grants for The Ministry of Health (Singapore).

Publications

(Google Scholar citation overview)

2012

14. dos Reis M, Inoue J, Hasegawa M, Asher RJ, Donoghue PCJ and Yang Z. (2012) Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc. Roy. Soc. B. (accepted)

13. Tamuri AU, dos Reis M and Goldstein RA. (2012) Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models. Genetics, 190:1101-1115. [pdf]

2011

12. 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) Allele mining and phylogenetic analyses of the eIF4E resistance gene in barley reveal exceptionally high sequence and haplotype diversity and a signature of positive selection. Mol. Ecol., 20:3653–3668. [pdf]

11. dos Reis M and Yang Z. (2011) Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times. Mol. Biol. Evol., 28:2161-2172. [pdf][R code]

10. dos Reis M, Tamuri AU, Hay AJ and Goldstein RA. (2011) Charting the host adaptation of influenza viruses. Mol. Biol. Evol., 28:1755-1767. [pdf]

9. Yang Z and dos Reis M. (2011) Statistical properties of the branch-site test of positive selection. Mol. Biol. Evol., 28:1217-1228. [pdf]

2010

8. Noël ES, dos Reis M, Arain Z and Ober EA. (2010) Analysis of the Albumin/alpha-Fetoprotein/Afamin/Group specific component gene family in the context of zebrafish liver differentation. Gene Expr. Patterns, 10:237-243. [pdf]

2009

7. Tamuri AU, dos Reis M, Hay AJ and Goldstein RA. (2009) Identifying changes in selective constraints: host shifts in influenza. PLoS Comp. Biol., 5:e1000564. [pdf]

6. dos Reis M, Hay AJ and Goldstein RA. (2009) Using non-homogeneous models to identify host shift events: application to the origin of the 1918 'Spanish' influenza virus. J. Mol. Evol., 69:333-345. [pdf] [Additional data]

5. dos Reis M and Wernisch L. (2009) Estimating translational selection in eukaryotic genomes. Mol. Biol. Evol., 26:451-461. [pdf] [Supporting material]

2006

4. Withers M, Wernisch L, and dos Reis M. (2006) Archaeology and evolution of transfer RNA genes in the Escherichia coli genome. RNA, 12:933-942. [pdf] [Supporting material]

2004

3. dos Reis M, Savva R and Wernisch L. (2004) Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res., 32:5036-5044. [pdf] [Software]

2003

2. Sheng G, dos Reis M, and Stern CD. (2003) Churchill, a zinc finger transcriptional activator, regulates the transition between gastrulation and neurulation. Cell, 115:603-613. [pdf] [Supporting material]

1. dos Reis M, Wernisch L, and 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 Res., 31:6976-6985. [pdf]

Software

CodonW and CodonR, software collection for codon usage analysis.