Mario Dos Reis

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  • Email mdosrei
  • ORCID ID: {{{OrcidID}}}
  • Tel. +44 (0)208 816 2300
  • Address: see Contact

Research Interests

Bioinformatics, molecular evolution and genomics.

Recent Publications

  • dos Reis M, Wernisch L, and Savva R. (2003) Unexpected correlations between gene expression and codon usage bias from microarray data for the whole E. coli K-12 genome. Nucleic Acids Res., 31: 6976-6985. PDF
  • 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
  • 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
  • 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

Research

I am currently starting work on the evolution of the influenza virus at NIMR, Mill Hill. The human Influenza A is a fast mutating RNA virus that continuously accumulates amino acid substitutions that affect the structure of its surface proteins, allowing it to evade the host immune system. This process, known as antigenic shift, allows the virus to cause the recurrent epidemics of flu in humans every winter. Sometimes, bird strains of the virus are occasionally able to cross the species barrier and infect humans, and if they adquire mutations that facilitate the infection from human to human, a flu pandemic such as the 1918 Spanish influenza can arise. Since the virus genome is made up of separate RNA fragments, mixed infections where different strains (possible from different species) co-infect a single host, can give way to the development of new strains from the repacking of the mixed set of RNA fragments. This might produce virus particles that can have substantially different antigenic properties. This process, known as antigenic shift, allows the virus to cause world wide flu pandemics when it is introduced into immunologically naive human populations. My work will be focused on the evolution of the RNA polymerase and NP genes of the virus, and its relationship to host shifts and the emergence of new epidemics.

My PhD project, which I am finishing, concerns the identification of putative factors that determine codon usage bias patterns across eukaryotes and prokaryotes. Since the first DNA sequences were available, it was quickly noticed that the usage of synonymous codons in protein coding genes is not random, and the first studies in this area showed that every genome seems to have a particular preference of codon choices. Although much research has been carried out in this area for the past 20 years, the real reasons underlying the idiosyncratic behavior of codon usage across most genomes remains an unanswered question in molecular evolution. I am currently developing statistical methods to test the effect of natural selection on codon usage bias in different genomes, with the hope of finding out an answer to this question.