Michael Golden

Post-doctoral Researcher

Department of Zoology

University of Oxford

Peter Medawar Building

South Parks Road

Oxford, OX1 3SY, UK

My research focuses on the impact of structural constraints on sequence evolution and the joint modelling of sequence and structure evolution, rather than just sequence alone. For example, modelling the impact of a conserved RNA secondary structure within an alignment of sequences on the patterns of sequence evolution, and modelling how the three-dimensional structures of proteins change as a function of their naturally evolving amino acid sequences.


I have especially focused on the nucleic acid secondary structures of single-stranded RNA and DNA viruses, many of which have genomes known to contain functionally important structures. These structures often show clear evidence of their evolutionary maintenance imprinted on the observed patterns of sequence evolution. Conversely, these patterns can be used to help identify structures with potential biological importance, and can thereby assist researchers in prioritising their computational or wet-lab experiments.

Golden M, García-Portugués E, Sørensen M, Mardia KV, Hamelryck T & Hein J (2017) A generative angular model of protein structure evolution. Molecular Biology & Evolution 34:2085-2100

Mauger DM, Golden M, Yamane D, Williford S, Lemon SM, Martin DP & Weeks KM (2015) Functionally conserved architecture of hepatitis C virus RNA genomes. Proceedings of the National Academy of Sciences USA 112:3692-3697

Golden M, Muhire, BM, Semegni Y & Martin DP (2014) Patterns of recombination in HIV-1M are influenced by selection disfavouring the survival of recombinants with disrupted genomic RNA and protein structures. PLOS One 9:e100400

Muhire BM, Golden M, Murrell B, Lefeuvre P, Lett JM, Gray A et al. (2014) Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses. Journal of Virology 88:1972-1989.

Golden M & Martin D (2012) DOOSS: a tool for visual analysis of data overlaid on secondary structures. Bioinformatics 29:271-272

Research Interests

Selected Publications