Dr Martin Simmen

My research is centred on computational/bioinformatics studies of different eukaryotic gene regulatory mechanisms.

Dr Martin Simmen


Hugh Robson Building

15 George Square

Edinburgh EH8 9XD

Contact details

 Work: +44 (0)131 651 1773

 Email: M.Simmen@ed.ac.uk


Personal profile

  • 2000 - present: Lecturer, School of Biomedical Sciences, University of Edinburgh
  • 1997 - 2000: Wellcome Trust Research Fellow in Mathematical Biology, Inst. of Cell & Molecular Biology, University of Edinburgh
  • 1995 - 1997: Postdoctoral Research Fellow, Inst. of Cell & Molecular Biology, University of Edinburgh
  • 1992 - 1995: MRC Computational Neuroscientist, Universities of Oxford and Edinburgh
  • 1992: PhD in Theoretical Physics (specializing in neural network models), University of Edinburgh
  • 1988: BSc (Hons) in Physics, University of Edinburgh

Research Theme


Dr Martin Simmen's research briefing

My research concerns the development and application of bioinformatics & computational/statistical approaches (usually in collaboration with experimental groups) to investigate diverse topics, including gene regulation, epigenetic mechanisms, the evolution of protein families and genomes, and synaptic morphology. 

Current experimental techniques often produce large and complex datasets and a large part of my work involves collaborating with experimental groups to ensure that appropriate quantitative approaches are used to analyse these, both to address key hypotheses and to generate novel hypotheses.

I also have an interest in the formal evaluation of the effectiveness of different types of undergraduate teaching in the biological/biomedical sciences.



Jones RA, Reich CD, Dissanayake KN, Kristmundsdottir F, Findlater GS, Ribchester RR, Simmen MW, Gillingwater TH (2016) NMJ-morph reveals principal components of synaptic morphology influencing structure-function relationships at the neuromuscular junction. Open Biology,  6 (12) Article Number: 160240

 McQueen HA, Shields C, Finnegan DJ, Higham J, Simmen MW (2014) PeerWise provides significant academic benefits to biological science students across diverse learning tasks, but with minimal instructor intervention, Biochemistry and Molecular Biology Education, 42:371-81.

 Maciver SK, Asif M, Simmen MW, Lorenzo-Morales, J (2013) A systematic analysis of Acanthamoeba genotype frequency correlated with source and pathogenicity: T4 is confirmed as a pathogen-rich genotype, European Journal of Protistology 49:217-221.

Vastermark A, Sallman Almen M, Simmen MW, Robert Fredriksson R, Schioth HB (2011) Functional specialization in nucleotide sugar transporters occurred through differentiation of the gene cluster EamA (DUF6) before the radiation of Viridiplantae. BMC Evolutionary Biology, 11: 123.

Fraser RM, Keszenman-Pereyra D, Simmen MW, Allan J (2009) High-resolution mapping of sequence-directed nucleosome positioning on genomic DNA, Journal of Molecular Biology 390: 292-305.

Simmen MW (2008) Genome-scale relationships between cytosine methylation and dinucleotide abundances in animals. Genomics 92: 33-40.

Fraser RM, Allan J, Simmen MW (2006) In silico approaches reveal the potential for DNA sequence-dependent histone octamer affinity to influence chromatin structure in vivo. Journal of Molecular Biology 364: 582-598.

Martin Simmen publication list (PDF)

Information for students:

Willingness to discuss research projects with undergraduate and postgraduate students: YES - please click here