Dr Amanda Clare

BA (Oxon), MSc( Edinburgh), PhD

Dr Amanda Clare

Senior Lecturer

Department of Computer Science

Contact Details

Profile

I am interested in all genomics questions and in particular, in what we can do with computers (algorithms, data structures and artificial intelligence) to help answer these questions. DNA/RNA sequencing allows us to inspect the genetic composition of microbes, animals, plants and viruses, but after we have obtained the sequences, what can we learn? How are communities changing over time? How are enzymes within a community specialised for different roles? Can we find new sources of anti-microbials? How can we detect genes in communities of organisms that have never been cultured? I'm also interested in the ethical and moral implications of genomic technologies, and in how the public will react to this information.

Teaching

Research

I am interested in all aspects of bioinformatics. Recent areas have included genomics and metagenomics, primer design, genome modification and ecological trait databases. I have a background in machine learning and data mining, particularly in the construction and interpretation of explanatory models. I also collaborate with text mining researchers to analyse the structure of science and scientific publications.

Research Groups

Publications

Clare, A & Daykin, JW 2019, 'Enhanced string factoring from alphabet orderings' Information Processing Letters, vol. 143, pp. 4-7. https://doi.org/10.1016/j.ipl.2018.10.011
Clare, A, Daykin, J, Mills, T & Zarges, C 2019, 'Evolutionary Search Techniques for the Lyndon Factorization of Biosequences' Paper presented at Workshop on Evolutionary Computation for Permutation Problems at GECCO 2019, Prague, Czech Republic, 13 Jul 2019 - 17 Jul 2019, pp. 1543-1550.
Nicholls, S, Aubrey, W, Edwards, A, de Grave, K, Huws, S, Leander, S, Soares, A, Creevey, C & Clare, A 2019 'Recovery of gene haplotypes from a metagenome' bioRxiv. https://doi.org/10.1101/223404
Clare, A & Daykin, J 2018, 'Alphabet Reordering for the Lyndon Factorization of Biological Strings'. https://doi.org/10.6084/m9.figshare.7029425.v1
Nicholls, S, Aubrey, W, Edwards, A, de Grave, K, Huws, S, Leander, S, Soares, A, Creevey, C & Clare, A 2018 'Computational haplotype recovery and long-read validation identifies novel isoforms of industrially relevant enzymes from natural microbial communities' bioRxiv. https://doi.org/10.1101/223404
More publications on the Research Portal