Dr Amanda Clare

BA (Oxon), MSc( Edinburgh), PhD (Aberytwyth)

Dr Amanda Clare

Senior Lecturer

Department of Computer Science

Contact Details

Profile

My research is in data analysis and data science, and in particular in bioinformatics and natural language processing/text analysis, but also the analysis of sequences in general, including time series and in the detection of anomalies. 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? How can we detect genes in communities of organisms that have never been cultured? I am interested in data and in comparing sets of data, whether genomic or text or sequences or counting categories, in understanding distributions, outliers and errors, and summarising the contents.

Research

My research is in data analysis and data science, and in particular in bioinformatics and natural language processing/text analysis, but also the analysis of sequences in general, including time series and in the detection of anomalies. 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? How can we detect genes in communities of organisms that have never been cultured? I am interested in data and in comparing sets of data, whether genomic or text or sequences or counting categories, in understanding distributions, outliers and errors, and summarising the contents.

Publications

Major, L, Clare, A, Daykin, J, Mora, B & Zarges, C 2024 'Heuristics for the Run-length Encoded Burrows-Wheeler Transform Alphabet Ordering Problem' arXiv. 10.48550/arXiv.2401.16435
Dimonaco, NJ, Clare, A, Kenobi, K, Aubrey, W & Creevey, CJ 2023, 'StORF-Reporter: Finding genes between genes', Nucleic Acids Research, vol. 51, no. 21, pp. 11504-11517. 10.1093/nar/gkad814, 10.6084/m9.figshare.23257871
Dimonaco, N, Aubrey, W, Clare, A, Kenobi, K & Creevey, C, StORF-Reporter, 2023, Software, Zenodo. 10.5281/zenodo.8335335
Dimonaco, NJ, Aubrey, W, Kenobi, K, Clare, A & Creevey, CJ 2022, 'No one tool to rule them all: Prokaryotic gene prediction tool annotations are highly dependent on the organism of study', Bioinformatics, vol. 38, no. 5, btab827, pp. 1198-1207. 10.1093/bioinformatics/btab827
Dimonaco, N, Aubrey, W, Kenobi, K, Clare, A & Creevey, C 2022 'StORF-Reporter: Finding Genes between Genes' bioRxiv. 10.1101/2022.03.31.486628
More publications on the Research Portal