Biological Sciences

People

Dr Daniel Barker

Location: Ashworth 3 GA55

Telephone: 651 7812

Email: Daniel.Barker@ed.ac.uk

Website: http://4273pi.org

Group members: Dr Heleen Plaisier

C.V.

YearDescription
2016+Lecturer in Bioinformatics, University of Edinburgh
2010-2015Lecturer in Biology, University of St Andrews
2005-2010Research Councils UK Academic Fellow in Evolutionary and Functional Genomics, University of St Andrews
2002-2005Research Fellow, University of Reading
2001-2002Developer, Ensembl project, Wellcome Trust Sanger Institute
1999-2001Software Engineer and Software Engineer II, Analog Devices Inc

Research groupings

Institute of Evolutionary Biology

Teaching

PGBI11006 Bioinformatics. Course Organiser.

PGBI11114 Research Proposal (Bioinformatics). Course Organiser.

PGBI11115 Comparative and Evolutionary Genomics. Course Organiser.

PGBI11003 Statistics and Data Analysis. Lecturer.

MSc Bioinformatics. Examination Board member.

Deputy Senior Tutor for Undergraduate Students, School of Biological Sciences.

Research interests

Bioinformatics education, phylogeny reconstruction and philosophy of science.

4273π - Software for Teaching and Learning Computational Biology. http://4273pi.org

LVB - Reconstructing Evolution with Parsimony and Simulated Annealing. http://lvb.bio.ed.ac.uk

Representative publications

McGill SE, Barker D (2017) Comparison of the protein-coding genomes of three deep-sea, sulfur-oxidising bacteria: "Candidatus Ruthia magnifica", "Candidatus Vesicomyosocius okutanii" and Thiomicrospira crunogena. BMC Research Notes, 10, 296. http://dx.doi.org/10.1186/s13104-017-2598-5

Darby C, Stolzer M, Ropp P, Barker D, Durand D (2017) Xenolog classification. Bioinformatics, 33, 640-649. http://dx.doi.org/10.1093/bioinformatics/btw686

Lim J-H, Latysheva NS, Iggo RD, Barker D (2016) Cluster analysis of p53 binding site sequences reveals subsets with different functions. Cancer Informatics, 15, 199-209. http://dx.doi.org/10.4137/CIN.S39968

Strobl MAR, Barker D (2016) On simulated annealing phase transitions in phylogeny reconstruction. Molecular Phylogenetics and Evolution, 101, 46-55. http://dx.doi.org/10.1016/j.ympev.2016.05.001

McDonagh JL, Barker D, Alderson RG (2016) Bringing computational science to the public. SpringerPlus, 5, 259. http://dx.doi.org/10.1186/s40064-016-1856-7

Barker D, Alderson RG, McDonagh JL, Plaisier H, Comrie MM, Duncan L, Muirhead GTP, Sweeney SD (2015) University-level practical activities in bioinformatics benefit voluntary groups of pupils in the last 2 years of school. International Journal of STEM Education, 2, 17. http://dx.doi.org/10.1186/s40594-015-0030-z

Wreggelsworth KM, Barker D (2015) A comparison of the protein-coding genomes of two green sulphur bacteria, Chlorobium tepidum TLS and Pelodictyon phaeoclathratiforme BU-1. BMC Research Notes, 8, 565. http://dx.doi.org/10.1186/s13104-015-1535-8

Robson JF, Barker D (2015) Comparison of the protein-coding gene content of Chlamydia trachomatis and Protochlamydia amoebophila using a Raspberry Pi computer. BMC Research Notes, 8, 561. http://dx.doi.org/10.1186/s13104-015-1476-2

Barker D (2015) Seeing the wood for the trees: philosophical aspects of classical, Bayesian and likelihood approaches in statistical inference and some implications for phylogenetic analysis. Biology & Philosophy, 30, 505-525. http://dx.doi.org/10.1007/s10539-014-9455-x  

Alderson RG, Barker D, Mitchell JBO (2014) One origin for metallo-β-lactamase activity, or two? An investigation assessing a diverse set of reconstructed ancestral sequences based on a sample of phylogenetic trees. Journal of Molecular Evolution, 79, 117-129. http://dx.doi.org/10.1007/s00239-014-9639-7

Barker D, Ferrier DEK, Holland PWH, Mitchell JBO, Plaisier H, Ritchie MG, Smart SD (2013) 4273π: bioinformatics education on low cost ARM hardware. BMC Bioinformatics, 14, 243. http://dx.doi.org/10.1186/1471-2105-14-243

Lim J-H, Iggo RD, Barker D (2013) Models incorporating chromatin modification data identify functionally important p53 binding sites. Nucleic Acids Research, 41, 5582-5593. http://dx.doi.org/10.1093/nar/gkt260