Information & Computational Sciences

Paul Shaw

paul_shawMeet Paul (Room: AF105 Ext: 8864) +441382568864

I was brought up in a small Perthshire village just a few miles from the James Hutton Institute Invergowrie site and went to high school and university in Dundee before getting my first scientific job at the Roslin Institute in Edinburgh. I worked at Roslin for three years on the development of a generic resource database for commercially farmed animals called ResSpecies before getting the opportunity to move back to what was at the time the Scottish Crop Research Institute (SCRI) in Invergowrie (now The James Hutton Institute).

Now I do mainly database stuff with a bit of everything else thrown in for good measure. Recently its been in the development of visualization tools for looking at plant pedigree and genetic resources data. At work I mainly work in barley but have had some collaborations with Prof. John Brown (UoD) and Craig Simpson in Arabidopsis alternative splicing and on the Seeds of Discovery Project which is looking at diversity in maize (Zea mays) and wheat (Triticum spp.), this is in collaboration with CIMMYT in Mexico and DArT in Australia. Our part of that is in the development of databases and visualization tools to help (primarily) Mexican plant breeders. For a more extensive list of what I am up to look at some of the links below to the applications and databases I am working on.

At work I would describe myself as pragmatic, it has also been said that I am not particularly tolerant of people making things more complicated than they actually are. I was once described in a school report as a ‘man of few words’ but I am not sure how much resemblance that has on me now!

You wont find me on Twitter, that is one game I have no interest in playing! But you will get me on the following social network sites.


Google Scholar

Ok, I gave in, I am now on twitter @cardinalb

I also have an official institute webpage which you can get at


BioVis 4th Symposium on Biological Data Visualization, ISMB 11-12 July 2014, Boston, USA – Best Paper Award for “Helium: Visualization of Large Scale Plant Pedigrees”.

Paul’s Publications

Click here for conference abstracts, posters and technical documents

16. Shaw, P.D., Kennedy, J., Graham, M., Milne, I. and Marshall, D.F. 2014. Helium: Visualization of large scale plant pedigrees. BMC Bioinformatics. In Press

15. Simpson, C., Lewandowska, D., Liney, M., Davidson, D., Chapman, S, Fuller, J., McNicol, J., Shaw, P. and Brown, J. 2014. Arabidopsis PTB1 and PTB2 proteins negatively regulate splicing of a mini-exon splicing reporter and affect alternative splicing of endogenous genes differentially. New Phytologist, doi:10.1111/nph.12821

14. Streitner, C, Simpson, C., Shaw, P,. Danisman, S., Brown, J., Staiger, D. 2013. Small changes in ambient temperature affect alternative splicing in Arabidopsisthaliana. Plant Signalling & Behaviour 8 (7).

13. Comadran, J., Kilian, B., Russell, J., Ramsay, L., Stein, N., Ganal, M., Shaw, P., Bayer, M., Thomas, W., Marshall, D., Hedley, P., Tondelli, A., Pecchioni, N., Francia, E., Korzun, V., Walther, A. and Waugh, R. 2012. Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barleyNature genetics, advance on. doi:10.1038/ng.2447

12. Streitner, C., Köster, T., Simpson, C.G., Shaw, P., Danisman, S., Brown, J.W.S., Staiger, D. 2012. An hnRNP-like RNA-binding protein affects alternative splicing by in vivointeraction with transcripts in Arabidopsis thalianaNucleic Acids Research. doi:10.1093/nar/gks873

11. Milne, I., Stephen, G., Bayer, M., Cock, P.J.A., Pritchard, L., Cardle, L., Shaw, P., Marshall, D.F. 2012. Using Tablet for visual exploration of second generation sequencing data. Briefings in Bioinformatics. doi: 10.1093/bib/bbs012

10. Wang, M., Jiang, N., Jia, T., Leach, L., Cockram, J., Comadran, J., Shaw, P.,Waugh, R., Luo, Z. 2011. Genome-wide association mapping of agronomic and morphologic traits in highly structured populations of barley cultivars. TAG Theoretical and Applied Genetics. DOI: 10.1007/s00122-011-1771-9

9. Bayer, M., Milne, I., Stephen, G., Shaw, P., Cardle, L., Wright, F., Marshall, D. 2011. Comparative visualization of genetic and physical maps with Strudel.Bioinformatics 27 (9), 1307-1308.

8. Cockram, J. et al., 2010. Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genomeProceedings of the National Academy of Sciences.

7. Milne, I., Shaw, P., Stephen, G., Bayer, M., Cardle, L., Thomas, W.T.B., Flavell, A.J., Marshall, D. 2010. Flapjack – Graphical Genotype Visualization.Bioinformatics.

6. Jing R., Vershinin A., Grzebyta J., Shaw P., Smykal P., Marshall D., Ambrose M.J., Ellis T.N., Flavell A.J. 2010. The genetic diversity and evolution of field pea (Pisum) studied by high throughput retrotransposon based insertion polymorphism (RBIP) marker analysis. BMC Evolutionary Biology 10(1), 44.

5. Milne, I., Bayer, M., Cardle, L., Shaw, P., Stephen, G., Wright, F. and Marshall, D. 2009. Tablet – Next generation sequence assembly visualization.Bioinformatics.

4. Kopecký, D., Bartoš, J., Lukaszewski, A.J., Baird, J.H., Cernoch, V., Kölliker, R., Rognli, O.A., Blois, H.,  Caig, V., Lübberstedt, T., Studer, B., Shaw, P., Doležel, J. and Kilian, A. 2009. Development and mapping of DArT markers within the Festuca – Lolium complexBMC Genomics 10, 473.

3. Brown, J.W.S., Shaw, P., Marshall, D.F. 2005. The Arabidopsis nucleolar protein databaseNucleic Acids Research 33, Database Issue, D633-D636.

2. Caldwell, D.G., McCallum, N., Shaw, P., Muehlbauer, G.J., Marshall, D.F., Waugh, R. 2004. A structured mutant population for forward and reverse genetics in Barley (Hordeum vulgare L.). Plant Journal 40(1), 143-50.

1. Brown, J.W.S., Echeverria, M., Liang-Hu, Qu., Lowe, T.M., Bachellerie, J.-P., Huttenhofer, A., Kastenmayer, J.P., Green, P.J., Shaw, P., Marshall, D.F. 2003.Plant snoRNA DatabaseNucleic Acids Research 31, 432-435.