Dr Paul Shaw

Senior Research Scientist
Information and Computational Sciences
E: Paul.Shaw@hutton.ac.uk
T: +44 (0)1382 568864
Paul focuses on software development for plant genetic resources, genetics and plant breeding. He leads several projects where his research contributes towards making experimental data including plant passport, pedigree, phenotypic and genotypic data available to collaborators, research and breeding communities using a suite of database and visualization tools that his team develops. He is particularly interested in biological visualization and how data can be effectively presented, explored and accessed in logical, digestible chunks in order to gain maximum impact and insight. He is also interested in how biological entities, such as plant accessions in pedigrees, and samples in plant breeding and genetics experiments, can be visualized and modelled using graphs.

Biography

Paul focuses on software development for plant genetic resources, genetics and plant breeding. He leads several projects where his research contributes towards making experimental data including plant passport, pedigree, phenotypic and genotypic data available to collaborators, research and breeding communities using a suite of database and visualization tools that his team develops. He is particularly interested in biological visualization and how data can be effectively presented, explored and accessed in logical, digestible chunks in order to gain maximum impact and insight. He is also interested in how biological entities, such as plant accessions in pedigrees, and samples in plant breeding and genetics experiments, can be visualized and modelled using graphs.

The main software resources his group develops and maintains include the informatics platforms Germinate (https://germinateplatform.github.io/get-germinate) for the storage of experimental data resulting from plant germplasm collections and Helium (https://ics.hutton.ac.uk/helium) for the visualization of complex plant pedigrees. His group is also active in the development of innovative mobile applications for the efficient collection of experimental data (https://cropgeeks.github.io/gridscore) and tools to help with general informatics requirements of genotyping platforms such as the barley 50K SNP platform and maintaining Hutton’s seed store and Underpinning Capacity collections.

He maintains regular interactions with the international plant genetic resources community both through research interests, collaborations and involvement in international groups such as the Divseek International Network (https://divseekintl.org) where Germinate is recognised as a ‘Thematic Hub` promoting the use of Germinate as a common and scalable data infrastructure platform and community focal point suited to a wide range of users who are primarily studying collections of germplasm of different sizes and complexities.

Paul works on a diverse set of projects involving other science departments at the Insitute including Cell and Molecular Sciences, Ecological Sciences and James Hutton Ltd.

Research

  • Information systems for plant genetic resources collections, plant genetics and breeding.
  • Development of visualization tools to help aid understanding of complex plant pedigrees.

Areas of Expertise

  • Database design and implementation.
  • Biological data visualization.
  • Large scale biological data handling and error checking.

Externaly funded research projects 

Other external projects

  • SusCrop-ERA-NET Associate Partner PROGRACE
  • SusCrop-ERA-NET Associate Partner WheatSecurity
  • 2020 – present DivSeek International Germinate Regional Hub coordinator.
  • 2020 – present SusCrop-ERA-NET Cofund on Sustainable Crop Production Associate Partner BRACE (agreement No 771134)

 

Publications

Journals

Books / chapters

  • Shaw, P.; Weise, S.; Obreza, M.; Raubach, S.; McCouch, S.; Kilian, B.; Werner, P. (2023) Database Solutions for Genebanks and Germplasm Collections, In: Ghamkhar, K.; Williams, W. M. & Brown, A.H.D. (eds.). Plant Genetics Resources for the 21st Century – The OMICS Era. New York: Apple Academic Press, Chapter 16, 25pp
  • Forster, B.P.; Franckowiak, J.D.; Lundqvist, U.; Thomas, W.T.B.; Leader, D.; Shaw, P.; Lyon, J.; Waugh, R. (2012) Mutant phenotyping and pre-breeding in barley., In: Shu, Q.Y., Forster, B.P. & Nakagawa, H. (eds.). Plant Mutation Breeding and Biotechnology. CAB International, Wallingford. Chapter 25, pp327-346.

Technical / contract reports

  • Thomas, W.T.B.; Comadran, J.; Ramsay, L.; Shaw, P.; Marshall, D.F.; Newton, A.C.; O’Sullivan, D.; Cockram, J.; Mackay, I.; Bayles, R.; White, J.; Kearsey, M.J.; Luo, Z.; Wang, M.; Tapsell, C.; Harrap, D.; Werner, P.; Klose, S.; Bury, P.; Wroth, J.; Argilllier, O.; Habgood, R.; Glew, M.; Bochard, A-M.; Gymer, P.; Vequaud, D.; Christerson, T.; Allvin, B,; Davies, N.; Broadbent, R.; Brosnan, J.; Bringhurst, T.; Booer, C.; Waugh, R. (2014) Association genetics of UK elite barley (AGOUEB)., Final Project Report to HGCA, No 528, 125pp.
  • Ramsay, L.; Thomas, W.T.B.; Comadran, J.; Marshall, D.F.; Shaw, P.; Waugh, R. (2011) Genetic diversity in modern barley varieties., Annual Report of the Scottish Crop Research Institute for 2010, pp23-24.
  • Milne, I.; Shaw, P.; Milne, L.; Bayer, M.; Stephen, G.; Marshall, D.F. (2010) Visualising genetic diversity., Annual Report of the Scottish Crop Research Institute for 2009, pp21-22.

Conference papers

  • Brooker, R.; Hewison, R.; Mitchell, C.; Newton, A.; Neilson, R.; Pakeman, R.; Raubach, S.; Shaw, P.; Verrall, S.; Karley, A. (2023) Crop mixtures as part of the sustainability toolbox for the distilling industry, World Distilled Spirits Conference, 9 May 2023, EICC, Edinburgh.
  • Shaw, P.; Milne, I.; Cardle, L.; Waugh, R.; Thomas, W.T.B.; Ramsay, L.; Comadran, J.; Stephen G.; Bayer, M.; Graham, M.; Kennedy J.; Oakey, H.; Marshall, D.F. (2012) Visualizing genetic transmission patterns in plant pedigrees., Plant and Animal Genome XX, San Diego, California, 14-18 January 2012.
  • Shaw, P.; Brown, J.W.S. (2010) Subnuclear structures in plants., Subnuclear Structures and Disease, Wellcome Trust Conference, Cambridge, 27-30 July 2010.
  • Shaw, P.; Cardle, L.; Milne, I.; Waugh, R.; Flavell, A.; Thomas, W.T.B.; Grzebyta, J.; Bayer, M.; Marshall, D.F. (2009) Germinate 2: A platform for Illumina SNP genotyping experiments and high volume phenotypic data., Plant & Animal Genome XVII, San Diego, California, 10-14 January 2009.
  • Brown, J.W.S.; Simpson, C.G.; Lewandowska, D.; Clark, G.; Fuller, J.; Kim, S.; Pendle, A.; Shaw, P.J.; Koroleva, O. (2009) The plant Nucleolus, mRNA and nonsense-mediated decay., Eurasnet UK RNA Splicing Workshop, Lake District, 23-25 January 2009, 10.
  • Marshall, D.F.; Close, T.; Ramsay, L.; Druka, A.; Thomas, W.T.B.; Flavell, A.J.; Shaw, P.; Milne, I.; Waugh, R. (2008) Barley genomics and genetic analysis – new trends in barley genomics., 10th International Barley Genetics Symposium, Alexandria, Egypt, 5-10 April 2008.
  • Brown, J.W.S.; Lewandowska, D.; Kim, S.; Pendle, A.; Koroleva, O.; Shaw, P.J. (2008) The Arabidopsis nucleolus accumulated aberrant mRNAs and UPF2 and UPF3 suggesting a role in nonsense-mediated decay., UK RNA Processing Meeting, Lake District, 18-20 January 2008.
  • Marshall, D.F.; Waugh, R.; Dicks, J.; Nwankwo, D.; Ellis, N.; Shaw, P.; Barnard, V.; Ambrose, M.; Flavell, A.J. (2008) New developments in the germinate project., Plant & Animal Genome XVI, San Diego, CA, 12-16 January 2008, 311 (Abstract).
  • Brown, J.W.S.; Kim, S.; Koroleva, O.; Pendle, A.; Lewandowska, D.; McKeown, P.; Shaw, P.J. (2007) The plant nucleolus functions in mRNA export and NMD., RNA Society Meeting. Madison, USA, 29 May – 2 June 2007.
  • Brown, J.W.S.; Kim, S.; Koroleva, O.; Pendle, A.; Lewandowska, D.; McKeown, P.; Shaw, P.J. (2007) The plant nucleolus functions in mRNA export and NMD., 6th Post-Transcriptional Regulation of Plant Gene Expression. Carry-le-Rouet, France, 10-13 May 2007.
  • Brown, J.W.S.; Kim, S.; Pendle, A.; Koroleva, O.; Lewandowska, D.; McKeown, P.; Shaw, P.J. (2007) Proteomic and RNomic analysis of Arabidopsis nucleoli indicate novel functions for the nucleolus., Keystone Meeting: Plant Cell Biology, Idaho, USA, 23-28 March 2007.
  • Shaw, P.J.; Pendle, A.; Koroleva, O.; Lewandowska, D.; Kim, S.; Brown, J.W.S. (2007) Novel functions for the nucleolus from proteomic and RNomic analysis of Arabidopsis nucleoli., Joint Bioinformatics and E-science, Proteomics and Cell Function Grantholders Workshop. BBSRC, Carden Park, Cheshire, 8-10 January 2007.
  • Kim, S.; Pendle, A.; Koroleva, O.; Lewandowska, D.; Shaw, P.J.; Brown, J.W.S. (2007) Proteomic and RNomic analyses of Arabidopsis nucleoli indicate novel functions for the nucleolus., Plant Science Scotland – Plant Biology, University of Glasgow, 5 January 2007.
  • Brown, J.W.S.; Kim, S.; Lewandowska, D.; Pendle, A.; Koroleva, O.; Shaw, P.J. (2006) Arabidopsis nucleoli are enriched in aberrantly spliced mRNAs., EMBO Workshop – The Nucleolus: New perspectives, York, 27-30 March 2006.
  • Brown, J.W.S.; Lewandowska, D.; Kim, S.; Pendle, A.; Koroleva, O.; Shaw, P.J. (2006) Novel functions for the nucleolus from proteomic and RNomic analysis of Arabidopsis nucleoli., UK RNA Processing Meeting. Lake District, 20-22 January 2006.
  • Brown, J.W.S.; Lewandowska, D.; Kim, S.; Pendle, A.; Koroleva, O.; Shaw, P.J. (2006) Proteomic and RNomic analysis of the nucleolus: novel functions in mRNA export and surveillance., 16th Penn State Symposium in Plant Physiology, Penn State, USA, 18-20 May 2006.
  • Kim, S.; Lewandowska, D.; Pendle, A.; Koroleva, O.; Shaw, P.J.; Brown, J.W.S. (2006) Novel functions for the nucleolus from proteomic and RNomic analysis of Arabidopsis nucleoli., RNA Society Meeting. Seattle, USA, 20-25 June 2006.
  • Marshall, D.F.; Shaw, P.; Cardle, L. (2005) The plant genomics database infrastructure at the Scottish Crop Research Institute., Plant & Animal Genome XII, San Diego, California, 15-19 January 2005 (Abstract).

Conference posters / abstracts

  • Shaw, P.; Raubach, S.; Macaulay, M.; Schreiber, M.; Milne, I.; Bayer, M.; Kilian, B. (2023) Going for BOLD Supporting the Biodiversity for Opportunities, Livelihoods and Development Project with Germinate and GridScore, Plant and Animal Genome 30, 13-18 January 2023. San Diego, USA & Online.
  • Raubach, S.; Shaw, P.D.; Brierley, J.; Torrance, L. (2018) Buntata – Potato disease identification on the go., Poster demonstration at Potatoes in Practice 2018, Balruddery Farm, Dundee, 9 August 2018.
  • Shaw, P.D.; Kennedy, J.; Graham, M.; Milne, I.; Marshall, D.F. (2014) Evaluation of Helium: Visualization of large scale plant pedigrees., BiVi (Biological Visualization) 1st Annual Meeting, Edinburgh Napier University, Edinburgh, 16-17 December 2014.
  • Stephen, G.; Milne, I.; Bayer, M.; Shaw, P.D.; Raubach, S.; Hearne, S.; Singh, S.; Wenzl, P.; Marshall, D. (2014) Graphical applications for visualizing and analysing genotype data sets., VizBi 2014, 2nd EMBO Conference on Visualizing Biological Data, EML-Heidelberg, Germany, 5-7 March 2014.
  • Milne, I.; Stephen, G.; Bayer, M.; Shaw, P.D.; Raubach, S.; Hearne, S.; Singh, S.; Wenzl, P.; Marshall, D. (2014) Graphical applications for visualizing and analysing genotype data sets., International Plant and Animal Genome XXII, San Diego, CA, USA, 11-15 January 2014.
  • Shaw, P.D.; Raubach, S.; Milne, I.; Stephen, G.; Wenzl, P.; Hearne, S.; Singh,; Marshall, D.F. (2014) Germinate: Wheat and maize databases for the Seeds of Discovery Project., International Plant and Animal Genome XXII Conference, San Diego, California, 11-15 January 2014.
  • Pritchard, L.; Bayer, M.; Cock, P.; Flores, P.; Jones, S.; Milne, I.; Shaw, P.; Marshall, D. (2014) James Hutton Institute Bioinformatics Grouping., Data Science Research Day, University of Edinburgh, 12 September 2014.
  • Shaw, P.; Thomas, B.; Ramsay, L.; Waugh, R.; Comadran, J.; Stephen, G.; Milne, I.; Graham, M.; Kennedy, J.; Marshall, D. (2013) Visualizing genetic transmission patterns in plant pedigrees., Plant and Animal Genome XXI, San Diego, CA, USA, 12-16 January 2013, P0974.
  • Milne, I.; Stephen, G.; Bayer, M.; Cardle, L.; Shaw, P.; Marshall, D. (2013) Optimisation of SNP and alternative splicing discovery using the Tablet NGS viewer., Plant and Animal Genome XXI, San Diego, CA, USA, 12-16 January 2013, P0971.
  • Thomas, W.T.B.; Comadran, J.; Ramsay, L.; Shaw, P.; Marshall, D.F.; Newton, A.C.; O’Sullivan, D.; Cockram, J.; Mackay, I.; Bayles, R.; Whitehead, C.; Bringhurst, T.; Brosnan, J.; Waugh, R. (2012) QTL controlling malting quality in UK barley., Molecular Mapping and Marker Assisted Selection, VetMed University, Vienna, Austria, 2 August 2012, No. 21 (Abstract).
  • Thomas, W.T.B.; Comadran, J.; Ramsay, L.; Shaw, P.; Marshall, D.F.; Newton, A.C.; O’Sullivan, D.; Cockram, J.; Mackay, I.; Bayles, R.; White, J.; Bringhurst, T.; Brosnan, J.; Waugh, R. (2012) Association genetics studies of progress in the development of UK elite malting barley., 11th International Barley Genetics Symposium, Hangzhou, China, 15-20 April 2012, No. 80 (Abstract).
  • Simpson, C.G.; Kalyna, M.; Shaw, P.; McNicol, J.W.; Marquez, Y.; Barta, A.; Brown, J.W.S. (2012) Arabidopsis ecotype alternative splicing variants., ICAR RNA Satellite Meeting, Vienna, Austria, 3-7 July 2012 (Poster).
  • Simpson, C.G.; Kalyna, M.; Fuller, J.; Shaw, P.; McNicol, J.; Marquez, Y.; Barta, A.; Brown, J.W.S. (2012) Arabidopsis ecotype alternative splicing variants., Plant RNA Workshop, Vienna, Austria, 8-9 July 2012 (Poster).
  • Shaw, P.; Kennedy J.; Milne, I.; Graham, M.; Marshall, D.F. (2012) Using a mathematical graph framework for visualization of inheritance patterns in commercial plant pedigrees., BioVis – 2nd IEEE Symposium on Biological Data Visualisation. Seattle, USA, 14-15 October 2012 (Poster).
  • Thomas, W.T.B.; Comadran, J.; Ramsay, L.; Shaw, P.; Marshall, D.; Newton, A.C.; O’Sullivan, D.; Cockram, J.; Mackay, I.; Bayles, R.; White, J.; Waugh, R.; AGOUEB Consortium. (2011) Detecting and mapping loci for disease resistance in UK elite barley cultivars., Fourth International Workshop on Barley Leaf Blights, West Park Centre, Dundee, 27-29 June 2011.
  • Thomas, W.T.B.; Comadran, J.; Ramsay, L.; Shaw, P.; Marshall, D.F.; Newton, A.C.; O’Sullivan, D.; Cockram, J.; Mackay, I.; Bayles, R.; White, J.; Bringhurst, T.; Brosnan, J.; Waugh, R.; (2011) Recent progress in the genetics of malting barley., World Distilled Spirits Conference Hilton hotel, Glasgow, 8-11 September 2011 (Abstract).
  • Thomas, W.T.B.; Comadran, J.; Ramsay, L.; Shaw, P.; Marshall, D.F.; Newton, A.C.; O’Sullivan, D.; Cockram, J.; Mackay, I.; Bayles, R.; White, J.; Waugh, R.; (2011) Detecting and mapping breeding progress in UK elite barley cultivars., North American Barley Researchers Workshop, Corvallis, USA, 6-8 June 2011 (Abstract).
  • Shaw, P.; Milne, I.; Cardle, L.; Waugh, R.; Flavell, A.J.; Stephen, G.; Bayer, M.; Graham, M.; Kennedy, J.; Marshall, D.F. (2011) Germinate 2 – Storage, visualization and analysis of high volume genotypic, phenotypic and pedigree data., Plant and Animal Genome XIX, San Diego, California, USA, 15-19 January 2011. (Poster)
  • Comadran, J.; Ramsay, L.; William, T.; Macaulay, M.; Marshall, D.F.; Shaw, P.; Cockram, J.; White, J.; Mackay, I.; Liu, Z.; Kearsey, M.J.; O’Sullivan, D.; Waugh, R. (2011) Genetic selection footprints in elite barley cultivars., Plant and Animal Genome XIX, San Diego, California, USA, 15-19 January 2011. (Poster)
  • Shaw, P.; Kennedy, J.; Graham, M.; Milne, I.; Marshall, D.F. (2011) Visualizing genetic transmission patterns in plant pedigrees., BioVis 2011, 1st IEEE Symposium on Biological Data Visialization, Providence, Rhode Island, 23-24 October 2011. (Poster)