Paul Shaw
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.
Current research interests
- 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
- The Global Crop Diversity Trust/Norwegian Government ‘BOLD’ Biodiversity for Opportunities, Livelihoods and Development 2021-2030 (PI)
- BBSRC International Partnering Award ‘BarleyEUNetwork’ BB/V018906/1 2021-2024 (Co-I)
- EU Horizon 2020 ‘BreedingValue’ ID:101000747” 2021-2025 (Co-I)
- Templeton World Charity Foundation/Global Crop Diversity Trust ‘Safeguarding crop diversity for food security: Pre-breeding complemented with Innovative Finance’ ID TWCF0400 2019-2022 (PI)
- INNOVATE UK Plant sensing to determine environmental impacts on developmental processes leading to crop yield ‘CherryBerry’ ID:104624 2019-2021 (Co-I)
- Global Crop Diversity Trust/Norwegian Government ‘Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives’ GS17010 2017-2021 (PI)
Other external projects
- 2020 – present DivSeek International Germinate Regional Hub coordinator.
- 2020 – present SusCrop-ERA-NET Cofund on Sustainable Crop Production Associate Partner BRACE (agreement No 771134)
ORCID
You can get an up to date list of my current publications from this link: https://orcid.org/0000-0002-0202-1150
Bibliography
- 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, 25pp
- Senger, E.; Osorio, S.; Olbricht, K.; Shaw, P.D.; Denoyes, B.; Davik, J.; Predieri, S.; Karhu, S.; Raubach, S.; Lippi, N.; Höfer, M.; Cockerton, H.; Pradal, C.; Kafkas, E.; Litthauer, S.; Usadel, B.; Mezzetti, B. (2022) Towards smart and sustainable development of modern berry cultivars in Europe, The Plant Journal, 111(5), pp. 1238-1251
- Raubach, S.; Schreiber, M.; Shaw, P.D. (2022) GridScore: a tool for accurate, cross-platform phenotypic data collection and visualization, BMC Bioinformatics, 23, Art. 214
- Arrieta Salgado, M.; Macaulay, M.; Colas, I.; Schreiber, M.; Shaw, P.; Waugh, R.; Ramsay, L. (2021) An Induced Mutation in HvRECQL4 Increases the Overall Recombination and Restores Fertility in a Barley HvMLH3 Mutant Background., Frontiers in Plant Science, 12, Art. 706560
- Raubach, S.; Kilian, B.; Dreher, K.; Amri, A.; Bassi, F.M.; Boukar, O.; Cook, D.; Cruickshank, A.; Fatokun, C.; El Haddad, N.; Humphries, A.; Jordan, D.; Kehel, Z.; Kumar, S.; Labarosa, S.J.; Nguyen, L.H.; Mace, E.; McCouch, S.; McNally, K.; Marshall, D.F.; Mikwa, E.O.; Milne, I.; Odeny, D.A.; Plazas, M.; Prohens, J.; Rieseberg, L.H.; Schafleitner, R.; Sharma, S.; Stephen, G.; Quang Tin, H.; Togola, A.; Warschefsky, E.; Werner, P.; Shaw, P. (2021) From bits to bites: advancement of the Germinate platform to support prebreeding informatics for crop wild relatives., Crop Science, 61, 1538-1566.
- Looseley, M.E.; Ramsay, L.; Bull, H.; Swanston, J.S.; Shaw, P.D.; Macaulay, M.; Booth, A.; Russell, J.R.; Waugh, R.; Thomas, W.T.B. (2020) Association mapping of malting quality traits in UK spring and winter barley cultivar collections, Theoretical and Applied Genetics, 133, 2567-2582.
- McCouch, S.; Navabi, K.; Abberton, M.; Anglin, N.L.; Barbieri, R.L.; Baum, M.; Bett, K.; Booker, H.; Brown, G.L.; Bryan, G.J.; Cattivelli, L.; Charest, D.; Eversole, K.; Freitas, M.; Ghamkhar, K.; Grattapaglia, D.; Henry, R.; Inglis, M.C.V.; Islam, T.; Kehel, Z.; Kersey, P.J.; King, G.J.; Kresovich, S.; Marden, E.; Mayes, S.; Ndjiondjop, M.N.; Nguyen, H.T.; Paiva, S.R.; Papa, R.; Phillips, P.W.B.; Rasheed, A.; Richards, C.; Rouard, M.; Sampaio, M.J.A.S.; Scholz, U.; Shaw, P.D.; Sherman, B.; Staton, S.E.; Stein, N.; Svensson, J.; Tester, M.; Valls, J.F.M.; Varshney, R.; Visscher, S.; von Wettberg, E.; Waugh, R. (2020) Mobilizing crop biodiversity., Molecular Plant, 13, 1341-1344.
- Sansaloni, C.; Franco, J.; Santos, B.; Percival-Alwyn, L.; Singh, S.; Petroli, C.; Campos, J.; Dreher, K.; Payne, T.; Marshall, D.; Kilian, B.; Milne, I.; Raubach, S.; Shaw, P.; Stephen, G.; Carling, J.; Saint Pierre, C.; Burgueño, J.; Crosa, J.; Li, H.; Guzman, C.; Kehel, Z.; Amri, A.; Kilian, A.; Wenzl, P.; Uauy, C.; Banziger, M.; Caccamo, M.; Pixley, K. (2020) Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints., Nature Communications, 11, Article No. 4572.
- Darrier, B.; Russel, J.; Milner, S.G.; Hedley, P.E.; Shaw, P.D.; Macaulay, M.; Ramsay, L.D.; Halpin, C.; Mascher, M.; Fleury, D.L.; Langridge, P.; Stein, N.; Waugh, R. (2019) A comparison of mainstream genotyping platforms for the evaluation and use of barley genetic resources., Frontiers in Plant Science, 10, Article No. 544.
- Selby, P.; Abbeloos, R.; Backlund, J.E.; Basterrechea Salido, M.; Bauchet, G.; Benites-Alfaro, O.; Birkett, C.; Calaminos, V.C.; Carceller, P.; Cornut, G.; Costa, B.V.; Edwards, J.D.; Finkers, R.; Gao, S.Y.; Ghaffar, M.; Glaser, P.; Guignon, V.; Hok, P.; Kilian, A.; König, P; Lagare, J.E.B.; Lange, M.; Laporte, M.-A.; Larmande, P.; LeBauer, D.; Lyon, D.; Marshall, D.; Matthews, D.; Milne, I.; Mistry, N.; Morales, N.; Mueller, L.; Neveu, P.; Papoutsoglou, E.; Pearce, B.; Perez-Masias, I.; Pommier, C.; Ramirez-Gonzalez, R.H.; Rathore, A.; Raquel, A.M.; Raubach, S; Rife, T.; Robbins, K.; Rouard, R.; Sarma, C.; Scholz, U.; Selby, P.; Sempere, G.; Shaw, P.; Simon, R.; Soldevilla, N.; Stephen, G.; Sun, Q.; Tovar, C.; Uszynski, G.; Verouden, M. (2019) BrAPI - an Application Programming Interface for plant breeding applications., Bioinformatics, 35, 4147-4155.
- Looseley, M.E.; Griffe, L.L.; Büttner, B.; Wright, K.M.; Middlefell-Williams, J.; Bull, H.; Shaw, P.D.; Macaulay, M.; Booth, A.; Schweizer, G.; Russell, J.R.; Waugh, R.; Thomas, W.T.B.; Avrova, A. (2018) Resistance to Rhynchosporium commune in a collection of European spring barley germplasm., Theoretical and Applied Genetics, 131, 2513-2528.
- Bayer, M.; Ganal, M.; Hedley, P.E.; Macaulay, M.; Plieske, J.; Ramsay, L.; Rapazote-Flores, P.; Russell, J.; Shaw, P.; Thomas, W.; Waugh, R. (2017) Development and evaluation of a barley 50k iSelect SNP array., Frontiers in Plant Science, 8, Article No. 1792.
- Shaw, P.D.; Raubach, S.; Hearne, S.J.; Dreher, K.; Bryan, G.; McKenzie, G.; Milne, I.; Stephen, G.; Marshall, D.F. (2017) Germinate 3: Development of a common platform to support the distribution of experimental data on crop wild relatives., Crop Science, 57, 1259-1273.
- Shaw, P.D.; Graham, M.; Kennedy, J.; Milne, I.; Marshall, D.F. (2014) Helium: visualization of large scale plant pedigrees., BMC Bioinformatics, 15, Article No. 259.
- Simpson, C.G.; Lewandowska, D.; Liney, M.; Davidson, D.; Chapman, S.; Fuller, J.; McNicol, J.; Shaw, P.; Brown, J.W.S. (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, 203, 424-436.
- 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.
- Milne, I.; Stephen, G.; Bayer, M.M.; Cock, P.J.A.; Pritchard, L.; Cardle, L.; Shaw, P.; Marshall, D.F. (2013) Using Tablet for visual exploration of second generation sequencing data., Briefings in Bioinformatics, 14, 193-202.
- Streitner, C.; Simpson, C.G.; Shaw, P.; Danisman, S.; Brown, J.W.S.; Staiger, D. (2013) Small changes in ambient temperature affect alternative splicing in Arabidopsis thaliana., Plant Signalling and Behaviour, 8, Article No. e24638.
- 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 vivo interaction with transcripts in Arabidopsis thaliana., Nucleic Acids Research, 40, 11240-11255.
- Comadran, J.; Kilian, B.; Russell, J.R.; Ramsay, L.; Stein, N.; Ganal, M.; Shaw, P.; Bayer, M.; Thomas, W.T.B.; Marshall, D.F.; Hedley, P.E.; Tondelli, A.; Pecchioni, N.; Francia, E.; Korzun, V.; Walther, A.; Waugh, R. (2012) Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley., Nature Genetics, 44, 1388-1392.
- 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.
- 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.
- Bayer, M.M.; Milne, I.; Stephen, G.; Shaw, P.; Cardle, L.; Wright, F.; Marshall, D.F. (2011) Comparative visualization of genetic and physical maps with Strudel., Bioinformatics, 27, 1307-1308.
- 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.; Bayer, M.M.; Cardle, L.; Shaw, P.; Stephen, G.; Wright, F.; Marshall, D.F. (2010) Tablet - next generation sequence assembly visualization., Bioinformatics, 26, 401-402.
- Jing, R.C.; Vershinin, A.V.; Grzebyta, J.; Shaw, P.; Smykal, P.; Marshall, D.F.; Ambrose, M.J.; Ellis, T.H.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(44).
- Shaw, P.; Brown, J.W.S. (2010) Subnuclear structures in plants., Subnuclear Structures and Disease, Wellcome Trust Conference, Cambridge, 27-30 July 2010.
- 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.
- Kopecky, D.; Bartos, J.; Lukaszewski, A.J.; Baird, J.H.; Cernoch, V.; Kolliker, R.; Rognli, O.A.; Blois, H.; Caig, V.; Lubberstedt, T.; Studer, B.; Shaw, P.; Dolexel, J.; Kilian, A. (2009) Development and mapping of DArT markers within the Festuca - Lolium complex., BMC Genomics, 10(473).
- 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.; 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.
- Senger, E.; Osorio, S.; Olbricht, K.; Shaw, P.D.; Denoyes, B.; Davik, J.; Predieri, S.; Karhu, S.; Raubach, S.; Lippi, N.; Höfer, M.; Cockerton, H.; Pradal, C.; Kafkas, E.; Litthauer, S.; Usadel, B.; Mezzetti, B. (2022) Towards smart and sustainable development of modern berry cultivars in Europe, The Plant Journal, 111(5), pp. 1238-1251
- Raubach, S.; Schreiber, M.; Shaw, P.D. (2022) GridScore: a tool for accurate, cross-platform phenotypic data collection and visualization, BMC Bioinformatics, 23, Art. 214
- Arrieta Salgado, M.; Macaulay, M.; Colas, I.; Schreiber, M.; Shaw, P.; Waugh, R.; Ramsay, L. (2021) An Induced Mutation in HvRECQL4 Increases the Overall Recombination and Restores Fertility in a Barley HvMLH3 Mutant Background., Frontiers in Plant Science, 12, Art. 706560
- Raubach, S.; Kilian, B.; Dreher, K.; Amri, A.; Bassi, F.M.; Boukar, O.; Cook, D.; Cruickshank, A.; Fatokun, C.; El Haddad, N.; Humphries, A.; Jordan, D.; Kehel, Z.; Kumar, S.; Labarosa, S.J.; Nguyen, L.H.; Mace, E.; McCouch, S.; McNally, K.; Marshall, D.F.; Mikwa, E.O.; Milne, I.; Odeny, D.A.; Plazas, M.; Prohens, J.; Rieseberg, L.H.; Schafleitner, R.; Sharma, S.; Stephen, G.; Quang Tin, H.; Togola, A.; Warschefsky, E.; Werner, P.; Shaw, P. (2021) From bits to bites: advancement of the Germinate platform to support prebreeding informatics for crop wild relatives., Crop Science, 61, 1538-1566.
- Looseley, M.E.; Ramsay, L.; Bull, H.; Swanston, J.S.; Shaw, P.D.; Macaulay, M.; Booth, A.; Russell, J.R.; Waugh, R.; Thomas, W.T.B. (2020) Association mapping of malting quality traits in UK spring and winter barley cultivar collections, Theoretical and Applied Genetics, 133, 2567-2582.
- McCouch, S.; Navabi, K.; Abberton, M.; Anglin, N.L.; Barbieri, R.L.; Baum, M.; Bett, K.; Booker, H.; Brown, G.L.; Bryan, G.J.; Cattivelli, L.; Charest, D.; Eversole, K.; Freitas, M.; Ghamkhar, K.; Grattapaglia, D.; Henry, R.; Inglis, M.C.V.; Islam, T.; Kehel, Z.; Kersey, P.J.; King, G.J.; Kresovich, S.; Marden, E.; Mayes, S.; Ndjiondjop, M.N.; Nguyen, H.T.; Paiva, S.R.; Papa, R.; Phillips, P.W.B.; Rasheed, A.; Richards, C.; Rouard, M.; Sampaio, M.J.A.S.; Scholz, U.; Shaw, P.D.; Sherman, B.; Staton, S.E.; Stein, N.; Svensson, J.; Tester, M.; Valls, J.F.M.; Varshney, R.; Visscher, S.; von Wettberg, E.; Waugh, R. (2020) Mobilizing crop biodiversity., Molecular Plant, 13, 1341-1344.
- Sansaloni, C.; Franco, J.; Santos, B.; Percival-Alwyn, L.; Singh, S.; Petroli, C.; Campos, J.; Dreher, K.; Payne, T.; Marshall, D.; Kilian, B.; Milne, I.; Raubach, S.; Shaw, P.; Stephen, G.; Carling, J.; Saint Pierre, C.; Burgueño, J.; Crosa, J.; Li, H.; Guzman, C.; Kehel, Z.; Amri, A.; Kilian, A.; Wenzl, P.; Uauy, C.; Banziger, M.; Caccamo, M.; Pixley, K. (2020) Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints., Nature Communications, 11, Article No. 4572.
- Darrier, B.; Russel, J.; Milner, S.G.; Hedley, P.E.; Shaw, P.D.; Macaulay, M.; Ramsay, L.D.; Halpin, C.; Mascher, M.; Fleury, D.L.; Langridge, P.; Stein, N.; Waugh, R. (2019) A comparison of mainstream genotyping platforms for the evaluation and use of barley genetic resources., Frontiers in Plant Science, 10, Article No. 544.
- Selby, P.; Abbeloos, R.; Backlund, J.E.; Basterrechea Salido, M.; Bauchet, G.; Benites-Alfaro, O.; Birkett, C.; Calaminos, V.C.; Carceller, P.; Cornut, G.; Costa, B.V.; Edwards, J.D.; Finkers, R.; Gao, S.Y.; Ghaffar, M.; Glaser, P.; Guignon, V.; Hok, P.; Kilian, A.; König, P; Lagare, J.E.B.; Lange, M.; Laporte, M.-A.; Larmande, P.; LeBauer, D.; Lyon, D.; Marshall, D.; Matthews, D.; Milne, I.; Mistry, N.; Morales, N.; Mueller, L.; Neveu, P.; Papoutsoglou, E.; Pearce, B.; Perez-Masias, I.; Pommier, C.; Ramirez-Gonzalez, R.H.; Rathore, A.; Raquel, A.M.; Raubach, S; Rife, T.; Robbins, K.; Rouard, R.; Sarma, C.; Scholz, U.; Selby, P.; Sempere, G.; Shaw, P.; Simon, R.; Soldevilla, N.; Stephen, G.; Sun, Q.; Tovar, C.; Uszynski, G.; Verouden, M. (2019) BrAPI - an Application Programming Interface for plant breeding applications., Bioinformatics, 35, 4147-4155.
- Looseley, M.E.; Griffe, L.L.; Büttner, B.; Wright, K.M.; Middlefell-Williams, J.; Bull, H.; Shaw, P.D.; Macaulay, M.; Booth, A.; Schweizer, G.; Russell, J.R.; Waugh, R.; Thomas, W.T.B.; Avrova, A. (2018) Resistance to Rhynchosporium commune in a collection of European spring barley germplasm., Theoretical and Applied Genetics, 131, 2513-2528.
- Bayer, M.; Ganal, M.; Hedley, P.E.; Macaulay, M.; Plieske, J.; Ramsay, L.; Rapazote-Flores, P.; Russell, J.; Shaw, P.; Thomas, W.; Waugh, R. (2017) Development and evaluation of a barley 50k iSelect SNP array., Frontiers in Plant Science, 8, Article No. 1792.
- Shaw, P.D.; Raubach, S.; Hearne, S.J.; Dreher, K.; Bryan, G.; McKenzie, G.; Milne, I.; Stephen, G.; Marshall, D.F. (2017) Germinate 3: Development of a common platform to support the distribution of experimental data on crop wild relatives., Crop Science, 57, 1259-1273.
- Shaw, P.D.; Graham, M.; Kennedy, J.; Milne, I.; Marshall, D.F. (2014) Helium: visualization of large scale plant pedigrees., BMC Bioinformatics, 15, Article No. 259.
- Simpson, C.G.; Lewandowska, D.; Liney, M.; Davidson, D.; Chapman, S.; Fuller, J.; McNicol, J.; Shaw, P.; Brown, J.W.S. (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, 203, 424-436.
- Milne, I.; Stephen, G.; Bayer, M.M.; Cock, P.J.A.; Pritchard, L.; Cardle, L.; Shaw, P.; Marshall, D.F. (2013) Using Tablet for visual exploration of second generation sequencing data., Briefings in Bioinformatics, 14, 193-202.
- Streitner, C.; Simpson, C.G.; Shaw, P.; Danisman, S.; Brown, J.W.S.; Staiger, D. (2013) Small changes in ambient temperature affect alternative splicing in Arabidopsis thaliana., Plant Signalling and Behaviour, 8, Article No. e24638.
- 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 vivo interaction with transcripts in Arabidopsis thaliana., Nucleic Acids Research, 40, 11240-11255.
- Comadran, J.; Kilian, B.; Russell, J.R.; Ramsay, L.; Stein, N.; Ganal, M.; Shaw, P.; Bayer, M.; Thomas, W.T.B.; Marshall, D.F.; Hedley, P.E.; Tondelli, A.; Pecchioni, N.; Francia, E.; Korzun, V.; Walther, A.; Waugh, R. (2012) Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley., Nature Genetics, 44, 1388-1392.
- Bayer, M.M.; Milne, I.; Stephen, G.; Shaw, P.; Cardle, L.; Wright, F.; Marshall, D.F. (2011) Comparative visualization of genetic and physical maps with Strudel., Bioinformatics, 27, 1307-1308.
- Milne, I.; Bayer, M.M.; Cardle, L.; Shaw, P.; Stephen, G.; Wright, F.; Marshall, D.F. (2010) Tablet - next generation sequence assembly visualization., Bioinformatics, 26, 401-402.
- Jing, R.C.; Vershinin, A.V.; Grzebyta, J.; Shaw, P.; Smykal, P.; Marshall, D.F.; Ambrose, M.J.; Ellis, T.H.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(44).
- Kopecky, D.; Bartos, J.; Lukaszewski, A.J.; Baird, J.H.; Cernoch, V.; Kolliker, R.; Rognli, O.A.; Blois, H.; Caig, V.; Lubberstedt, T.; Studer, B.; Shaw, P.; Dolexel, J.; Kilian, A. (2009) Development and mapping of DArT markers within the Festuca - Lolium complex., BMC Genomics, 10(473).
- Brown, J.W.S.; Shaw, P.J.; Shaw, P.; Marshall, D.F. (2005) Arabidopsis nucleolar protein database (AtNoPDB)., Nucleic Acids Research, 33, D633-D636.
- 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, 143-150.
- Brown, J.W.S.; Echeverria, M.; Qu, L.; Lowe, T.M.; Bachellerie, J.; Huttenhofer, A.; Kastenmayer, J.P.; Green, P.J.; Shaw, P.; Marshall, D.F. (2003) Plant snoRNA database., Nucleic Acids Research, 31, 432-435.
- Streitner, C.; Simpson, C.G.; Shaw, P.; Danisman, S.; Brown, J.W.S.; Staiger, D. (2013) Small changes in ambient temperature affect alternative splicing in Arabidopsis thaliana., Plant Signalling and Behaviour, 8, Article No. e24638.
- 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, 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.
- 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.
- 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).
