Paul Shaw Poster, Conference Abstracts and Technical Documents

Book Chapters

1. 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., Nakagawa, M. & Forster, B.P. (eds.). Mutation Techniques in Plants – Principles and Applications. Chapter 25.

Visualization Focussed Conference Abstracts

3. Shaw, P.D., Kennedy, J., Graham, M., Marshall, D., Evaluation of Helium: Visualization of Large Scale Plant Pedigrees. BioVis 2013 3rd IEEE Symposium on Biological Data Visualization. Atlanta, GA, 13-14 October 2013.

2. Shaw, P.D., Kennedy, J., Graham, M., Milne, I., Marshall, D.F. 2012. Using a Mathematical Graph Framework for Visualization of Inheritance Patterns in Commercial Plant Pedigrees. BioVis 2012 2nd IEEE Symposium on Biological Data Visualization. Seattle, WA, 14 – 15 October 2012.

1. Shaw, P.D., 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 Visualization. Providence, RI, 23 – 24 October 2011.

Biological Focussed Conference Abstracts

34. Dreher, K. Hearne, S., Willcox, M., Singh, S., Saint Pierre, C., Chen, J., Prashant, V., Shaw, P., Milne, I., Stephen, G., Raubach, S., Marshall, D. and Wenzl, P. 2014. Seeds of Discovery project at CIMMYT yields rich data for maize and wheat research. Plant Biology 2014, Portland, Oregon, USA, 12-16 July 2014.

33. Shaw, P.D, Kennedy, J., Graham, M., Milne, I. and Marshall, D.F. 2014. Helium: Visualization of Large Plant Pedigrees. Monogram Network Meeting, Reading, UK, 27-28 March 2014.

32. Stephen, G., Milne, I, Bayer, M., Shaw, P.D., Raubach, S., Hearne, S., Singh, S., Wenzl, P. and Marshall, D. 2014. Graphical applications for visualization and analysis of genotypic data sets. VIZBI, Heidelberg, Germany, 5th-7th March 2014.

31. Shaw, P., Raubach, S., Milne, I,. Stephen, G., Wenzl, P., Hearne, S., Singh, S, Marshall, D. 2014. Germinate: Wheat and Maize Databases for the Seeds of Discovery Project. Plant and Animal Genome XXII, San Diego, CA, 11-15 January 2014

30. Milne, I., Stephen, G., Bayer, M., Shaw, P., Raubach, S., Hearne, S,. Singh, S., Wenzl, P., Marshall, D. 2014. Graphical Applications for Visualizing and Analysing Genotype Data Sets. Plant and Animal Genome XXII, San Diego, CA, 11-15 January 2014

29. 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 & Animal Genome XXI, San Diego, CA, 12-16 January 2013

28. Milne, I., Stephen, G., Bayer, M., Cardle, L., Shaw, P., Marshall D. Optimisation of SNP and Alternative Splicing Discovery using the Tablet NGS Viewer. Plant & Animal Genome XXI, San Diego, CA, 12-16 January 2013

27. Wenzl, P., et. al. Seeds of Discovery: Unlocking the Genetic Potential of Maize and Wheat Genetic Resources. Plant & Animal Genome XXI, San Diego, CA, 12-16 January 2013

26. Simpson, C., Kalyna, M., Shaw, P., McNicol, J., Marquez, Y., Barta, A., Brown, J.W.S. 2012. Arabidopsis Ecotype Alternative Splicing Variants. ICAR RNA Satellite Meeting, Vienna, Austria.

25. 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. 2012. Visualizing Genetic Transmission Patterns in Plant Pedigrees. Plant & Animal Genome XX, San Deigo, CA, 14-18 January 2012

24. 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 23-24.

23. Thomas, W.T.B., Comadran, J., Ramsay, L., Shaw, P., Marshall, D.J., Newton, A.C., O’Sullivan, D., Cockram, J., Mackay, I., Bayles, R., White, J., Waugh, R. & AGOUEB 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

22. Comadran, J., Ramsay, L., Thomas, W., Macaulay, M., Marshall, D.,Shaw, P., Cockram, J., White, J., Liu, Z., the AGOUEB Consortium, Kearsey, M., O’Sullivan, D., Waugh, R. 2011. Genetic Selection Footprints in Elite Barley Cultivars. Plant & Animal Genome XIX, San Diego, CA, 15-19 January 2011

21. Shaw, P., Milne, I., Cardle, L., Waugh, R., Flavell, A., Stephen, G., Bayer, M., Graham, M., Kennedy, J. and Marshall, D.F. 2011. Germinate 2 – Storage, Visualization and Analysis of High Volume Genotypic, Phenotypic and Pedigree Data. Plant & Animal Genome XIX, San Diego, CA, 15-19 January 2011

20. Marshall, D.F., Milne, I., Milne, L., Shaw, P., Bayer, M., Stephen, G., Ramsay, L., Thomas, W., Russell, J., Flavell, A. and Waugh, R. 2010. SCRI visualization tools: an eagle eye view of large cereal data. 20th International Triticeae Mapping Initiative, Beijing, China, 1-5 September 2010

19. Flavell, A.J., Jing, R., Vershinin, A.V., Grzebyta, J., Shaw, P., Smykal, P., Marshall, D.F., Ambrose, M.J. & Ellis, T.H.N. 2010. The genetic diversity and evolution of field pea (Pisum) studied by high-throughput retrotransposon-based insertion polymorphism (RBIP) marker analysis. 2nd International Symposium: Genomics of Plant Genetic Resources, Bologna, Italy, 24-27 April 2010

18. Comadran, J., Ramsay, L., Thomas, W.T.B., Macaulay, M., Marshall, D.F., Shaw, P., Cockram, J., White, J., Mackay, I., Liu, Z., Kearsey, M.J., O’Sullivan, D. & Waugh, R. 2010. Association genetic analysis of UK elite barley platform. Monogram Network Workshop, Norwich, 2-4 March 2010

17. Marshall, D.F., Milne, I., Bayer, M., Shaw, P., Cardle, L., Stephen, G., Ramsay, L., Comadran, J., Thomas, W.T.B., Russell, J.R., Flavell, A.J. & Waugh, R. 2010. What you see is what you get: SCRI visualization tools for SNP discovery, genotype analysis and comparative mapping. Plant & Animal Genome XVIII, San Diego, California, USA, 9-13 January 2010

16. Marshall, D.F., Milne, I., Bayer, M., Shaw, P., Cardle, L., Stephen, G., Ramsay, L., Comadran, J., Thomas, W.T.B., Russell, J., Flavell, A. and Waugh, R. 2010. Tablet, Flapjack and Strudel: SCRI visualization tools to support SNP discovery, genotype analysis and comparative mapping.Plant & Animal Genome XVIII, San Diego, CA, 9-13 January 2010

15. Marshall, D.F., Milne, I., Stephen, G., Cardle, L., Bayer, M., and Shaw, P.2010. What you see is what you get: Visualizing next generation sequence assembly and alignment data in tablet. GARNish 8-9.

14. Shaw, P., Cardle, L., Milne, I., Waugh, R., Flavell, A., Stephen, G., Bayer, M., Graham, M., Kennedy, J. and Marshall, D.F. 2010. Germinate 2 – storage, visualization and analysis of high volume genotypic, phenotypic and pedigree data. Plant & Animal Genome XVIII, San Diego, CA, 9-13 January 2010

13. Ramsay, L., Comadran, J., Marshall, D.F., Thomas, W.T.B., Shaw, P., MacKenzie, K., Druka, A. & Waugh, R. 2009. Association genetics in barley. 9th International Plant Molecular Biology Congress, St Louis, MO, USA, 25-30 October 2009

12. Comadran, J., Ramsay, L., Thomas, W.T.B., Macaulay, M., Marshall, D.F., Shaw, P., Cockram, J., White, J., Mackay, I., Liu, Z., Kearsey, M.J., O’Sullivan, D. & Waugh, R. 2009. UK spring barley association panel. The Rank Prize Funds Mini-Symposium on Domestication of Cereals and Exploitation of Genetic Diversity in Improvement, Grasmere, 21-24 September 2009

11. 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 21-22.

10. 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, CA, 10-14 January 2009

9. Milne, I., Bayer, M., Shaw, P., Cardle, L. and Marshall, D.F. 2009. Flapjack – a high performance application for graphical genotyping. Plant & Animal Genome XVII, San Diego, CA, 10-14 January 2009

8. 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.

7. 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

6. Shaw, P., Rostocks, N., Leader, D., Waugh, R., Cardle, L. and Marshall, D.F. 2006. Barley mutant and SNP databases at SCRI. Plant & AnimalGenome XIII, San Diego, CA, 14-18 January 2006

5. 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, CA, 15-19 January 2005

4. Cardle, L., Shaw, P., Brown, J.W.S., O’Parka, K. and Marshall, D.F. 2004. The development of an integrated suite of plant databases at the SCRI.Plant & Animal Genome XI, San Diego, CA, 10-14 January 2004

3. Papworth, R., Black, I., Law, A., Leckie, S., Russell, G., Shaw, P., Speed, D. and Alan Archibald. 2001.Integrated bioinformatics resources for genome analysis in farm animals. 2001.Chicken Genomics Workshop, Manchester, UK, December 2001.

2. Law, A.S., Nicholson, D., Shaw, P. & Archibald, A.L. 2001. ResSpecies: a generic database for genetic linkage or QTL mapping. Plant & AnimalGenome IX, San Diego, CA, 13-17 January 2001

1. Law, A.S., Nelson, J.P., Papworth, R., Shaw, P., Cai, Y., Russell, G., Black, I., Leckie, S. and Archibald, A.L. 2000. Bioinformatics resources forgenome analysis in farm animals. Plant & Animal Genome VIII, San Diego, CA, 9-12 January 2000