As well as a variety of internal meetings, I attended a couple of receptions, the first of which was at BIS – largely for industrialists and partner organisations. This was very useful, and I met a number of folk who would not normally see themselves as close to our interests. The second was an annual event (though a first for me) where ‘scientists meet the media’ at the Royal Society. Again I made a number of potentially important contacts that will help get the BBSRC message out.
The main visit of the week was to Harper Adams University College. Harper Adams is a major provider of agricultural education, training and knowledge transfer, as well as (largely applied) research. This was thus an exceptionally interesting visit. Without seeking to pick out specific areas, I note that Harper Adams runs the only UK degree courses in Agricultural Engineering, and I saw some very interesting work at the interface of engineering and agriculture, especially in the areas of using modern technology to plant, sense, weed, and harvest agricultural crops. The whole area of ‘precision agriculture’ is going to provide an important contribution to increasing the productivity of food and non-food crops, and we can expect it to expand significantly.
Another very interesting and important area was represented by the OpenFields project. This seeks to make available, in an accessible and structured format, the many and dispersed outputs of agricultural research (sensu lato) in a manner somewhat akin to that available for biomedical publications via UKPMC.
A lot of papers I read last week seemed to be about genomics. Thus, there was a long-heralded paper (long-heralded in that the code has been available at sourceforge for a while) on the development and very effective use of ‘coloured’ de Bruijn graphs in genome assembly, and one on the rise and benefits of analysing ‘your own’ genomics data. Another showed that what was found might be significantly affected by the platform that generated the data; this might or might not be affected by the analyses applied. Because everything is in one sense connected to everything else in biochemical networks, one might wonder whether all genes and gene-finding algorithms might have predictive value; scarily in some circumstances they might. However, the benefits of sequencing multiple cultivars of agricultural crops for finding genes underlying important traits is starting to become clear. Continuing analyses of the so-called ‘missing heritability’ lead to a reaffirmation of the importance of epistasis – a systems biology property – in the understanding of genotype-phenotype interactions.
I also note a useful report on “Understanding the UK Agricultural Research Contribution to International Development and Food Security”, and an interesting piece on the use of Search Engine Optimisation to help get one’s website messages out. A different and maybe more effective method of networking.
- Iqbal, Z., Caccamo, M., Turner, I., Flicek, P. & McVean, G. (2012). De novo assembly and genotyping of variants using colored de Bruijn graphs. Nature Genet, online; DOI:10.1038/ng.1028
- Kell DB (2002) Genotype:phenotype mapping: genes as computer programs. Trends Genet 18:555-559
- Lam, H. Y. K., Clark, M. J., Chen, R., Chen, R., Natsoulis, G., O’Huallachain, M., Dewey, F. E., Habegger, L., Ashley, E. A., Gerstein, M. B., Butte, A. J., Ji, H. P. & Snyder, M. (2012). Performance comparison of whole-genome sequencing platforms. Nature Biotechnol 30, 78-83
- Maclean, D. & Kamoun, S. (2012). Big data in small places. Nature Biotechnol 30, 33-34
- Maher, B. (2008). The case of the missing heritability. Nature 456, 18-21
- Micklos D, Lauter S, Nisselle A (2011) Lessons from a science education portal. Science 334:1657-1658
- Reumers, J., Rijk, P. D., Zhao, H., Liekens, A., Smeets, D., Cleary, J., Loo, P. V., Bossche, M. V. D., Catthoor, K., Sabbe, B., Despierre, E., Vergote, I., Hilbush, B., Lambrechts, D. & Del-Favero, J. (2012). Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing. Nature Biotechnol 30, 61-68
- Venet, D., Dumont, J. E. & Detours, V. (2011). Most random gene expression signatures are significantly associated with breast cancer outcome. PLoS Comput Biol 7, e1002240. Full free text
- Xu, X. et mult al. (2012). Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotechnol 30, 105-111
- Zuk O, Hechter E, Sunyaev SR, Lander ES: The mystery of missing heritability: Genetic interactions create phantom heritability. Proc Natl Acad Sci U S A 2012, online
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