Intelligent Data Ecosystems

TitleIntelligent Data Ecosystems
TypeScience Department
InstituteRothamsted Research
HeadChris Baker
Executive AssistantSally Murdoch

Outputs

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Changes in organic carbon to clay ratios in different soils and land uses in England and Wales over time

A - Papers appearing in refereed journals
Prout, J. M., Shepherd, K. D., McGrath, S. P., Kirk, G. J. D., Hassall, K. L. and Haefele, S. M. 2022. Changes in organic carbon to clay ratios in different soils and land uses in England and Wales over time. Scientific Reports. 12, p. 5162. https://doi.org/10.1038/s41598-022-09101-3

The impact of drought length and intensity on N cycling gene abundance, transcription and the size of an N2O hot moment from a temperate grassland soil

A - Papers appearing in refereed journals
Barrat, H., Clark, I. M., Evans, J., Chadwick, D. R. and Cardenas, L. M. 2022. The impact of drought length and intensity on N cycling gene abundance, transcription and the size of an N2O hot moment from a temperate grassland soil. Soil Biology and Biochemistry. 168 (May), p. 108606. https://doi.org/10.1016/j.soilbio.2022.108606

CO2 fluxes from three different temperate grazed pastures using Eddy covariance measurements

A - Papers appearing in refereed journals
Cardenas, L. M., Olde, L., Loick, N., Griffith, B. A., Hill, T., Evans, J., Cowan, N., Segura, C., Sint, H. M., Harris, P., McCalmont, J., Zhu, S., Dobermann, A. and Lee, M. R. F. 2022. CO2 fluxes from three different temperate grazed pastures using Eddy covariance measurements. Science of the Total Environment. 831 (20 July), p. 154819. https://doi.org/10.1016/j.scitotenv.2022.154819

Stochastic modelling of bird flocks – accounting for the cohesiveness of collective motion

A - Papers appearing in refereed journals
Reynolds, A. M., McIvor, G. E., Thornton, A., Yang, P. and Ouellette, N. T. 2022. Stochastic modelling of bird flocks – accounting for the cohesiveness of collective motion. Journal of the Royal Society Interface. 19, p. 20210745. https://doi.org/10.1098/rsif.2021.0745

A Near-Chromosome Level Genome Assembly of the European Hoverfly, Sphaerophoria Rueppellii (Diptera: Syrphidae), and a Comparative Analysis of Insecticide Resistance-Related Gene Families in Hemipteran Crop Pests and Pollinators

A - Papers appearing in refereed journals
Bailey, E., Field, L. M., Rawlings, C. J., King, R., Mohareb, F., Hassani-Pak, K., Hughes, D. J., Williamson, M. S., Ganko, E., Buer, B. and Nauen, R. 2022. A Near-Chromosome Level Genome Assembly of the European Hoverfly, Sphaerophoria Rueppellii (Diptera: Syrphidae), and a Comparative Analysis of Insecticide Resistance-Related Gene Families in Hemipteran Crop Pests and Pollinators. BMC Genomics. 23 (1), p. 198. https://doi.org/10.1186/s12864-022-08436-5

Rothamsted Research PhD Student Symposium 1st and 2nd March 2022 Handbook , Posters

C2 - Non-edited contributions to conferences
Mead, A. 2022. Rothamsted Research PhD Student Symposium 1st and 2nd March 2022 Handbook , Posters.

The potential of fluorescence imaging to distinguish insect pest and non-pest species

A - Papers appearing in refereed journals
Shortall, C. R., Perryman, S. A. M., Halsey, K. and West, J. S. 2022. The potential of fluorescence imaging to distinguish insect pest and non-pest species. Outlooks on Pest Management. 33 (1 February), pp. 13-16(4). https://doi.org/10.1564/v33_feb_05

Exploring the effects of land management change on productivity, carbon and nutrient balance: Application of an Ensemble Modelling Approach to the upper River Taw observatory, UK

A - Papers appearing in refereed journals
Hassall, K. L., Coleman, K., Dixit, P., Granger, S. J., Zhang, Y., Sharp, R., Wu, L., Whitmore, A. P., Richter, G. M., Collins, A. L. and Milne, A. E. 2022. Exploring the effects of land management change on productivity, carbon and nutrient balance: Application of an Ensemble Modelling Approach to the upper River Taw observatory, UK. Science of the Total Environment. 824, p. 153824. https://doi.org/10.1016/j.scitotenv.2022.153824

A comprehensive sugar beet virus yellows model

G - Articles in popular magazines and other technical publications
Bell, J. R. and Mead, A. 2022. A comprehensive sugar beet virus yellows model. British Sugar Beet Review. 90, pp. 12-15.

Functionally characterized arthropod pest and pollinator cytochrome P450s associated with xenobiotic metabolism

A - Papers appearing in refereed journals
Katsavou, E., Riga, M., Ioannidis, P., King, R., Zimmer, C. T. and Vontas, J. 2022. Functionally characterized arthropod pest and pollinator cytochrome P450s associated with xenobiotic metabolism. Pesticide Biochemistry and Physiology. 181 (supp 2), p. 105005. https://doi.org/10.1016/j.pestbp.2021.105005

Genetic diversity in nitrogen fertilizer responses and N gas emission in modern wheat

A - Papers appearing in refereed journals
Oszvald, M., Hassall, K. L., Hughes, D. J., Torres-Ballesteros, A., Clark, I. M., Riche, A. B. and Heuer, S. 2022. Genetic diversity in nitrogen fertilizer responses and N gas emission in modern wheat. Frontiers in Plant Science. 13, p. 816475. https://doi.org/10.3389/fpls.2022.816475

Is it possible to attain the same soil organic matter content in arable agriculture soils as under natural vegetation?

A - Papers appearing in refereed journals
Powlson, D. S., Poulton, P. R., Glendining, M. J., Macdonald, A. J. and Goulding, K. W. T. 2022. Is it possible to attain the same soil organic matter content in arable agriculture soils as under natural vegetation? Outlook on Agriculture. 51 (1), pp. 91-104. https://doi.org/10.1177/00307270221082113

Ethylene augments root hypoxia tolerance through amelioration of reactive oxygen species and growth cessation

A - Papers appearing in refereed journals
Liu, Z., Hartman, S., Van Veen, H., Zhang, H., Leeggangers, H. A. C. F., Martopawiro, S., Bosman, F., De Deugd, F., Su, P., Hummel, M., Rankenberg, T., Hassall, K. L., Bailey-Serres, J., Theodoulou, F. L., Voesenek, L. A. C. J. and Sasidharan, R. 2022. Ethylene augments root hypoxia tolerance through amelioration of reactive oxygen species and growth cessation. bioRxiv. https://doi.org/10.1101/2022.01.21.477196

A scaffold-level genome assembly of a minute pirate bug, Orius laevigatus, and a comparative analysis of insecticide resistance-related gene families with hemipteran crop pests

A - Papers appearing in refereed journals
Bailey, E., Field, L. M., Rawlings, C. J., King, R., Mahareb, F., Hassani-Pak, K., Hughes, D. J., Williamson, M. S., Ganko, E., Buer, B. and Nauen, R. 2022. A scaffold-level genome assembly of a minute pirate bug, Orius laevigatus, and a comparative analysis of insecticide resistance-related gene families with hemipteran crop pests. BMC Genomics. 23 (45). https://doi.org/10.1186/s12864-021-08249-y

Can the right composition and diversity of farmed species improve food security among smallholder farmers?

A - Papers appearing in refereed journals
MacLaren, C., Aliyu, K. T., Waswa, W., Storkey, J., Claessens, L., Vanlauwe, B. and Mead, A. 2022. Can the right composition and diversity of farmed species improve food security among smallholder farmers? Frontiers in Sustainable Food Systems. 6, p. 744700. https://doi.org/10.3389/fsufs.2022.744700

The legacy effect of synthetic N fertiliser

A - Papers appearing in refereed journals
Vonk, W. J., Hijbeek, R., Glendining, M. J., Powlson, D. S., Bhogal, A., Merbach, I., Silva, J. V., Poffenbarger, H. J., Dhillon, J., Sieling, K. and Ten Berge, H. F. M. 2022. The legacy effect of synthetic N fertiliser. European Journal of Soil Science. p. e13238. https://doi.org/10.1111/ejss.13238

Combining targeted grass traits with red clover improves grassland performance and reduces need for nitrogen fertilisation

A - Papers appearing in refereed journals
Carswell, A. M., Sanchez-Rodriguez, A. F., Saunders, K. S., Le Cocq, K., Shaw, R., Cotton, J., Zhang, Y., Evans, J., Chadwick, D. R., Jones, D. L. and Misselbrook, T. H. 2022. Combining targeted grass traits with red clover improves grassland performance and reduces need for nitrogen fertilisation. European Journal of Agronomy. 133, p. 126433. https://doi.org/10.1016/j.eja.2021.126433

Establishing long-term nitrogen response of global cereals to assess sustainable fertilizer rates

A - Papers appearing in refereed journals
Van Grinsven, H. J. M., Ebanyat, P., Glendining, Margaret, Gu, B., Hijbeek, R., Lam, S. K., Lassaletta, L., Mueller, N. D., Pacheco, F. S., Quemada, M., Bruulsema, T. W., Jacobsen, B. H. and Ten Berge, H. F. M. 2022. Establishing long-term nitrogen response of global cereals to assess sustainable fertilizer rates. Nature Food. 3, pp. 122-132. https://doi.org/10.1038/s43016-021-00447-x

High-quality, haplotype-phased de novo assembly of the highly heterozygous fig genome, a major genetic resource for fig breeding

Conference paper
Usai, G., Mascagni, T., Giordani, A., Vangelisti, A., Bosi, E., Zuccolo, A., Ceccarelli, M., King, R., Hassani-Pak, K., Solorzano Zambrano, L., Cavallini, A. and Natali, L. 2021. High-quality, haplotype-phased de novo assembly of the highly heterozygous fig genome, a major genetic resource for fig breeding. VI International Symposium on Fig. International Society of Horticultural Science (ISHS). https://doi.org/10.17660/ActaHortic.2021.1310.4

Daisychain Search and Interactive Visualisation of Homologs in Genome Assemblies

A - Papers appearing in refereed journals
Schliebs, O., Chan, C-K. K., Bayer, P. E., Petereit, J., Singh, A., Hassani-Pak, K., Batley, J. and Edwards, D. 2021. Daisychain Search and Interactive Visualisation of Homologs in Genome Assemblies. Agronomy. 11 (12), p. 2587. https://doi.org/10.3390/agronomy11122587

Laboratory phenomics predicts field performance and identifies superior indica haplotypes for early seedling vigour in dry direct-seeded rice

A - Papers appearing in refereed journals
Menard, G. N., Sandhu, N., Anderson, D., Catolos, M., Hassall, K. L., Eastmond, P. J., Kumar, A. and Kurup, S. 2021. Laboratory phenomics predicts field performance and identifies superior indica haplotypes for early seedling vigour in dry direct-seeded rice. Genomics. 113 (6), pp. 4227-4236. https://doi.org/10.1016/j.ygeno.2021.11.006

In silico characterisation of the complete Ly6 protein family in Fasciola gigantica supported through transcriptomics of the newly-excysted juveniles

A - Papers appearing in refereed journals
Davey, S. D., Chalmers, I. W., Fernandez-Fuentes, N., Swain, M. T., Smith, D., Abbas Abidi, S. M., Saifullah, M. K., Raman, M., Ravikumar, G., McVeigh, P., Maule, A. G., Brophy, P. M. and Morphew, R. M. 2021. In silico characterisation of the complete Ly6 protein family in Fasciola gigantica supported through transcriptomics of the newly-excysted juveniles. Molecular Omics. https://doi.org/10.1039/D1MO00254F

Impacts of field margin orientation on populations of soil-dwelling invertebrates in relation to the direction and intensity of field traffic

A - Papers appearing in refereed journals
Carlesso, L., Beadle, A., Cook, S. M., Hartwell, G., Mead, A., Ritz, K., Sparkes, D., Wu, L. and Murray, P. J. 2021. Impacts of field margin orientation on populations of soil-dwelling invertebrates in relation to the direction and intensity of field traffic. Soil Use and Management. https://doi.org/10.1111/sum.12768

Revisiting strategies to incorporate gender-responsiveness into maize breeding in southern Africa

A - Papers appearing in refereed journals
Cairns, J. E., Baudron, F., Hassall, K. L., Ndhlela, T., Nyagumbo, I., McGrath, S. P. and Haefele, S. M. 2021. Revisiting strategies to incorporate gender-responsiveness into maize breeding in southern Africa. Outlook on Agriculture. https://doi.org/10.1177/00307270211045410

High-quality, haplotype-phased de novo assembly of the highly heterozygous fig genome, a major genetic resource for fig breeding

A - Papers appearing in refereed journals
Usai, G., Mascagni, F., Giordani, T., Vangelisti, A., Bosi, E., Zuccolo, A., Ceccarelli, M., King, R., Hassani-Pak, K., Solorzano, L. S., Cavallini, A. and Natali, L. 2021. High-quality, haplotype-phased de novo assembly of the highly heterozygous fig genome, a major genetic resource for fig breeding. Acta Horticulturae. (1310), pp. 21-28. https://doi.org/10.17660/ActaHortic.2021.1310.4

Soil methane (CH4) fluxes in cropland with permanent pasture and riparian buffer strips with different vegetation

A - Papers appearing in refereed journals
Dlamini, J., Cardenas, L. M., Tesfamariam, E. H., Dunn, R. M., Hawkins, J. M. B., Blackwell, M. S. A., Evans, J. and Collins, A. L. 2021. Soil methane (CH4) fluxes in cropland with permanent pasture and riparian buffer strips with different vegetation. Journal of Plant Nutrition and Soil Science. https://doi.org/10.1002/jpln.202000473

Comparative compositions of metabolites and dietary fibre components in doughs and breads produced from bread wheat, emmer and spelt and using yeast and sourdough processes.

A - Papers appearing in refereed journals
Shewry, P. R., America, A. H. P., Lovegrove, A., Wood, A., Plummer, A., Evans, J., Van den Broeck, H. C., Gilissen, L., Mumm, R., Ward, J. L., Proos, Z., Kuiper, P., Longin, C. F. H., Andersson, A. A. M., Van Straaten, J. P., Jonkers, D. and Brouns, F. 2021. Comparative compositions of metabolites and dietary fibre components in doughs and breads produced from bread wheat, emmer and spelt and using yeast and sourdough processes. Food Chemistry. 374 (16 April 2022), p. 131710. https://doi.org/10.1016/j.foodchem.2021.131710

Investigating the origins and evolution of a glyphosate-resistant weed invasion in South America

A - Papers appearing in refereed journals
Gaines, T., Slavov, G., Hughes, D. J., Kupper, A., Sparks, C., Oliva, J., Vila-Aiub, M., Alejandro Garcia, M., Aldo Merotto Jr and Neve, P. 2021. Investigating the origins and evolution of a glyphosate-resistant weed invasion in South America. Molecular Ecology. 30 (21), pp. 5360-5372. https://doi.org/10.1111/mec.16221

High-altitude migration of Psylloidea (Hemiptera) over England

A - Papers appearing in refereed journals
Greenslade, A. F. C., Chapman, J. W. and Reynolds, D. R. 2021. High-altitude migration of Psylloidea (Hemiptera) over England. Entomologist's gazette. 72 (3), pp. 189-198. https://doi.org/10.31184/G00138894.723.1817

Land management legacy affects abundance and function of the acdS gene in wheat root associated pseudomonads

A - Papers appearing in refereed journals
Ruscoe, H., Taketani, R., Clark, I. M., Lund, G., Hughes, D. J., Dodd, I., Hirsch, P. R. and Mauchline, T. H. 2021. Land management legacy affects abundance and function of the acdS gene in wheat root associated pseudomonads. Frontiers in Microbiology. 12, p. 611339. https://doi.org/10.3389/fmicb.2021.611339

Uncovering Trait Associations Resulting in Maximal Seed Yield in Winter and Spring Oilseed Rape

A - Papers appearing in refereed journals
Siles-Suarez, L., Hassall, K. L., Sanchis-Gritsch, C., Eastmond, P. J. and Kurup, S. 2021. Uncovering Trait Associations Resulting in Maximal Seed Yield in Winter and Spring Oilseed Rape. Frontiers in Plant Science. 12 (6 September), p. 697576. https://doi.org/10.3389/fpls.2021.697576

Agrochemicals interact synergistically to increase bee mortality

A - Papers appearing in refereed journals
Siviter, H., Bailes, E. J., Martin, C. D., Oliver, T., Koricheva, J., Leadbeater, E. and Brown, M. J. F. 2021. Agrochemicals interact synergistically to increase bee mortality. Nature. 596, pp. 389-392. https://doi.org/10.1038/s41586-021-03787-7

The distribution of soil micro-nutrients and the effects on herbage micro-nutrient uptake and yield in three different pasture systems

A - Papers appearing in refereed journals
Thomas, C. L., Darch, T., Harris, P., Beaumont, D. A. and Haefele, S. M. 2021. The distribution of soil micro-nutrients and the effects on herbage micro-nutrient uptake and yield in three different pasture systems. Agronomy. 11 (9), p. 1731. https://doi.org/10.3390/agronomy11091731

Elucidating the performance of hybrid models for predicting extreme water flow events through variography and wavelet analyses

A - Papers appearing in refereed journals
Curceac, S., Milne, A. E., Atkinson, P. M., Wu, L. and Harris, P. 2021. Elucidating the performance of hybrid models for predicting extreme water flow events through variography and wavelet analyses. Journal of Hydrology. 598 (July), p. 126442. https://doi.org/10.1016/j.jhydrol.2021.126442

Changes in agricultural climate in South-Eastern England from 1892 to 2016 and differences in cereal and permanent grassland yield

A - Papers appearing in refereed journals
Addy, J., Ellis, R. H., Macdonald, A. J., Semenov, M. A. and Mead, A. 2021. Changes in agricultural climate in South-Eastern England from 1892 to 2016 and differences in cereal and permanent grassland yield. Agricultural and Forest Meteorology. 308-309, p. 108560. https://doi.org/10.1016/j.agrformet.2021.108560

Metagenomic approaches reveal differences in genetic diversity and relative abundance of nitrifying bacteria and archaea in contrasting soils

A - Papers appearing in refereed journals
Clark, I. M., Hughes, D. J., Fu, Q., Abadie, M. and Hirsch, P. R. 2021. Metagenomic approaches reveal differences in genetic diversity and relative abundance of nitrifying bacteria and archaea in contrasting soils . Scientific Reports. 11, p. 15905. https://doi.org/10.1038/s41598-021-95100-9

Exploring the diversity of promoter and 5’UTR sequences in ancestral, historic and modern wheat

A - Papers appearing in refereed journals
Hammond-Kosack, M., King, R., Kanyuka, K. and Hammond-Kosack, K. E. 2021. Exploring the diversity of promoter and 5’UTR sequences in ancestral, historic and modern wheat . Plant Biotechnology Journal. https://doi.org/10.1111/pbi.13672

Environmental drivers of annual population fluctuations in a trans-Saharan insect migrant

A - Papers appearing in refereed journals
Hu, G., Stefanescu, C., Oliver, T. H., Roy, D. B., Brereton, T., Van Swaay, C., Reynolds, D. R. and Chapman, J. W. 2021. Environmental drivers of annual population fluctuations in a trans-Saharan insect migrant. Proceedings of the National Academy of Sciences. 118 (26), p. e2102762118. https://doi.org/10.1073/pnas.2102762118

Understanding the thermodynamic properties of insect swarms

A - Papers appearing in refereed journals
Reynolds, A. M. 2021. Understanding the thermodynamic properties of insect swarms. Scientific Reports. 11, p. 14979. https://doi.org/10.1038/s41598-021-94582-x

Weierstrassian Levy walks are a by-product of crawling

A - Papers appearing in refereed journals
Reynolds, A. M. 2021. Weierstrassian Levy walks are a by-product of crawling. European Physical Journal E. 44, p. 96. https://doi.org/10.1140/epje/s10189-021-00100-2