Computational and Analytical Sciences

TitleComputational and Analytical Sciences
TypeScience Department
InstituteRothamsted Research
HeadChris Rawlings
Executive AssistantSally Murdoch

Outputs

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ACE: Application for Conditional probability Elicitation

J - Computer programs

Hassall, K. L. 2019. ACE: Application for Conditional probability Elicitation. GitHub Rothamsted Research.

A Possible Connection Between Plant Longevity and the Absence of Protein Fibrillation: Basis for Identifying Aggregation Inhibitors in Plants

A - Papers appearing in refereed journals

Mohammed-Beigi, H., Kjaer, L., Eskandari, H., Aliakbari, F., Christiansen, G., Ruvo, G., Ward, J. L. and Otzen, D.E. 2019. A Possible Connection Between Plant Longevity and the Absence of Protein Fibrillation: Basis for Identifying Aggregation Inhibitors in Plants. Frontiers in Plant Science. p. 10:148.

New bioactive metabolites from the elicited marine sponge-derived bacterium Actinokineospora spheciospongiae sp. nov.

A - Papers appearing in refereed journals

Tawfike, A., Attia, E. Z., Desoukey, S. Y., Hajjar, D., Makki, A. A., Schupp, P. J., Edrada-Ebel, R. and Abdelmohsen, U. R. 2019. New bioactive metabolites from the elicited marine sponge-derived bacterium Actinokineospora spheciospongiae sp. nov. AMB Express. 9 (12).

Isolation of anticancer and anti-trypanosome secondary metabolites from the endophytic fungus Aspergillus flocculus via bioactivity guided isolation and MS based metabolomics

A - Papers appearing in refereed journals

Tawfike, A. F, Romli, M., Clements, C., Abbott, G., Young, L., Schumacher, M., Diederich, M., Farag, M. and Edrada-Ebel, R. 2019. Isolation of anticancer and anti-trypanosome secondary metabolites from the endophytic fungus Aspergillus flocculus via bioactivity guided isolation and MS based metabolomics. Journal of Chromatography B. (1106-1107), pp. 71-83.

Improved isotopic model based on 15N tracing and Rayleigh-type isotope fractionation for simulating differential sources of N2O emissions in a clay grassland soil

A - Papers appearing in refereed journals

Castellano-Hinojosa, A., Loick, N., Dixon, E. R., Matthews, P., Lewicka-Szczebak, D., Well, R., Bol, R., Charteris, A. and Cardenas, L. M. 2019. Improved isotopic model based on 15N tracing and Rayleigh-type isotope fractionation for simulating differential sources of N2O emissions in a clay grassland soil. Rapid Communications In Mass Spectrometry.

Responses of carbon, nitrogen and phosphorus to two consecutive drying–rewetting cycles in soils

A - Papers appearing in refereed journals

Pezzola, D., Cardenas, L. M., Mian, I.A., Carswell, A. M., Donovan, N., Dhanoa, D. and Blackwell, M. S. A. 2019. Responses of carbon, nitrogen and phosphorus to two consecutive drying–rewetting cycles in soils. Journal of Plant Nutrition and Soil Science.

Metabolomic-Guided Isolation of Bioactive Natural Products from Curvularia sp., an Endophytic Fungus of Terminalia laxiflora

A - Papers appearing in refereed journals

Tawfike, A. F., Abbott, G., Young, L. and Edrada-Ebel, R. 2018. Metabolomic-Guided Isolation of Bioactive Natural Products from Curvularia sp., an Endophytic Fungus of Terminalia laxiflora. Planta Medica. 84 (3), pp. 182-190.

Final grain weight is not limited by the activity of key starch-synthesising enzymes during grain filling in wheat

A - Papers appearing in refereed journals

Fahy, B., Siddiqui, H., David, L., Powers, S. J., Borrill, P., Uauy, C. and Smith, A. 2018. Final grain weight is not limited by the activity of key starch-synthesising enzymes during grain filling in wheat. Journal of Experimental Botany. 69 (22), p. 5461–5475.

Understanding the Relative Impacts of Climate Change on Crop Production using Data from the Rothamsted Long-Term Experiments

F - Theses

Addy, J. 2018. Understanding the Relative Impacts of Climate Change on Crop Production using Data from the Rothamsted Long-Term Experiments. F - Theses University of Reading CAS

Replacing a permanent pasture and its effect in the first year on a commercial dairy farm

A - Papers appearing in refereed journals

Rivero-Viera, J., Orr, R. J., Coumbe, J., Willson, B., Evans, J. and Lee, M. R. F. 2018. Replacing a permanent pasture and its effect in the first year on a commercial dairy farm. Agro Sur. 46 (1), pp. 3-12.

Pyrolysis temperature during biochar production alters its subsequent utilization by microorganisms in an acid arable soil

A - Papers appearing in refereed journals

Luo, Y., Dungait, J. A. J., Zhao, X., Brookes, P. C., Durenkamp, M., Li, G. and Lin, Q. 2018. Pyrolysis temperature during biochar production alters its subsequent utilization by microorganisms in an acid arable soil. Land Degradation & Development. 29 (7), pp. 2183-2188.

More on midges

G - Articles in popular magazines and other technical publications

Reynolds, A. M. 2018. More on midges. IOP Publishing.

Rothamsted Long-term experiments : guide to the classical and other long-term experiments, datasets and sample archive

E - Books edited/written by staff member, alone/with others

Macdonald, A. J., Poulton, P. R., Clark, I. M., Scott, T., Glendining, M. J., Perryman, S. A. M., Storkey, J., Bell, J. R., Shield, I. F., Mcmillan, V. E. and Hawkins, J. M. B. Macdonald, A. J. (ed.) 2018. Rothamsted Long-term experiments : guide to the classical and other long-term experiments, datasets and sample archive. Rothamsted Research, Harpenden.

Dry matter losses and quality changes during short rotation coppice willow storage in chip or rod form

A - Papers appearing in refereed journals

Whittaker, C., Yates, N. E., Powers, S. J., Misselbrook, T. H. and Shield, I. F. 2018. Dry matter losses and quality changes during short rotation coppice willow storage in chip or rod form. Biomass & Bioenergy. 112, pp. 29-36.

The tethered flight technique as a tool for studying life‐history strategies associated with migration in insects

A - Papers appearing in refereed journals

Minter, M., Pearson, A. J., Lim, K. S., Wilson, K., Chapman, J. W. and Jones, C. M. 2018. The tethered flight technique as a tool for studying life‐history strategies associated with migration in insects. Ecological Entomology. 43 (4).

Ongoing changes in migration phenology and winter residency at Bracken Bat Cave

A - Papers appearing in refereed journals

Stepanian, P. M. and Wainwright, C. E. 2018. Ongoing changes in migration phenology and winter residency at Bracken Bat Cave. Global Change Biology.

Loop-mediated isothermal amplification (LAMP) assays for rapid detection of Pyrenopeziza brassicae (light leaf spot of brassicas)

A - Papers appearing in refereed journals

King, K. M., Krivova, V., Canning, G. G. M., Hawkins, N. J., Kaczmarek, A. M., Perryman, S. A. M., Dyer, P. S., Fraaije, B. A. and West, J. S. 2018. Loop-mediated isothermal amplification (LAMP) assays for rapid detection of Pyrenopeziza brassicae (light leaf spot of brassicas). Plant Pathology. 67 (1), pp. 167-174.

Does repeated biochar incorporation induce further soil priming effect?

A - Papers appearing in refereed journals

Luo, Y., Lin, Q. M., Durenkamp, M. and Kuzyakov, Y. 2018. Does repeated biochar incorporation induce further soil priming effect? Journal of Soils and Sediments. 18 (1), pp. 128-135.

Effects of variety, year of cultivation and sulphur supply on the accumulation of free asparagine in the grain of commercial wheat varieties

A - Papers appearing in refereed journals

Curtis, T. Y., Powers, S. J., Wang, R. and Halford, N. G. 2018. Effects of variety, year of cultivation and sulphur supply on the accumulation of free asparagine in the grain of commercial wheat varieties. Food Chemistry. 239 (15 January), pp. 304-313.

Fluctuating environments drive insect swarms into a new state that is robust to perturbations

A - Papers appearing in refereed journals

Reynolds, A. M. 2018. Fluctuating environments drive insect swarms into a new state that is robust to perturbations. EPL. 124, p. 38001.

Incorporating terminal velocities into Lagrangian stochastic models of particle dispersal in the atmospheric boundary layer

A - Papers appearing in refereed journals

Reynolds, A. M. 2018. Incorporating terminal velocities into Lagrangian stochastic models of particle dispersal in the atmospheric boundary layer. Scientific Reports. 8, p. 16843.

Host shift induces changes in mate choice of the seed predator Acanthoscelides obtectus via altered chemical signalling

A - Papers appearing in refereed journals

Vuts, J., Woodcock, C. M., Koenig, L., Powers, S. J., Pickett, J. A., Szentesi, A. and Birkett, M. A. 2018. Host shift induces changes in mate choice of the seed predator Acanthoscelides obtectus via altered chemical signalling. PLOS ONE. 13 (11), p. e0206144.

KnetMaps: a BioJS component to visualize biological knowledge networks

A - Papers appearing in refereed journals

Singh, A., Rawlings, C. J. and Hassani-Pak, K. 2018. KnetMaps: a BioJS component to visualize biological knowledge networks. F1000Research. 7, p. 1651.

Sequence diversity and Identification of novel puroindoline and grain softness protein alleles in Elymus, Agropyron and related species

A - Papers appearing in refereed journals

Wilkinson, M. D., King, R. and Grimaldi, R. 2018. Sequence diversity and Identification of novel puroindoline and grain softness protein alleles in Elymus, Agropyron and related species. Diversity. 10 (4), p. 114.

Genetic interactions between ABA signalling and the Arg/N-end rule pathway during Arabidopsis seedling establishment

A - Papers appearing in refereed journals

Zhang, H., Gannon, L., Jones, P. D., Rundle, C. A., Hassall, K. L., Gibbs, D. J., Holdsworth, M. J. and Theodoulou, F. L. 2018. Genetic interactions between ABA signalling and the Arg/N-end rule pathway during Arabidopsis seedling establishment. Scientific Reports. 8, p. 15192.

Genomic index selection provides a pragmatic framework for setting and refining multi-objective breeding targets in Miscanthus

A - Papers appearing in refereed journals

Slavov, G. T., Davey, C. L., Bosch, M., Robson, P. R. H., Donnison, I. S. and MacKay, I. J. 2018. Genomic index selection provides a pragmatic framework for setting and refining multi-objective breeding targets in Miscanthus. Annals of Botany. pp. 1-9.

Breeding progress and preparedness for mass-scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow, and poplar

A - Papers appearing in refereed journals

Clifton-Brown, J., Harfouche, A., Casler, M. D., Jones, H. D., Macalpine, W. J., Murphy-Bokern, D., Smart, L. B., Adler, A., Ashman, C., Awty-Carroll, D., Bastien, C., Bopper, S., Botnari, V., Brancourt-Hulmel, M., Chen, Z., Clark, L. V., Cosentino, S., Dalton, S., Davey, C., Dolstra, O., Donnison, I., Flavell, R., Greef, J., Hanley, S. J., Hastings, A., Hertzberg, M., Hsu, T., Huang, L., Iurato, A., Jensen, E., Jin, X., Jørgensen, U., Kiesel, A., Kim, D., Liu, J., McCalmont, J. P., McMahon, B. G., Mos, M., Robson, P., Sacks, E. J., Sandu, A., Scalici, G., Schwarz, K., Scordia, D., Shafiei, R., Shield, I. F., Slavov, G., Stanton, B. J., Swaminathan, K., Taylor, G., Torres, A. F., Trindade, L. M., Tschaplinski, T., Tuskan, J., Yamada, T., Yu, C. Y., Zalesny, R., Zong, J. and Lewandowski, I. 2018. Breeding progress and preparedness for mass-scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow, and poplar. Global Change Biology Bioenergy.

Characterizing animal anatomy and internal composition for electromagnetic modelling in radar entomology

A - Papers appearing in refereed journals

Mirkovic, D., Stepanian, P. M., Wainwright, C. E., Reynolds, D. R. and Menz, M. H. M. 2018. Characterizing animal anatomy and internal composition for electromagnetic modelling in radar entomology. Remote Sensing in Ecology and Conservation.

Olfactory-cued navigation in shearwaters: linking movement patterns to mechanisms

A - Papers appearing in refereed journals

Abolaffio, M., Reynolds, A. M., Cecere, J. G., Paiva, V. H. and Focardi, S. 2018. Olfactory-cued navigation in shearwaters: linking movement patterns to mechanisms. Scientific Reports. 8 (11590).

The anaplerotic node is essential for the intracellular survival of Mycobacterium tuberculosis

A - Papers appearing in refereed journals

Basu, P., Sandhu, N., Bhatt, A., Singh, A., Balhana, R., Gobe, I., Crowhurst, N. A., Mendum, T. A., Gao, L., Ward, J. L., Beale, M. H., McFadden J. and Beste, D. J. V. 2018. The anaplerotic node is essential for the intracellular survival of Mycobacterium tuberculosis. Journal of Biological Chemistry. 293 (15), pp. 5695-5704.

The adaptation of Fusarium culmorum to DMI Fungicides Is Mediated by Major Transcriptome Modifications in Response to Azole Fungicide, Including the Overexpression of a PDR Transporter (FcABC1)

A - Papers appearing in refereed journals

Hellin, P., King, R., Urban, M., Hammond-Kosack, K. E. and Legreve, A 2018. The adaptation of Fusarium culmorum to DMI Fungicides Is Mediated by Major Transcriptome Modifications in Response to Azole Fungicide, Including the Overexpression of a PDR Transporter (FcABC1). Frontiers in Microbiology. 9 (1385).

Higher flight activity in the offspring of migrants compared to residents in a migratory insect

A - Papers appearing in refereed journals

Dällenbach, L. J., Glauser, A., Lim, K. S., Chapman, J. W. and Menz, M. H. M. 2018. Higher flight activity in the offspring of migrants compared to residents in a migratory insect. Proceedings of the Royal Society B: Biological Sciences. 285 (1881).

Towards FAIRer Biological Knowledge Networks Using a Hybrid Linked Data and Graph Database Approach

A - Papers appearing in refereed journals

Brandizi, M., Singh, A., Rawlings, C. J. and Hassani-Pak, K. 2018. Towards FAIRer Biological Knowledge Networks Using a Hybrid Linked Data and Graph Database Approach. Journal of Integrative Bioinformatics. 15 (3), pp. 1-10.

Passive particles Lévy walk through turbulence mirroring the diving patterns of marine predators

A - Papers appearing in refereed journals

Reynolds, A. M. 2018. Passive particles Lévy walk through turbulence mirroring the diving patterns of marine predators. Journal of Physics Communications. 2 (8), p. 085003.

Dissecting Wheat Grain Yield Drivers in a Mapping Population in the UK

A - Papers appearing in refereed journals

Pennacchi, J. P., Carmo-Silva, E., Andralojc, P. J., Feuerhelm, D,, Powers, S. J. and Parry, M. A. J. 2018. Dissecting Wheat Grain Yield Drivers in a Mapping Population in the UK. Agronomy. 8 (94).

Temperature and nitrogen supply interact to determine protein distribution gradients in the wheat grain endosperm

A - Papers appearing in refereed journals

Savill, G. P., Michalski, A., Powers, S. J., Wan, Y., Tosi, P., Buchner, P. H. and Hawkesford, M. J. 2018. Temperature and nitrogen supply interact to determine protein distribution gradients in the wheat grain endosperm. Journal of Experimental Botany. 69 (12), pp. 3117-3126.

New insights in the composition of wax and sterol esters in common and mutant sunflower oils revealed by ESI-MS/MS

A - Papers appearing in refereed journals

Broughton, R., Ruíz-Lopez, N., Hassall, K. L., Martínez-Force, E., Garcés, R., Salas, J. J. and Beaudoin, F. 2018. New insights in the composition of wax and sterol esters in common and mutant sunflower oils revealed by ESI-MS/MS. Food Chemistry. 269, pp. 70-79.

Levy foraging patterns of rural humans

A - Papers appearing in refereed journals

Reynolds, A. M., Ceccon, E., Baldauf, C., Medeiros, T. K. and Miramontes, O. 2018. Levy foraging patterns of rural humans. PLOS ONE. 13 (6), p. e0199099.

Distinguishing between apparent and actual randomness: a preliminary examination with Australian ants

A - Papers appearing in refereed journals

Reynolds, A. M., Ferdous, M. J. and Cheng, K. 2018. Distinguishing between apparent and actual randomness: a preliminary examination with Australian ants. Behavioral Ecology and Sociobiology. 72 (113).

The contribution of cattle urine and dung to nitrous oxide emissions: Quantification of country specific emission factors and implications for national inventories

A - Papers appearing in refereed journals

Chadwick, D. R., Cardenas, L. M., Dhanoa, M. S., Donovan, N., Misselbrook, T. H., Williams, J. R., Thorman, R. E., McGeough, K. L., Watson, C. J., Bell, M., Anthony, S. G. and Rees, R. M. 2018. The contribution of cattle urine and dung to nitrous oxide emissions: Quantification of country specific emission factors and implications for national inventories. Science of The Total Environment. 635, pp. 607-617.