Bioinformatics and genomic and phenomic platform development

2021

A deep learning-integrated micro-CT image analysis pipeline for quantifying rice lodging resistance-related traits

Wu, D., Wu, D., Feng, H., Duan, L., Dai, G., Liu, X., Wang, K., Yang, P., Chen, G., Gay, A. P., Doonan, J. H., Niu, Z., Xiong, L. & Yang, W., 08 Maw 2021, Yn: Plant Communications. 2, 2, 100165.

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34 Dyfyniadau (Scopus)

177 Wedi eu Llwytho i Lawr (Pure)

2020

Drought priming effects on alleviating the photosynthetic limitations of wheat cultivars (Triticum aestivum L.) with contrasting tolerance to abiotic stresses

Mendanha, T., Rosenqvist, E., Nordentoft Hyldgaard, B., Doonan, J. H. & Ottosen, C. O., 27 Tach 2020, Yn: Journal of Agronomy and Crop Science. 206, 6, t. 651-664 14 t.

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19 Dyfyniadau (Scopus)

331 Wedi eu Llwytho i Lawr (Pure)

Genotypic variations in leaf and whole-plant water use efficiencies are closely related in bread wheat genotypes under well-watered and water-limited conditions during grain filling

del Pozo, A., Méndez-Espinoza, A. M., Romero-Bravo, S., Garriga, M., Estrada, F., Alcaíno, M., Camargo-Rodriguez, A. V., Corke, F. M. K., Doonan, J. H. & Lobos, G. A., 16 Ion 2020, Yn: Scientific Reports. 10, 1, 460.

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28 Dyfyniadau (Scopus)

146 Wedi eu Llwytho i Lawr (Pure)

Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors

Gordon, S. P., Contreras-Moreira, B., Levy, J. J., Djamei, A., Czedik-Eysenberg, A., Tartaglio, V. S., Session, A., Martin, J., Cartwright, A., Katz, A., Singan, V. R., Goltsman, E., Barry, K., Dinh-Thi, V. H., Chalhoub, B., Diaz-Perez, A., Sancho, R., Lusinska, J., Wolny, E. & Nibau, C. & 13 eraill, Doonan, J. H., Mur, L. A. J., Plott, C., Jenkins, J., Hazen, S. P., Lee, S. J., Shu, S., Goodstein, D., Rokhsar, D., Schmutz, J., Hasterok, R., Catalan, P. & Vogel, J. P., 29 Gorff 2020, Yn: Nature Communications. 11, 1, 16 t., 3670.

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63 Dyfyniadau (Scopus)

312 Wedi eu Llwytho i Lawr (Pure)

High-Throughput Genome-Wide Genotyping To Optimize the Use of Natural Genetic Resources in the Grassland Species Perennial Ryegrass (Lolium perenne L.)

Keep, T., Sampoux, J. P., Blanco-Pastor, J. L., Dehmer, K. J., Hegarty, M. J., Ledauphin, T., Litrico, I., Muylle, H., Roldán-Ruiz, I., Roschanski, A. M., Ruttink, T., Surault, F., Willner, E. & Barre, P., 01 Medi 2020, Yn: G3 (Bethesda, Md.). 10, 9, t. 3347-3364 18 t.

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20 Dyfyniadau (Scopus)

143 Wedi eu Llwytho i Lawr (Pure)

Semi-Automated Field Plot Segmentation From UAS Imagery for Experimental Agriculture

Robb, C., Hardy, A., Doonan, J. H. & Brook, J., 09 Rhag 2020, Yn: Frontiers in Plant Science. 11, 13 t., 591886.

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15 Dyfyniadau (Scopus)

154 Wedi eu Llwytho i Lawr (Pure)

2019

A comparative assessment of the performance of a stay-green sorghum (Sorghum bicolor (L) Moench) introgression line developed by marker-assisted selection and its parental lines

Galyuon, I. K., Gay, A., Hash, C. T., Bidinger, F. R. & Howarth, C., 26 Meh 2019, Yn: African Journal of Biotechnology. 18, 26, t. 548-563 16 t., 7118D0361330.

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283 Wedi eu Llwytho i Lawr (Pure)

Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne)

Fradera-Sola, A., Thomas, A., Gasior, D., Harper, J., Hegarty, M., Armstead, I. & Fernandez Fuentes, N., 30 Gorff 2019, Yn: PLoS One. 14, 7, e0220518.

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4 Dyfyniadau (Scopus)

193 Wedi eu Llwytho i Lawr (Pure)

Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species

Maughan, P. J., Lee, R., Walstead, R., Vickerstaff, R. J., Fogarty, M. C., Brouwer, C. R., Reid, R. R., Jay, J. J., Bekele, W. A., Jackson, E. W., Tinker, N. A., Langdon, T., Schlueter, J. A. & Jellen, E. N., 22 Tach 2019, Yn: BMC Biology. 17, 1, 92.

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55 Dyfyniadau (Scopus)

174 Wedi eu Llwytho i Lawr (Pure)

Integrating a newly developed BAC-based physical mapping resource for Lolium perenne with a genome-wide association study across a L. Perenne European ecotype collection identifies genomic contexts associated with agriculturally important traits

Harper, J., de Vega, J., Swain, S., Heavens, D., Gasior, D., Thomas, A., Evans, C., Lovatt, A., Lister, S., Thorogood, D., Skot, L., Hegarty, M., Blackmore, T., Kudrna, D., Byrne, S., Asp, T., Powell, W., Fernandez-Fuentes, N. & Armstead, I., 08 Mai 2019, Yn: Annals of Botany. 123, 6, t. 977-992 16 t., mcy230.

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6 Dyfyniadau (Scopus)

192 Wedi eu Llwytho i Lawr (Pure)

Physiological and biochemical basis for stay-green trait in sorghum

Galyuon, I. K. A., Gay, A., Borrell, A. K. & Howarth, C. J., 2019, Yn: African Crop Science Journal. 27, 4, t. 653, 677

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168 Wedi eu Llwytho i Lawr (Pure)

Rapid UHPLC-MS metabolite profiling and phenotypic assays reveal genotypic impacts of nitrogen supplementation in oats

Allwood, J. W., Xu, Y., Martinez-Martin, P., Palau, R., Cowan, S., Goodacre, R., Marshall, A., Stewart, D. & Howarth, C., 12 Maw 2019, Yn: Metabolomics. 15, 3, 42.

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16 Dyfyniadau (Scopus)

335 Wedi eu Llwytho i Lawr (Pure)

Water-Saving Traits Can Protect Wheat Grain Number Under Progressive Soil Drying at the Meiotic Stage: A Phenotyping Approach

Faralli, M., Williams, K., Han, J., Corke, F., Doonan, J. & Kettlewell, P. S., 01 Rhag 2019, Yn: Journal of Plant Growth Regulation. 38, 4, t. 1562-1573 12 t.

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19 Dyfyniadau (Scopus)

145 Wedi eu Llwytho i Lawr (Pure)

2018

Haplotype based genotyping-by-sequencing in oat genome research

Bekele, W. A., Wight, C. P., Chao, S., Howarth, C. & Tinker, N. A., 25 Maw 2018, Yn: Plant Biotechnology Journal. 16, 8, t. 1452-1463 12 t.

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86 Dyfyniadau (Scopus)

225 Wedi eu Llwytho i Lawr (Pure)

Identification of Stipules reduced, a leaf morphology gene in pea (Pisum sativum)

Moreau, C., Hofer, J. M., Eléouët, M., Sinjushin, A., Ambrose, M., Skøt, K., Blackmore, T., Swain, M., Hegarty, M., Balanza, V., Ferrándiz, C. & Ellis, T. H. N., 01 Hyd 2018, Yn: New Phytologist. 220, 1, t. 288-299 12 t.

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25 Dyfyniadau (Scopus)

204 Wedi eu Llwytho i Lawr (Pure)

Mapping of easy to screen SSR markers for selection of RFLP markers-bracketed downy mildew resistance QTLs in pearl millet

Taunk, J., Sehgal, D., Yadav, N., Howarth, C., Yadav, R. & Yadav, R., 01 Meh 2018, Yn: European Journal of Plant Pathology. 151, 2, t. 401-411 11 t.

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6 Dyfyniadau (Scopus)

166 Wedi eu Llwytho i Lawr (Pure)

2017

Deep sequencing of Suppression Subtractive Hybridisation drought and recovery libraries of the non-model crop Trifolium repens L.

Bisaga, M., Lowe, M., Hegarty, M., Abberton, M. & Ravagnani, A., 23 Chwef 2017, Yn: Frontiers in Plant Science. 8, 213.

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6 Dyfyniadau (Scopus)

205 Wedi eu Llwytho i Lawr (Pure)

Expression of a fungal ferulic acid esterase in suspension cultures of tall fescue (Festuca arundinacea) decreases cell wall feruloylation and increases rates of cell wall digestion

Morris, P., Dalton, S., Langdon, T., Hauck, B. & Buanafina, M. M. D. O., 01 Mai 2017, Yn: Plant Cell, Tissue and Organ Culture. 129, 2, t. 181-193 13 t.

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5 Dyfyniadau (Scopus)

213 Wedi eu Llwytho i Lawr (Pure)

iFrag: A Protein-Protein Interface Prediction Server Based on Sequence Fragments

Garcia-Garcia, J., Valls-Comamala, V., Guney, E., Andreu, D., Muñoz , F. J., Fernandez-Fuentes, N. & Oliva, B., 03 Chwef 2017, Yn: Journal of Molecular Biology. 429, 3, t. 382-389 8 t.

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34 Dyfyniadau (Scopus)

174 Wedi eu Llwytho i Lawr (Pure)

Linking Auxin with Photosynthetic Rate via Leaf Venation

Mcadam, S. A. M., Eléouët, M. P., Best, M., Brodribb, T. J., Murphy, M. C., Cook, S. D., Dalmais, M., Dimitriou, T., Gélinas-Marion, A., Gill, W. M., Hegarty, M., Hofer, J. M. I., Maconochie, M., Mcadam, E. L., McGuiness, P., Nichols, D. S., Ross, J. J., Sussmilch, F. C. & Urquhart, S., 30 Medi 2017, Yn: Plant Physiology. 175, 1, t. 351-360 10 t.

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49 Dyfyniadau (Scopus)

191 Wedi eu Llwytho i Lawr (Pure)

The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics

Cooper, L., Meier, A., Laporte, M.-A., Elser, J. L., Mungall, C., Sinn, B. T., Cabaliere, D., Carbon, S., Dunn, N. A., Smith, B., Qu, B., Preece, J., Zhang, E., Todorovic, S., Gkoutos, G., Doonan, J., Stevenson, D. W., Arnaud, E. & Jaiswal, P., 23 Tach 2017, Yn: Nucleic Acids Research. gkx1152.

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134 Dyfyniadau (Scopus)

198 Wedi eu Llwytho i Lawr (Pure)

2016

Automated estimation of tiller number in wheat by ribbon detection

Boyle, R. D., Corke, F. M. K. & Doonan, J. H., Gorff 2016, Yn: Machine Vision and Applications. 27, 5, t. 637-646 10 t.

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13 Dyfyniadau (Scopus)

297 Wedi eu Llwytho i Lawr (Pure)

Genetic diversity of stay-green sorghums and their derivatives revealed by microsatellites

Galyuon, I. K. A. & Howarth, C., 22 Meh 2016, Yn: African Journal of Biotechnology. 15, 25, t. 1363-1374

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184 Wedi eu Llwytho i Lawr (Pure)

Implementation of genomic prediction in Lolium perenne (L.) breeding populations

Grinberg, N., Lovatt, A., Hegarty, M., Macfarlane, A. C., Skot, K., Kelly, R., Blackmore, T., Thorogood, D., King, R. D., Armstead, I., Powell, W. & Skot, L., 12 Chwef 2016, Yn: Frontiers in Plant Science. 7, FEB2016, 10 t., 133.

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52 Dyfyniadau (Scopus)

213 Wedi eu Llwytho i Lawr (Pure)

Insight into the machinery that oils chromatin dynamics

Wright, R. H. G., Fernandez-Fuentes, N., Oliva, B. & Beato, M., 28 Tach 2016, Yn: Nucleus. 7, 6, t. 532-539

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7 Dyfyniadau (Scopus)

InteractoMIX: A suite of computational tools to exploit interactomes in biological and clinical research

Poglayen, D., Marín-López, M. A., Bonet, J., Fornes, O., Garcia-Garcia, J., Planas-Iglesias, J., Segura, J., Oliva, B. & Fernandez-Fuentes, N., 09 Meh 2016, Yn: Biochemical Society Transactions. 44, 3, t. 917-924 8 t.

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4 Dyfyniadau (Scopus)

102 Wedi eu Llwytho i Lawr (Pure)

MetaPred2CS: A sequence-based meta-predictor for protein-protein interactions of prokaryotic two-component system proteins

Kara, A., Vickers, M., Swain, M., Whitworth, D. & Fernandez-Fuentes, N., 01 Tach 2016, Yn: Bioinformatics. 32, 21, t. 3339-3341 3 t.

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2 Dyfyniadau (Scopus)

90 Wedi eu Llwytho i Lawr (Pure)

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Lensink, M. F., Velankar, S., Kryshtafovych, A., Huang, S.-Y., Schneidman-Duhovny, D., Sali, A., Segura, J., Fernandez-fuentes, N., Viswanath, S., Elber, R., Grudinin, S., Popov, P., Neveu, E., Lee, H., Baek, M., Park, S., Heo, L., Rie Lee, G., Seok, C. & Qin, S. & 30 eraill, Zhou, H.-X., Ritchie, D. W., Maigret, B., Devignes, M.-D., Ghoorah, A., Torchala, M., Chaleil, R. A. G., Bates, P. A., Ben-Zeev, E., Eisenstein, M., Negi, S. S., Weng, Z., Vreven, T., Pierce, B. G., Borrman, T. M., Yu, J., Ochsenbein, F., Guerois, R., Vangone, A., Rodrigues, J. P. G. L. M., Van Zundert, G., Nellen, M., Xue, L., Karaca, E., Melquiond, A. S. J., Visscher, K., Kastritis, P. L., Bonvin, A. M. J. J., Xu, X. & Qiu, L., 20 Medi 2016, Yn: Proteins: Structure, Function and Genetics. 84, S1, t. 323-348

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125 Dyfyniadau (Scopus)

234 Wedi eu Llwytho i Lawr (Pure)

The GH51 α-l-arabinofuranosidase from Paenibacillus sp. THS1 is multifunctional, hydrolyzing main-chain and side-chain glycosidic bonds in heteroxylans.

Bouraoui, H., Desrousseaux, M.-L., Ioannou, E., Alvira, P., Manaï, M., Rémond,, C., Dumon, C., Fernandez-Fuentes, N. & O'Donohue, M. J., 08 Gorff 2016, Yn: Biotechnology for Biofuels. 9, 140.

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28 Dyfyniadau (Scopus)

199 Wedi eu Llwytho i Lawr (Pure)

2015

A synteny-based draft genome sequence of the forage grass Lolium perenne

Byrne, S. L., Nagy, I., Pfeifer, M., Armstead, I., Swain, S., Studer, B., Campbell, J., Czaban, A., Hentrup, S., Panitz, F., Bendixen, C., Hedegaard, J., Caccamo, M., Asp, T. & Mayer, K., 13 Tach 2015, Yn: Plant Journal. 84, 4, t. 816-826 11 t.

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136 Dyfyniadau (Scopus)

187 Wedi eu Llwytho i Lawr (Pure)

Genetic identification of Kazakhstan Oat varieties

Nurpeissov, M., Abugaliyeva, A. & Langdon, T., 01 Rhag 2015, Yn: Biosciences Biotechnology Research Asia. 12, 3, t. 2227-2233 7 t.

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2 Dyfyniadau (Scopus)

Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor

Kara, A., Vickers, M., Swain, M., Whitworth, D. E. & Fernandez-Fuentes, N., 2015, Yn: BMC Bioinformatics. 16, 1, 297.

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2 Dyfyniadau (Scopus)

159 Wedi eu Llwytho i Lawr (Pure)

Human IgG1 Responses to Surface Localised Schistosoma mansoni Ly6 Family Members Drop following Praziquantel Treatment

Chalmers, I. W., Fitzsimmons, C. M., Brown, M., Pierrot, C., Jones, F. M., Wawrzyniak, J. M., Fernandez-Fuentes, N., Tukahebwa, E. M., Dunne, D. W., Khalife, J. & Hoffmann, K. F., Gorff 2015, Yn: PLoS Neglected Tropical Diseases. 9, 7, t. e0003920 e0003920.

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14 Dyfyniadau (Scopus)

210 Wedi eu Llwytho i Lawr (Pure)

VORFFIP-Driven Dock: V-D ²OCK, a fast, accurate protein docking strategy

Segura, J., Marín-López, M. A., Jones, P. F., Oliva, B., Fernandez-fuentes, N. & Keskin, O. (Golygydd), 12 Maw 2015, Yn: PLoS One. 10, 3, e0118107.

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20 Dyfyniadau (Scopus)

139 Wedi eu Llwytho i Lawr (Pure)

2014

ArchDB 2014: Structural classification of loops in proteins

Bonet, J., Planas-Iglesias, J., Garcia-Garcia, J., Marín-López, M. A., Fernandez-Fuentes, N. & Oliva, B., 01 Ion 2014, Yn: Nucleic Acids Research. 42, D1, t. D315-D319 5 t.

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39 Dyfyniadau (Scopus)

231 Wedi eu Llwytho i Lawr (Pure)

Conformational flexibility of the oncogenic protein LMO2 primes the formation of the multi-protein transcription complex

Sewell, H., Tanaka, T., Omari, K. E., Mancini, E. J., Cruz, A., Fernandez-Fuentes, N., Chambers, J. & Rabbitts, T. H., 10 Ion 2014, Yn: Scientific Reports. 4, 3643.

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16 Dyfyniadau (Scopus)

167 Wedi eu Llwytho i Lawr (Pure)

Frag’r’Us: Knowledge-based sampling of protein backbone conformations for de novo structure-based protein design

Bonet, J., Segura, J., Planas-Iglesias, J., Oliva, B. & Fernandez-Fuentes, N., 01 Gorff 2014, Yn: Bioinformatics. 30, 13, t. 1935-1936

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17 Dyfyniadau (Scopus)

179 Wedi eu Llwytho i Lawr (Pure)

Objective Definition of Rosette Shape Variation Using a Combined Computer Vision and Data Mining Approach

Camargo-Rodriguez, A., Papadopoulou, D., Spyropoulou, Z., Vlachonasios, K., Doonan, J. H., Gay, A. P. & Candela, H. (Golygydd), 07 Mai 2014, Yn: PLoS One. 9, 5, t. e96889 11 t., e96889.

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