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 Mar 2021, In: Plant Communications. 2, 2, 100165.

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34 Citations (Scopus)

138 Downloads (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 Nov 2020, In: Journal of Agronomy and Crop Science. 206, 6, p. 651-664 14 p.

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19 Citations (Scopus)

247 Downloads (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 Jan 2020, In: Scientific Reports. 10, 1, 460.

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28 Citations (Scopus)

130 Downloads (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 others, 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 Jul 2020, In: Nature Communications. 11, 1, 16 p., 3670.

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63 Citations (Scopus)

260 Downloads (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 Sept 2020, In: G3 (Bethesda, Md.). 10, 9, p. 3347-3364 18 p.

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20 Citations (Scopus)

121 Downloads (Pure)

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

Robb, C., Hardy, A., Doonan, J. H. & Brook, J., 09 Dec 2020, In: Frontiers in Plant Science. 11, 13 p., 591886.

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15 Citations (Scopus)

134 Downloads (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 Jun 2019, In: African Journal of Biotechnology. 18, 26, p. 548-563 16 p., 7118D0361330.

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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 Jul 2019, In: PLoS ONE. 14, 7, e0220518.

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4 Citations (Scopus)

183 Downloads (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 Nov 2019, In: BMC Biology. 17, 1, 92.

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55 Citations (Scopus)

155 Downloads (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 May 2019, In: Annals of Botany. 123, 6, p. 977-992 16 p., mcy230.

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6 Citations (Scopus)

169 Downloads (Pure)

Physiological and biochemical basis for stay-green trait in sorghum

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

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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 Mar 2019, In: Metabolomics. 15, 3, 42.

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16 Citations (Scopus)

312 Downloads (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 Dec 2019, In: Journal of Plant Growth Regulation. 38, 4, p. 1562-1573 12 p.

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19 Citations (Scopus)

117 Downloads (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 Mar 2018, In: Plant Biotechnology Journal. 16, 8, p. 1452-1463 12 p.

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87 Citations (Scopus)

202 Downloads (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 Oct 2018, In: New Phytologist. 220, 1, p. 288-299 12 p.

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26 Citations (Scopus)

185 Downloads (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 Jun 2018, In: European Journal of Plant Pathology. 151, 2, p. 401-411 11 p.

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6 Citations (Scopus)

160 Downloads (Pure)

2017

Assembly and annotation of a physical map-based draft genome of the forage grass Lolium perenne (P0920)

Beynon, S., 14 Jan 2017.

Research output: Contribution to conference › Poster

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 Feb 2017, In: Frontiers in Plant Science. 8, 213.

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6 Citations (Scopus)

192 Downloads (Pure)

Editorial: Plant Phenotyping and Phenomics for Plant Breeding

Lobos, G. A., Camargo-Rodriguez, A., del Pozo, A., Araus, J. L., Ortiz, R. & Doonan, J., 22 Dec 2017, In: Frontiers in Plant Science. 8, 2181.

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61 Citations (Scopus)

159 Downloads (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 May 2017, In: Plant Cell, Tissue and Organ Culture. 129, 2, p. 181-193 13 p.

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5 Citations (Scopus)

190 Downloads (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 Feb 2017, In: Journal of Molecular Biology. 429, 3, p. 382-389 8 p.

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34 Citations (Scopus)

161 Downloads (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 Sept 2017, In: Plant Physiology. 175, 1, p. 351-360 10 p.

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50 Citations (Scopus)

171 Downloads (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 Nov 2017, In: Nucleic Acids Research. gkx1152.

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134 Citations (Scopus)

182 Downloads (Pure)

2016

Automated estimation of tiller number in wheat by ribbon detection

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

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13 Citations (Scopus)

289 Downloads (Pure)

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

Galyuon, I. K. A. & Howarth, C., 22 Jun 2016, In: African Journal of Biotechnology. 15, 25, p. 1363-1374

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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 Feb 2016, In: Frontiers in Plant Science. 7, FEB2016, 10 p., 133.

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52 Citations (Scopus)

183 Downloads (Pure)

Insight into the machinery that oils chromatin dynamics

Wright, R. H. G., Fernandez-Fuentes, N., Oliva, B. & Beato, M., 28 Nov 2016, In: Nucleus. 7, 6, p. 532-539

Research output: Contribution to journal › Article › peer-review

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7 Citations (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 Jun 2016, In: Biochemical Society Transactions. 44, 3, p. 917-924 8 p.

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4 Citations (Scopus)

99 Downloads (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 Nov 2016, In: Bioinformatics. 32, 21, p. 3339-3341 3 p.

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2 Citations (Scopus)

86 Downloads (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 others, 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 Sept 2016, In: Proteins: Structure, Function and Genetics. 84, S1, p. 323-348

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125 Citations (Scopus)

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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 Jul 2016, In: Biotechnology for Biofuels. 9, 140.

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28 Citations (Scopus)

179 Downloads (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 Nov 2015, In: Plant Journal. 84, 4, p. 816-826 11 p.

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136 Citations (Scopus)

185 Downloads (Pure)

Genetic identification of Kazakhstan Oat varieties

Nurpeissov, M., Abugaliyeva, A. & Langdon, T., 01 Dec 2015, In: Biosciences Biotechnology Research Asia. 12, 3, p. 2227-2233 7 p.

Research output: Contribution to journal › Article › peer-review

2 Citations (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, In: BMC Bioinformatics. 16, 1, 297.

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2 Citations (Scopus)

145 Downloads (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., Jul 2015, In: PLoS Neglected Tropical Diseases. 9, 7, p. e0003920 e0003920.

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14 Citations (Scopus)

198 Downloads (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. (Editor), 12 Mar 2015, In: PLoS ONE. 10, 3, e0118107.

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20 Citations (Scopus)

130 Downloads (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 Jan 2014, In: Nucleic Acids Research. 42, D1, p. D315-D319 5 p.

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39 Citations (Scopus)

199 Downloads (Pure)

Challenges of Crop Phenomics in the Post-genomic Era

Gegas, V. C., Gay, A., Camargo-Rodriguez, A. & Doonan, J., 22 Jan 2014, Phenomics. Hancock, J. (ed.). 1 ed. Boca Raton: Taylor & Francis, p. 142-171 30 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

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 Jan 2014, In: Scientific Reports. 4, 3643.

Research output: Contribution to journal › Article › peer-review

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16 Citations (Scopus)

147 Downloads (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 Jul 2014, In: Bioinformatics. 30, 13, p. 1935-1936

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17 Citations (Scopus)

166 Downloads (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. (Editor), 07 May 2014, In: PLoS ONE. 9, 5, p. e96889 11 p., e96889.

Research output: Contribution to journal › Article › peer-review

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28 Citations (Scopus)

169 Downloads (Pure)

2013

A modular perspective of protein structures: application to fragment based loop modeling

Fernandez-Fuentes, N. & Fiser, A., 2013, Protein Supersecondary Structures. Kister, A. E. (ed.). Springer Nature, Vol. 932. p. 141-158 18 p. (Methods in Molecular Biology; vol. 932).

Research output: Chapter in Book/Report/Conference proceeding › Chapter