Article

Adiyaman, R., Edmunds, N. S., Genc, A. G., Alharbi, S. M. A. and McGuffin, L. ORCID: https://orcid.org/0000-0003-4501-4767 (2023) Improvement of protein tertiary and quaternary structure predictions using the ReFOLD refinement method and the AlphaFold2 recycling process. Bioinformatics Advances, 3 (1). vbad078. ISSN 2635-0041 doi: https://doi.org/10.1093/bioadv/vbad078

AlOuda, S. K., Sasikumar, P., AlThunayan, T., Alaajam, F., Khan, S., Sahli, K. A., Abohassan, M. S., Pollitt, A. ORCID: https://orcid.org/0000-0001-8706-5154, Jung, S. M. and Gibbins, J. M. ORCID: https://orcid.org/0000-0002-0372-5352 (2023) Role of heat shock protein 47 in platelet glycoprotein VI dimerisation and signaling. Research and Practice in Thrombosis and Haemostasis, 7 (6). 102177. ISSN 2475-0379 doi: https://doi.org/10.1016/j.rpth.2023.102177

Bye, A. P. ORCID: https://orcid.org/0000-0002-2061-2253, Kriek, N., Sage, T., Rawlings, S. J., Prodger, C., Kesavan, M., Lees, C., Booth, S., Cowen, L. G., Shefferd, K., Desborough, M. J., Gibbins, J. M. ORCID: https://orcid.org/0000-0002-0372-5352 and Eyre, T. A. (2023) Pirtobrutinib results in reversible platelet dysfunction compared to ibrutinib and acalabrutinib. Haematologica, 108 (5). ISSN 1592-8721 doi: https://doi.org/10.3324/haematol.2022.281402

Cheung, H. Y. F., Zou, J., Tantiwong, C., Fernandez, D. I., Huang, J., Ahrends, R., Roest, M., Cavill, R., Gibbins, J. ORCID: https://orcid.org/0000-0002-0372-5352 and Heemskerk, J. W. M. (2023) High-throughput assessment identifying major platelet Ca2+ entry pathways via tyrosine kinase-linked and G protein-coupled receptors. Cell Calcium, 112. 102738. ISSN 0143-4160 doi: https://doi.org/10.1016/j.ceca.2023.102738

Dodd, J., Sweby, P. K. ORCID: https://orcid.org/0009-0003-8488-0251, Mayes, S., Murchie, E. H., Karunaratne, A. S., Massawe, F. and Tindall, M. J. (2023) A multiscale mathematical model describing the growth and development of bambara groundnut. Journal of Theoretical Biology, 560. 111373. ISSN 0022-5193 doi: https://doi.org/10.1016/j.jtbi.2022.111373

Edmunds, N. S., Alharbi, S. M.A., Genc, A. G., Adiyaman, R. and McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767 (2023) Estimation of model accuracy in CASP15 using the ModFOLDdock server. Proteins: Structure, Function, and Bioinformatics, 91 (12). pp. 1871-1878. ISSN 1097-0134 doi: https://doi.org/10.1002/prot.26532

Gelzinis, J. A., Szahaj, M. K., Bekendam, R. H., Wurl, S. E., Pantos, M. M., Verbetsky, C. A., Dufresne, A., Shea, M., Howard, K. C., Tsodikov, O. V., Garneau‐Tsodikova, S., Zwicker, J. I. and Kennedy, D. R. ORCID: https://orcid.org/0000-0002-4359-6911 (2023) Targeting thiol isomerase activity with zafirlukast to treat ovarian cancer from the bench to clinic. The FASEB Journal, 37 (5). e22914. ISSN 1530-6860 doi: https://doi.org/10.1096/fj.202201952r

Gerencer, M. and McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767 (2023) Are the integrin binding motifs within SARS CoV-2 spike protein and MHC class II alleles playing the key role in COVID-19? Frontiers in Immunology, 14. ISSN 1664-3224 doi: https://doi.org/10.3389/fimmu.2023.1177691

Gibbins, J. M. ORCID: https://orcid.org/0000-0002-0372-5352 (2023) Adding fuel to the flames in pre-eclampsia: the platelet connection. Journal of Thrombosis and Haemostasis, 21 (7). pp. 1750-1752. ISSN 1538-7933 doi: https://doi.org/10.1016/j.jtha.2023.03.031

Kuravi, S. J., Ahmed, N. S., Taylor, K. A. ORCID: https://orcid.org/0000-0002-4599-7727, Capes, E. M., Bye, A. ORCID: https://orcid.org/0000-0002-2061-2253, Unsworth, A. J., Gibbins, J. M. ORCID: https://orcid.org/0000-0002-0372-5352 and Pugh, N. (2023) Delineating zinc influx mechanisms during platelet activation. International Journal of Molecular Sciences, 24 (14). 11689. ISSN 1422-0067 doi: https://doi.org/10.3390/ijms241411689

Lovegrove, J. A. ORCID: https://orcid.org/0000-0001-7633-9455, O'Sullivan, D. M. ORCID: https://orcid.org/0000-0003-4889-056X, Tosi, P. ORCID: https://orcid.org/0000-0003-4171-6120, Millan, E. ORCID: https://orcid.org/0000-0002-2421-2855, Todman, L. C. ORCID: https://orcid.org/0000-0003-1232-294X, Bishop, J. ORCID: https://orcid.org/0000-0003-2114-230X, Chatzifragkou, A. ORCID: https://orcid.org/0000-0002-9255-7871, Clegg, M. E., Hammond, J. ORCID: https://orcid.org/0000-0002-6241-3551, Jackson, K. G. ORCID: https://orcid.org/0000-0002-0070-3203, Jones, P. J. ORCID: https://orcid.org/0000-0003-3464-5424, Lignou, S. ORCID: https://orcid.org/0000-0001-6971-2258, Macready, A. L. ORCID: https://orcid.org/0000-0003-0368-9336, McMeel, Y., Parker, J. ORCID: https://orcid.org/0000-0003-4121-5481, Rodriguez-Garcia, J. ORCID: https://orcid.org/0000-0002-4986-3144, Sharp, P., Shaw, L. J., Smith, L. G. ORCID: https://orcid.org/0000-0002-9898-9288 and Tebbit, M. (2023) 'Raising the pulse': the environmental, nutritional and health benefits of pulse-enhanced foods. Nutrition Bulletin, 48 (1). pp. 134-143. ISSN 1471-9827 doi: https://doi.org/10.1111/nbu.12601

Markey, O., Garcimartín, A., Vasilopoulou, D., Kliem, K. E. ORCID: https://orcid.org/0000-0002-0058-8225, Fagan, C. C. ORCID: https://orcid.org/0000-0002-2101-8694, Humphries, D. J., Todd, S. ORCID: https://orcid.org/0000-0002-9981-923X, Givens, D. I. ORCID: https://orcid.org/0000-0002-6754-6935, Lovegrove, J. A. ORCID: https://orcid.org/0000-0001-7633-9455 and Jackson, K. G. ORCID: https://orcid.org/0000-0002-0070-3203 (2023) Impact of dairy fat manipulation on endothelial function and lipid regulation in human aortic endothelial cells exposed to human plasma samples: an in vitro investigation from the RESET study. European Journal of Nutrition. ISSN 1436-6215 doi: https://doi.org/10.1007/s00394-023-03284-9

McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767, Edmunds, N. S., Genc, A. G., Alharbi, S. M. A., Salehe, B. R. and Adiyaman, R. (2023) Prediction of protein structures, functions and interactions using the IntFOLD7, MultiFOLD and ModFOLDdock servers. Nucleic Acids Research, 51 (W1). W274-W280. ISSN 1362-4962 doi: https://doi.org/10.1093/nar/gkad297

Mitchell, J. L., Khan, D., Rana, R. H., Kriek, N., Unsworth, A. J., Sage, T., Bye, A. P. ORCID: https://orcid.org/0000-0002-2061-2253, Laffan, M., Shapiro, S., Thakurta, A., Grech, H., Ramasamy, K. and Gibbins, J. M. ORCID: https://orcid.org/0000-0002-0372-5352 (2023) Multiple myeloma and its treatment contribute to increased platelet reactivity. Platelets, 34 (1). 2264940. ISSN 1369-1635 doi: https://doi.org/10.1080/09537104.2023.2264940

Nelson, M. R., Gibbins, J. M. ORCID: https://orcid.org/0000-0002-0372-5352 and Dunster, J. L. ORCID: https://orcid.org/0000-0001-8986-4902 (2023) Platelet-driven routes to chaos in a model of hepatitis. Chaos, Solitons & Fractals, 170. 113338. ISSN 1873-2887 doi: https://doi.org/10.1016/j.chaos.2023.113338

Pushpass, R.-A. G., Alzoufairi, S., Mancini, A., Quilter, K., Fava, F., Delaiti, S., Vrhovsek, U., Christensen, C., Joyce, S. A., Tuohy, K. M., Jackson, K. G. ORCID: https://orcid.org/0000-0002-0070-3203 and Lovegrove, J. A. ORCID: https://orcid.org/0000-0001-7633-9455 (2023) Chronic consumption of probiotics, oats and apples have differential effects on postprandial bile acid profile and cardiometabolic disease risk markers compared to an isocaloric control (cornflakes): a randomized trial. The American Journal of Clinical Nutrition, 117 (2). ISSN 0002-9165 doi: https://doi.org/10.1016/j.ajcnut.2022.10.013

Ranjbar, J., Njoroge, W. ORCID: https://orcid.org/0009-0003-1365-5129, Gibbins, J. M. ORCID: https://orcid.org/0000-0002-0372-5352, Roach, P. ORCID: https://orcid.org/0000-0003-4135-9733, Yang, Y. ORCID: https://orcid.org/0000-0002-1362-6040 and Harper, A. G. S. ORCID: https://orcid.org/0000-0003-2413-4823 (2023) Developing biomimetic hydrogels of the arterial wall as a prothrombotic substrate for in vitro human thrombosis models. Gels, 9 (6). 477. ISSN 2310-2861 doi: https://doi.org/10.3390/gels9060477

Sellem, L., Eichelmann, F., Jackson, K. G. ORCID: https://orcid.org/0000-0002-0070-3203, Wittenbecher, C., Schultze, M. and Lovegrove, J. A. ORCID: https://orcid.org/0000-0001-7633-9455 (2023) Replacement of dietary saturated with unsaturated fatty acids is associated with beneficial effects on lipidome metabolites: a secondary analysis of a randomized trial. American Journal of Clinical Nutrition, 117 (6). pp. 1248-1261. ISSN 0002-9165 doi: https://doi.org/10.1016/j.ajcnut.2023.03.024

Tantiwong, C., Dunster, J. L. ORCID: https://orcid.org/0000-0001-8986-4902, Cavill, R., Tomlinson, M. G., Wierling, C., Heemskerk, J. W. M. and Gibbins, J. M. ORCID: https://orcid.org/0000-0002-0372-5352 (2023) An agent-based approach for modelling and simulation of glycoprotein VI receptor diffusion, localisation and dimerisation in platelet lipid rafts. Scientific Reports, 13. 3906. ISSN 2045-2322 doi: https://doi.org/10.1038/s41598-023-30884-6

Thienel, M., Müller-Reif, J. B., Zhang, Z., Ehreiser, V., Huth, J., Shchurovska, K., Kilani, B., Schweizer, L., Geyer, P. E., Zweibel, M., Novotny, J., Lüsebrink, E., Little, G., Orban, M., Nicolai, L., El Nemr, S., Titova, A., Spannagl, M., Kindberg, J., Evans, A. L., Mach, O., Vogel, M., Tiedt, S., Ormanns, S., Kessler, B., Dueck, A., Friebe, A., Godsk Jørgensen, P., Majzoub-Altweck, M., Blutke, A., Polzin, A., Stark, K., Kääb, S., Maier, D., Gibbins, J. M. ORCID: https://orcid.org/0000-0002-0372-5352, Limper, U., Frobert, O., Mann, M., Massberg, S. and Petzold, T. (2023) Immobility-associated thromboprotection is conserved across mammalian species from bear to human. Science, 380 (6641). pp. 178-187. ISSN 1095-9203 doi: https://doi.org/10.1126/science.abo5044

Tindall, M. J. ORCID: https://orcid.org/0000-0001-6069-5260, Cucurull-Sanchez, L., Mistry, H. and Yates, J. W.T. (2023) Quantitative systems pharmacology and machine learning: a match made in heaven or hell? The Journal of Pharmacology and Experimental Therapeutics, 387 (1). pp. 92-99. ISSN 1521-0103 doi: https://doi.org/10.1124/jpet.122.001551

Verdier, H., Thomas, P., Batista, J. ORCID: https://orcid.org/0000-0001-5406-6353, Kempster, C. ORCID: https://orcid.org/0000-0001-5721-1050, McKinney, H., Gleadall, N. ORCID: https://orcid.org/0000-0002-1132-1059, Danesh, J., Mumford, A. ORCID: https://orcid.org/0000-0002-5523-511X, Heemskerk, J. W. M. ORCID: https://orcid.org/0000-0002-2848-5121, Ouwehand, W. H. ORCID: https://orcid.org/0000-0002-7744-1790, Downes, K., Astle, W. J. ORCID: https://orcid.org/0000-0001-8866-6672 and Turro, E. ORCID: https://orcid.org/0000-0002-1820-6563 (2023) A signature of platelet reactivity in CBC scattergrams reveals genetic predictors of thrombotic disease risk. Blood, 142 (22). pp. 1895-1908. ISSN 1528-0020 doi: https://doi.org/10.1182/blood.2023021100

Book or Report Section

Adiyaman, R. and McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767 (2023) Using local protein model quality estimates to guide a molecular dynamics-based refinement strategy. In: Filipek, S. (ed.) Homology Modeling: Methods and Protocols. Methods in Molecular Biology. Springer Nature, New York, pp. 119-140. ISBN 9781071629734 doi: https://doi.org/10.1007/978-1-0716-2974-1_7

Alharbi, S. M. A. and McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767 (2023) Machine learning methods for predicting protein contacts. In: Kurgan, L. (ed.) Machine Learning in Bioinformatics of Protein Sequences: Algorithms, Databases and Resources for Modern Protein Bioinformatics. World Scientific, pp. 155-181. ISBN 9789811258572 doi: https://doi.org/10.1142/9789811258589_0006

Maghrabi, A. H. A., Aldowsari, F. M. F. and McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767 (2023) Quality estimates for 3D protein models. In: Filipek, S. (ed.) Homology Modeling: Methods and Protocols. Methods in Molecular Biology, 2627. Springer Nature, New York, pp. 101-118. ISBN 9781071629734 doi: https://doi.org/10.1007/978-1-0716-2974-1_6

Conference or Workshop Item

Stowell, J. D., Mela, D. J., Coppens, P., Lovegrove, J. A. ORCID: https://orcid.org/0000-0001-7633-9455, McArdle, H. J., van der Sman, F. J. P., Verhagen, H., Young, H. A. and Young, I. S. (2023) Dietary supplements, 'functional' and 'super' foods: Science, regulations and roles in the diet”. Royal Society of Medicine, London, 29 November 2022. In: Meeting on “Dietary supplements, 'functional' and 'super' foods: Science, regulations and roles in the diet”, 29 November 2022, Royal Society of Medicine, London. doi: https://doi.org/10.31219/osf.io/9z3x2

Thesis

Aldaghmi, A. S. M. (2023) Understanding the mechanisms of the regulation of platelet function by thiol isomerase enzymes. PhD thesis, University of Reading. doi: https://doi.org/10.48683/1926.00119425

De Simone, I. (2023) Novel mechanisms of platelet activation and sustained signalling through GPVI and PAR1. PhD thesis, University of Reading. doi: https://doi.org/10.48683/1926.00112631

Provenzale, I. (2023) The modulatory roles of collagen and endothelial cells on platelet function. PhD thesis, University of Reading. doi: https://doi.org/10.48683/1926.00118921