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All Outputs (39)

Monitoring university student response to social distancing policy during the SARS-CoV-2 pandemic using Bluetooth: the RADAR study (2024)
Journal Article
Bolton, K. J., Mendez-Villalon, A., Nanji, H., Jia, R., Ayling, K., Figueredo, G., & Vedhara, K. (2024). Monitoring university student response to social distancing policy during the SARS-CoV-2 pandemic using Bluetooth: the RADAR study. Mathematics in Medical and Life Sciences, 1(1), Article 2425096. https://doi.org/10.1080/29937574.2024.2425096

Aim: We use the Remote Assessment of Disease and Relapses platform (RADAR) to collect Bluetooth contact and location data from university students. We test the ability of this technology to objectively capture social interaction, explore the propensi... Read More about Monitoring university student response to social distancing policy during the SARS-CoV-2 pandemic using Bluetooth: the RADAR study.

The Challenges and Lessons Learned Building a New UK Infrastructure for Finding and Accessing Population-Wide COVID-19 Data for Research and Public Health Analysis: The CO-CONNECT Project (2024)
Journal Article
Jefferson, E., Milligan, G., Johnston, J., Mumtaz, S., Cole, C., Best, J., Giles, T. C., Cox, S., Masood, E., Horban, S., Urwin, E., Beggs, J., Chuter, A., Reilly, G., Morris, A., Seymour, D., Hopkins, S., Sheikh, A., & Quinlan, P. (2024). The Challenges and Lessons Learned Building a New UK Infrastructure for Finding and Accessing Population-Wide COVID-19 Data for Research and Public Health Analysis: The CO-CONNECT Project. Journal of Medical Internet Research, 26, Article e50235. https://doi.org/10.2196/50235

The COVID-19-Curated and Open Analysis and Research Platform (CO-CONNECT) project worked with 22 organizations across the United Kingdom to build a federated platform, enabling researchers to instantaneously and dynamically query federated datasets t... Read More about The Challenges and Lessons Learned Building a New UK Infrastructure for Finding and Accessing Population-Wide COVID-19 Data for Research and Public Health Analysis: The CO-CONNECT Project.

PIMMS-Dash: Accessible analysis, interrogation, and visualisation of high-throughput transposon insertion sequencing (TIS) data (2024)
Journal Article
Blanchard, A. M., Taylor, A., Warry, A., Shephard, F., Curwen, A., Leigh, J. A., Emes, R. D., & Egan, S. A. (2024). PIMMS-Dash: Accessible analysis, interrogation, and visualisation of high-throughput transposon insertion sequencing (TIS) data. Computational and Structural Biotechnology Journal, 23, 3780-3783. https://doi.org/10.1016/j.csbj.2024.10.025

Motivation: Current methods for visualising and interrogating high-throughput transposon insertion mutagenesis sequencing (TIS) data requires a significant time investment in learning bioinformatics, often producing static figures that do not facilit... Read More about PIMMS-Dash: Accessible analysis, interrogation, and visualisation of high-throughput transposon insertion sequencing (TIS) data.

Association between Nutritional Status Assessed by Body Mass Index and Crohn’s Disease Phenotype: A Nation-Wide Analysis (2024)
Journal Article
Ndzo, J., Vuyyuru, S. K., Trimble, T., Yan, K., Figueredo, G., & Moran, G. W. (in press). Association between Nutritional Status Assessed by Body Mass Index and Crohn’s Disease Phenotype: A Nation-Wide Analysis. Journal of Crohn's and Colitis,

Background & Aims:

Incidence of obesity and Crohn’s disease (CD) is increasing globally. Therefore, understanding any associations between adiposity and disease phenotype is crucial. We aimed explore the relationship between nutritional status me... Read More about Association between Nutritional Status Assessed by Body Mass Index and Crohn’s Disease Phenotype: A Nation-Wide Analysis.

Comparative judgement modeling to map forced marriage at local levels (2024)
Journal Article
Seymour, R., Nyarko-Agyei, A., Mccabe, H., Severn, K., Sirl, D., Kypraios, T., & Taylor, A. (in press). Comparative judgement modeling to map forced marriage at local levels. Annals of Applied Statistics,

Forcing someone into marriage against their will is a violation of their human rights. In 2021, the county of Nottinghamshire, UK, launched a strategy to tackle forced marriage and violence against women and girls. We set out to map the risk of force... Read More about Comparative judgement modeling to map forced marriage at local levels.

MicroRNA biogenesis is broadly disrupted by inhibition of the splicing factor SF3B1 (2024)
Journal Article
Downie Ruiz Velasco, A., Parsons, A. L., Heatley, M. C., Martin, A. R., Smart, A. D., Shah, N., & Jopling, C. L. (2024). MicroRNA biogenesis is broadly disrupted by inhibition of the splicing factor SF3B1. Nucleic Acids Research, 52(15), 9210-9229. https://doi.org/10.1093/nar/gkae505

In animals, microRNA (miRNA) biogenesis begins with cotranscriptional cleavage of the primary (pri-)miRNA by the Microprocessor complex. Cotranscriptional splicing has been shown to influence Microprocessor cleavage when miRNAs are hosted in introns... Read More about MicroRNA biogenesis is broadly disrupted by inhibition of the splicing factor SF3B1.

Comparative transcriptome reprogramming in oak galls containing asexual or sexual generations of gall wasps (2024)
Journal Article
Bellows, E., Heatley, M., Shah, N., Archer, N., Giles, T., & Fray, R. (2024). Comparative transcriptome reprogramming in oak galls containing asexual or sexual generations of gall wasps. Plant Biology, 26(5), 798-810. https://doi.org/10.1111/plb.13670

Oak gall wasps have evolved strategies to manipulate the developmental pathways of their host to induce gall formation. This provides shelter and nutrients for the developing larva. Galls are entirely host tissue; however, the initiation, development... Read More about Comparative transcriptome reprogramming in oak galls containing asexual or sexual generations of gall wasps.

PIMMS-Dash: Accessible analysis, interrogation, and visualisation of high-throughput transposon insertion sequencing (TIS) data (2024)
Preprint / Working Paper
Blanchard, A. M., Taylor, A., Warry, A., Shephard, F., Curwen, A., Leigh, J. A., Emes, R. D., & Egan, S. A. (2024). PIMMS-Dash: Accessible analysis, interrogation, and visualisation of high-throughput transposon insertion sequencing (TIS) data

Motivation Current methods for visualising and interrogating high-throughput transposon insertion mutagenesis sequencing (TIS) data requires a significant time investment in learning bioinformatics, often producing static figures that do not facilita... Read More about PIMMS-Dash: Accessible analysis, interrogation, and visualisation of high-throughput transposon insertion sequencing (TIS) data.

Compartmentalization proteomics revealed endolysosomal protein network changes in a goat model of atrial fibrillation (2024)
Journal Article
Ayagama, T., Charles, P. D., Bose, S. J., Boland, B., Priestman, D. A., Aston, D., Berridge, G., Fisher, R., Cribbs, A. P., Song, Q., Mirams, G. R., Amponsah, K., Heather, L., Galione, A., Herring, N., Kramer, H., Capel, R. A., Platt, F. M., Schotten, U., Verheule, S., & Burton, R. A. (2024). Compartmentalization proteomics revealed endolysosomal protein network changes in a goat model of atrial fibrillation. iScience, 27(6), Article 109609. https://doi.org/10.1016/j.isci.2024.109609

Endolysosomes (EL) are known for their role in regulating both intracellular trafficking and proteostasis. EL facilitate the elimination of damaged membranes, protein aggregates, membranous organelles and play an important role in calcium signaling.... Read More about Compartmentalization proteomics revealed endolysosomal protein network changes in a goat model of atrial fibrillation.

Antibody prevalence after three or more COVID-19 vaccine doses in individuals who are immunosuppressed in the UK: a cross-sectional study from MELODY (2023)
Journal Article
Pearce, F. A., Lim, S. H., Bythell, M., Lanyon, P., Hogg, R., Taylor, A., Powter, G., Cooke, G. S., Ward, H., Chilcot, J., Thomas, H., Mumford, L., McAdoo, S. P., Pettigrew, G. J., Lightstone, L., & Willicombe, M. (2023). Antibody prevalence after three or more COVID-19 vaccine doses in individuals who are immunosuppressed in the UK: a cross-sectional study from MELODY. The Lancet Rheumatology, 5(8), E461-E473. https://doi.org/10.1016/S2665-9913%2823%2900160-1

Background:
In the UK, additional COVID-19 vaccine booster doses and treatments are offered to people who are immunosuppressed to protect against severe COVID-19, but how best to choose the individuals that receive these vaccine booster doses and t... Read More about Antibody prevalence after three or more COVID-19 vaccine doses in individuals who are immunosuppressed in the UK: a cross-sectional study from MELODY.

AI4Green: An Open-Source ELN for Green and Sustainable Chemistry (2023)
Journal Article
Boobier, S., Davies, J. C., Derbenev, I. N., Handley, C. M., & Hirst, J. D. (2023). AI4Green: An Open-Source ELN for Green and Sustainable Chemistry. Journal of Chemical Information and Modeling, 63(10), 2895–2901. https://doi.org/10.1021/acs.jcim.3c00306

An Electronic Laboratory Notebook (ELN) combining features, including data archival, collaboration tools, and green and sustainability metrics for organic chemistry, is presented. AI4Green is a web-based application, available as open-source code and... Read More about AI4Green: An Open-Source ELN for Green and Sustainable Chemistry.

AI4Green: An Open-Source ELN for Green and Sustainable Chemistry (2023)
Preprint / Working Paper
Boobier, S., Davies, J., Derbenev, I., Handley, C., & Hirst, J. AI4Green: An Open-Source ELN for Green and Sustainable Chemistry

An Electronic Laboratory Notebook (ELN) combining features, including data archival, collaboration tools, and green and sustainability metrics for organic chemistry, is presented. AI4Green is a web-based application, available as open-source code and... Read More about AI4Green: An Open-Source ELN for Green and Sustainable Chemistry.

Identifying new biomarkers of aggressive Group 3 and SHH medulloblastoma using 3D hydrogel models, single cell RNA sequencing and 3D OrbiSIMS imaging (2023)
Journal Article
Linke, F., Johnson, J. E. C., Kern, S., Bennett, C. D., Lourdusamy, A., Lea, D., Clifford, S. C., Merry, C. L. R., Stolnik, S., Alexander, M. R., Peet, A. C., Scurr, D. J., Griffiths, R. L., Grabowska, A. M., Kerr, I. D., & Coyle, B. (2023). Identifying new biomarkers of aggressive Group 3 and SHH medulloblastoma using 3D hydrogel models, single cell RNA sequencing and 3D OrbiSIMS imaging. Acta Neuropathologica Communications, 11(1), Article 6. https://doi.org/10.1186/s40478-022-01496-4

The most common malignant brain tumour in children, medulloblastoma (MB), is subdivided into four clinically relevant molecular subgroups, although targeted therapy options informed by understanding of different cellular features are lacking. Here, b... Read More about Identifying new biomarkers of aggressive Group 3 and SHH medulloblastoma using 3D hydrogel models, single cell RNA sequencing and 3D OrbiSIMS imaging.

Differential remodelling in small and large murine airways revealed by novel whole lung airway analysis (2023)
Journal Article
Tatler, A. L., Philp, C. J., Hill, M. R., Cox, S., Bullock, A. M., John, A., Middlewick, R., Stephenson, K. E., Goodwin, A. T., Billington, C. K., O'Dea, R. D., Johnson, S. R., & Brook, B. S. (2023). Differential remodelling in small and large murine airways revealed by novel whole lung airway analysis. American Journal of Physiology-Lung Cellular and Molecular Physiology, 324(3), L271-L284. https://doi.org/10.1152/ajplung.00034.2022

Airway remodelling occurs in chronic asthma leading to increased airway smooth muscle (ASM) mass and extra-cellular matrix (ECM) deposition. Whilst extensively studied in murine airways, studies report only selected larger airways at one time point m... Read More about Differential remodelling in small and large murine airways revealed by novel whole lung airway analysis.

Dynamic early warning scores for predicting clinical deterioration in patients with respiratory disease (2022)
Journal Article
Gonem, S., Taylor, A., Figueredo, G., Forster, S., Quinlan, P., Garibaldi, J. M., McKeever, T. M., & Shaw, D. (2022). Dynamic early warning scores for predicting clinical deterioration in patients with respiratory disease. Respiratory Research, 23, Article 203. https://doi.org/10.1186/s12931-022-02130-6

Background: The National Early Warning Score-2 (NEWS-2) is used to detect patient deterioration in UK hospitals but fails to take account of the detailed granularity or temporal trends in clinical observations. We used data-driven methods to develop... Read More about Dynamic early warning scores for predicting clinical deterioration in patients with respiratory disease.

cellmlmanip and chaste_codegen: automatic CellML to C++ code generation with fixes for singularities and automatically generated Jacobians (2022)
Journal Article
Hendrix, M., Clerx, M., Tamuri, A. U., Keating, S. M., Johnstone, R. H., Cooper, J., & Mirams, G. R. (2022). cellmlmanip and chaste_codegen: automatic CellML to C++ code generation with fixes for singularities and automatically generated Jacobians. Wellcome Open Research, 6, Article 261. https://doi.org/10.12688/wellcomeopenres.17206.2

Hundreds of different mathematical models have been proposed for describing electrophysiology of various cell types. These models are quite complex (nonlinear systems of typically tens of ODEs and sometimes hundreds of parameters) and software packag... Read More about cellmlmanip and chaste_codegen: automatic CellML to C++ code generation with fixes for singularities and automatically generated Jacobians.

A Hybrid Architecture (CO-CONNECT) to Facilitate Rapid Discovery and Access to Data Across the United Kingdom in Response to the COVID-19 Pandemic: Development Study (2022)
Journal Article
Jefferson, E., Cole, C., Mumtaz, S., Cox, S., Giles, T., Adejumo, S., Urwin, E., Lea, D., McDonald, C., Best, J., Masood, E., Milligan, G., Johnston, J., Horban, S., Birced, I., Hall, C., Jackson, A., Collins, C., Rising, S., Dodsley, C., …Quinlan, P. (2022). A Hybrid Architecture (CO-CONNECT) to Facilitate Rapid Discovery and Access to Data Across the United Kingdom in Response to the COVID-19 Pandemic: Development Study. Journal of Medical Internet Research, 24(12), Article e40035. https://doi.org/10.2196/40035

Background:
COVID-19 data have been generated across the United Kingdom as a by-product of clinical care and public health provision, as well as numerous bespoke and repurposed research endeavors. Analysis of these data has underpinned the United Ki... Read More about A Hybrid Architecture (CO-CONNECT) to Facilitate Rapid Discovery and Access to Data Across the United Kingdom in Response to the COVID-19 Pandemic: Development Study.

chaste codegen: automatic CellML to C++ code generation with fixes for singularities and automatically generated Jacobians (2022)
Journal Article
Hendrix, M., Clerx, M., Tamuri, A. U., Keating, S. M., Johnstone, R. H., Cooper, J., & Mirams, G. R. (2022). chaste codegen: automatic CellML to C++ code generation with fixes for singularities and automatically generated Jacobians. Wellcome Open Research, 6, Article 261. https://doi.org/10.12688/wellcomeopenres.17206.1

Hundreds of different mathematical models have been proposed for describing electrophysiology of various cell types. These models are quite complex (nonlinear systems of typically tens of ODEs and sometimes hundreds of parameters) and software packag... Read More about chaste codegen: automatic CellML to C++ code generation with fixes for singularities and automatically generated Jacobians.

Cluster analyses of the TCGA and a TMA dataset using the coexpression of HSP27 and CRYAB improves alignment with clinical-pathological parameters of breast cancer and suggests different epichaperome influences for each sHSP (2022)
Journal Article
Quinlan, P. R., Figeuredo, G., Mongan, N., Jordan, L. B., Bray, S. E., Sreseli, R., Ashfield, A., Mitsch, J., van den Ijssel, P., Thompson, A. M., & Quinlan, R. A. (2022). Cluster analyses of the TCGA and a TMA dataset using the coexpression of HSP27 and CRYAB improves alignment with clinical-pathological parameters of breast cancer and suggests different epichaperome influences for each sHSP. Cell Stress and Chaperones, 27(2), 177-188. https://doi.org/10.1007/s12192-022-01258-0

Our cluster analysis of the Cancer Genome Atlas for co-expression of HSP27 and CRYAB in breast cancer patients identified three patient groups based on their expression level combination (high HSP27 + low CRYAB; low HSP27 + high CRYAB; similar HSP27 ... Read More about Cluster analyses of the TCGA and a TMA dataset using the coexpression of HSP27 and CRYAB improves alignment with clinical-pathological parameters of breast cancer and suggests different epichaperome influences for each sHSP.