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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., …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 tre... 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)
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., …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., …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.

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., …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., …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.

Findability of UK health datasets available for research: a mixed methods study (2022)
Journal Article
Griffiths, E., Joseph, R. M., Tilston, G., Thew, S., Kapacee, Z., Dixon, W., & Peek, N. (2022). Findability of UK health datasets available for research: a mixed methods study. BMJ Health & Care Informatics, 29(1), Article e100325. https://doi.org/10.1136/bmjhci-2021-100325

Objective How health researchers find secondary data to analyse is unclear. We sought to describe the approaches that UK organisations take to help researchers find data and to assess the findability of health data that are available for research.... Read More about Findability of UK health datasets available for research: a mixed methods study.

Towards a more reliable interpretation of machine learning outputs for safety-critical systems using feature importance fusion (2021)
Journal Article
Rengasamy, D., Rothwell, B. C., & Figueredo, G. P. (2021). Towards a more reliable interpretation of machine learning outputs for safety-critical systems using feature importance fusion. Applied Sciences, 11(24), Article 11854. https://doi.org/10.3390/app112411854

When machine learning supports decision-making in safety-critical systems, it is important to verify and understand the reasons why a particular output is produced. Although feature importance calculation approaches assist in interpretation, there is... Read More about Towards a more reliable interpretation of machine learning outputs for safety-critical systems using feature importance fusion.

minoTour, real-time monitoring and analysis for nanopore sequencers (2021)
Journal Article
Munro, R., Santos, R., Payne, A., Forey, T., Osei, S., Holmes, N., & Loose, M. (2022). minoTour, real-time monitoring and analysis for nanopore sequencers. Bioinformatics, 38(4), 1133-1135. https://doi.org/10.1093/bioinformatics/btab780

Summary: MinoTour offers a LIMS system for Oxford Nanopore Technology sequencers, with real-time metrics and analysis available permanently for review. Integration of unique real-time automated analysis can reduce the time required to answer biologic... Read More about minoTour, real-time monitoring and analysis for nanopore sequencers.

Kernel Methods for Predicting Yields of Chemical Reactions (2021)
Journal Article
Haywood, A. L., Redshaw, J., Hanson-Heine, M. W., Taylor, A., Brown, A., Mason, A. M., …Hirst, J. D. (2022). Kernel Methods for Predicting Yields of Chemical Reactions. Journal of Chemical Information and Modeling, 62(9), 2077-2092. https://doi.org/10.1021/acs.jcim.1c00699

The use of machine learning methods for the prediction of reaction yield is an emerging area. We demonstrate the applicability of support vector regression (SVR) for predicting reaction yields, using combinatorial data. Molecular descriptors used in... Read More about Kernel Methods for Predicting Yields of Chemical Reactions.

LINE-1 transcription in round spermatids is associated with accretion of 5-carboxylcytosine in their open reading frames (2021)
Journal Article
Blythe, M. J., Kocer, A., Rubio-Roldan, A., Giles, T., Abakir, A., Ialy-Radio, C., …Ruzov, A. (2021). LINE-1 transcription in round spermatids is associated with accretion of 5-carboxylcytosine in their open reading frames. Communications Biology, 4, Article 691. https://doi.org/10.1038/s42003-021-02217-8

Chromatin of male and female gametes undergoes a number of reprogramming events during the transition from germ cell to embryonic developmental programs. Although the rearrangement of DNA methylation patterns occurring in the zygote has been extensiv... Read More about LINE-1 transcription in round spermatids is associated with accretion of 5-carboxylcytosine in their open reading frames.

Single-Cell Tracking on Polymer Microarrays Reveals the Impact of Surface Chemistry on Pseudomonas aeruginosa Twitching Speed and Biofilm Development (2020)
Journal Article
Carabelli, A. M., Isgró, M., Sanni, O., Figueredo, G. P., Winkler, D. A., Burroughs, L., …Alexander, M. R. (2020). Single-Cell Tracking on Polymer Microarrays Reveals the Impact of Surface Chemistry on Pseudomonas aeruginosa Twitching Speed and Biofilm Development. ACS Applied Bio Materials, 3(12), 8471–8480. https://doi.org/10.1021/acsabm.0c00849

© 2020 American Chemical Society. Bacterial biofilms exhibit up to 1000 times greater resistance to antibiotic or host immune clearance than planktonic cells. Pseudomonas aeruginosa produces retractable type IV pili (T4P) that facilitate twitching mo... Read More about Single-Cell Tracking on Polymer Microarrays Reveals the Impact of Surface Chemistry on Pseudomonas aeruginosa Twitching Speed and Biofilm Development.

Study protocol for a multicentre longitudinal mixed methods study to explore the Outcomes of ChildrEn and fAmilies in the first year after paediatric Intensive Care: the OCEANIC study (2020)
Journal Article
Manning, J. C., Latour, J. M., Curley, M. A. Q., Draper, E. S., Jilani, T., Quinlan, P. R., …Coad, J. (2020). Study protocol for a multicentre longitudinal mixed methods study to explore the Outcomes of ChildrEn and fAmilies in the first year after paediatric Intensive Care: the OCEANIC study. BMJ Open, 10(5), Article e038974. https://doi.org/10.1136/bmjopen-2020-038974

Introduction Annually in the UK, 20 000 children become very ill or injured and need specialist care within a paediatric intensive care unit (PICU). Most children survive. However, some children and their families may experience problems after they h... Read More about Study protocol for a multicentre longitudinal mixed methods study to explore the Outcomes of ChildrEn and fAmilies in the first year after paediatric Intensive Care: the OCEANIC study.

An innovative approach to multi-method integrated assessment modelling of global climate change (2020)
Journal Article
Siebers, P. O., Lim, Z. E., Figueredo, G. P., & Hey, J. (2020). An innovative approach to multi-method integrated assessment modelling of global climate change. Journal of Artificial Societies and Social Simulation, 23(1), https://doi.org/10.18564/jasss.4209

© 2020, University of Surrey. All rights reserved. Modelling and simulation play an increasingly significant role in exploratory studies for informing policy makers on climate change mitigation strategies. There is considerable research being done in... Read More about An innovative approach to multi-method integrated assessment modelling of global climate change.

Fuzzy Hot Spot Identification for Big Data: An Initial Approach (2019)
Conference Proceeding
Triguero, I., Tickle, R., Figueredo, G. P., Mesgarpour, M., Ozcan, E., & John, R. I. (2019). Fuzzy Hot Spot Identification for Big Data: An Initial Approach. In 2019 IEEE International Conference on Fuzzy Systems (FUZZ-IEEE). https://doi.org/10.1109/FUZZ-IEEE.2019.8858979

Hot spot identification problems are present across a wide range of areas, such as transportation, health care and energy. Hot spots are locations where a certain type of event occurs with high frequency. A recent big data approach is capable of iden... Read More about Fuzzy Hot Spot Identification for Big Data: An Initial Approach.

PAS3-HSID: a Dynamic Bio-Inspired Approach for Real-Time Hot Spot Identification in Data Streams (2019)
Journal Article
Tickle, R., Triguero, I., Figueredo, G. P., Mesgarpour, M., & John, R. I. (2019). PAS3-HSID: a Dynamic Bio-Inspired Approach for Real-Time Hot Spot Identification in Data Streams. Cognitive Computation, 11(3), 434–458. https://doi.org/10.1007/s12559-019-09638-y

© 2019, Springer Science+Business Media, LLC, part of Springer Nature. Hot spot identification is a very relevant problem in a wide variety of areas such as health care, energy or transportation. A hot spot is defined as a region of high likelihood o... Read More about PAS3-HSID: a Dynamic Bio-Inspired Approach for Real-Time Hot Spot Identification in Data Streams.

Complete Genome Sequences of Seven Vibrio cholerae Phages Isolated in China (2017)
Journal Article
Bhandare, S. G., Warry, A., Emes, R. D., Su, J., Barrow, P. A., & Atterbury, R. J. (2017). Complete Genome Sequences of Seven Vibrio cholerae Phages Isolated in China. Genome Announcements, 5(47), Article e01019-17. https://doi.org/10.1128/genomeA.01019-17

The complete genome sequences of seven closely related Vibrio cholerae phages isolated from environmental sites in southeastern China are reported here. Phages QH, CJY, H1, H2, H3, J2, and J3 are members of the Podoviridae family and are highly simil... Read More about Complete Genome Sequences of Seven Vibrio cholerae Phages Isolated in China.