Publications

Ariño H, Bae SK, Chaturvedi J, Wang T and Roberts A (2023) Identifying encephalopathy in patients admitted to an intensive care unit: Going beyond structured information using natural language processing. Front. Digit. Health 5:1085602. doi: https://doi.org/10.3389/fdgth.2023.1085602

Chaturvedi, J., et al. (2022) ‘Extracting Information about Pain from Free-Text of Mental Health Electronic Health Records', 20th Congress of the European Psychiatric Association Section, Cambridge UK

Chaturvedi, J., et al. (2022) ‘Annotations of Mentions of Pain in Mental Health Records', IASP 2022 World Congress of Pain, Toronto Canada

Chaturvedi, J., et al. (2022) 'Sample Size in Healthcare Natural Language Processing', 5th Healthcare Text Analytics Conference: HealTAC 2022 (online)

Chaturvedi, J. (2022) 'Combining Empirical and Knowledge-based Methods for Clinical Modelling of Electronic Health Record Text', 20th International Conference on Artificial Intelligence in Medicine (Doctoral Consortium), Halifax Canada

Godfrey, T., Batra, R., Douthwaite, S., Edgeworth, J., Miles, S., Zschaler, S. (2022). A Methodology for DSML-Assisted Participatory Agent-Based Enterprise Modelling. In: Barn, B.S., Sandkuhl, K. (eds) The Practice of Enterprise Modeling. PoEM 2022. Lecture Notes in Business Information Processing, vol 456. Springer, Cham. https://doi.org/10.1007/978-3-031-21488-2_13

Participatory Agent-Based Modelling in Healthcare – A Domain-Specific Modelling Language Approach. ACM Student Research Competition Track, MODELS 2022

Nordio G. et al. (2022). Digital data repository and automatic analysis framework for FDOPA PET neuroimaging. Preprint. http://dx.doi.org/10.1101/2022.04.14.488129

Easmin R. et al. (2022) Bitbox: A Cloud-based data sharing solution for medical images. Conference: 2022 44th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC). https://doi.org/10.1109/EMBC48229.2022.9871689

Giacomel A. et al. (2022) Integrating neuroimaging and gene expression data: the Imaging Transcriptomics toolbox. STAR PROTOCOL  https://doi.org/10.1016/j.xpro.2022.101315

 Giacomel A. et al (2021) Generation of a Normative Dopamine Neuroreceptor Template from [11C]PHNO PET Imaging Modelling Population Variability. NeuroReceptor Mapping 2021

Giacomel A. et al (2022) Towards a Normative Model of the Dopamine Neuroreceptor System using [11C]-(+)-PHNO PET Imaging. Brain and BrainPET 2022

Giacomel A. et al. (2022) The Imaging Transcriptomics Tollbox. https://doi.org/10.5281/zenodo.6364963

Mandreoli, F., Ferrari, D., et. al. (2022) Real-world data mining meets clinical practice: Research challenges and perspective, Frontiers in Big Data https://doi.org/10.3389/fdata.2022.1021621

Ferrari D., et al. (2022) Multi-Objective Symbolic Regression for Data-Driven Scoring System Management, IEEE International Conference on Data Mining (ICDM 2022, Orlando FL)

Wang, W., et al., (2022) Real-world effectiveness of steroids in severe COVID-19: a retrospective cohort study, BMC Infectious Diseases https://doi.org/10.1186/s12879-022-07750-3

Farran, D., Bean, D., Wang, T., Msosa, Y., Casetta, C., Dobson, R., ... & Gaughran, F. (2022). Anticoagulation for atrial fibrillation in people with serious mental illness in the general hospital setting. Journal of psychiatric research, 153, 167-173 https://doi.org/10.1016/j.jpsychires.2022.06.044

Farran, D., Feely, O., Ashworth, M., & Gaughran, F. (2022). Anticoagulation therapy and outcomes in patients with atrial fibrillation and serious mental illness: A systematic review and meta-analysis. Journal of Psychiatric Research, 156, 737-753 https://doi.org/10.1016/j.jpsychires.2022.11.002

Bearne, L. M., Volkmer, B., Peacock, J., Sekhon, M., Fisher, G., Holmes, M. N. G., ... & MOSAIC Trial Collaboration. (2022). Effect of a home-based, walking exercise behavior change intervention vs usual care on walking in adults with peripheral artery disease: the MOSAIC randomized clinical trial. JAMA, 327(14), 1344-1355. https://doi.org/10.1001/jama.2022.3391

Farran, D., Feely, O., Ashworth, M., & Gaughran, F. (2022). Corrigendum to “Anticoagulation therapy and outcomes in patients with atrial fibrillation and serious mental illness: A systematic review and meta-analysis”.  https://doi.org/10.1016/j.jpsychires.2022.12.016

Farran, D., Bean, D., Wang, T., Msosa, Y., Casetta, C., Dobson, R., ... & Gaughran, F. (2022). Corrigendum to "Anticoagulation for atrial fibrillation in people with serious mental illness in the general hospital setting". https://doi.org/10.1016/j.jpsychires.2022.12.015

Kabiljo R, Bowles H, Marriott H, et al. (2022). RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data. iScience. 25(11):105289.  https://doi.org/10.1016/j.isci.2022.105289

Marriott H., et al. (2022). Genetic data of 10,996 ALS patients and 7,403 controls shows that missense variants in the tail domain of NEFH increase the risk of ALS. European Network to Cure ALS (ENCALS) 2022, Edinburgh, Scotland.

Marriott H., et al. (2022). Unsupervised hierarchical clustering of postmortem motor cortex expression data identifies distinct molecular phenotypes which replicate the major mechanisms of ALS pathogenesis. 33rd International Symposium on ALS/MND. Virtual.

Serna-Pascual M., et al. (2021) SPAR (Symmetric Projection Attractor Reconstruction): Identifying novel respiratory biomarkers from waveform morphology and variability https://doi.org/10.1183/13993003.congress-2021.PA3217

Serna-Pascual M., et al. (2022) Hidden Disease Signs in the Pattern of Breathing https://stemforbritain.org.uk/2022-winners

Serna-Pascual M., et al. (2022) Symmetric Projection Attractor Reconstruction: Analysis of waveform morphology predicts COPD exacerbations doi 10.1183/13993003.congress-2022.3645

Serna-Pascual M., et al. (2022) Symmetric Projection Attractor Reconstruction (SPAR): advanced respiratory pattern analysis provides additional biomarkers of COPD http://dx.doi.org/10.1136/thorax-2022-BTSabstracts.73

Guy P Hunt, Luigi Grassi, Rafael Henkin, Fabrizio Smeraldi, Thomas P Spargo, Renata Kabiljo, Sulev Koks, Zina Ibrahim, Richard J B Dobson, Ammar Al-Chalabi, Michael R Barnes, Alfredo Iacoangeli, GEOexplorer: a webserver for gene expression analysis and visualisation, Nucleic Acids Research, Volume 50, Issue W1, 5 July 2022, Pages W367–W374, https://doi.org/10.1093/nar/gkac364

Hunt, G.P. et al. (2021) “GEOexplorer: An R/bioconductor package for gene expression analysis and visualisation.”  https://doi.org/10.1101/2021.10.06.459411

Guy P Hunt, Luigi Grassi, Rafael Henkin, Fabrizio Smeraldi, Thomas P Spargo, Renata Kabiljo, Sulev Koks, Zina Ibrahim, Richard J B Dobson, Ammar Al-Chalabi, Michael R Barnes, Alfredo Iacoangeli, GEOexplorer: a webserver for gene expression analysis and visualisation, 33rd International Symposium on ALS/MND. Virtual.

Guy P Hunt, Luigi Grassi, Rafael Henkin, Fabrizio Smeraldi, Thomas P Spargo, Renata Kabiljo, Sulev Koks, Zina Ibrahim, Richard J B Dobson, Ammar Al-Chalabi, Michael R Barnes, Alfredo Iacoangeli, GEOexplorer: a webserver for gene expression analysis and visualisation, European Network to Cure ALS

Chaturvedi J, et al. (2023) Development of a Corpus Annotated with Mentions of Pain in Mental Health Records [Internet]. JMIR Preprints. [cited 2023 Feb 1]. Available from: https://preprints.jmir.org/preprint/45849 [Under Review]  http://doi.org/10.2196/preprints.45849

Kell G, Marshall I, Wallace B, Jaun A. What Would it Take to get Biomedical QA Systems into Practice? In: Proceedings of the 3rd Workshop on Machine Reading for Question Answering [Internet]. Punta Cana, Dominican Republic: Association for Computational Linguistics; 2021. p. 28–41. Available from: https://aclanthology.org/2021.mrqa-1.3  https://10.18653/v1/2021.mrqa-1.3

Gilchrist, L. et al. (2022). Investigating the genetic overlap between different depression symptoms and Alzheimer's Disease.

Green, R. et al. (2022) Investigating Associations Between Blood Metabolites, Later Life Brain Imaging Measures, And Genetic Risk For Alzheimer’s Disease. https://www.medrxiv.org/content/10.1101/2022.01.29.22270098v3

Slade, S et al. (2022) American College of Cardiology and American Heart Association blood pressure categories - a systematic review in the first half of pregnancy. https://doi.org/10.1016/j.ajog.2022.10.004

Slade, S et al. (2023) American College of Cardiology and American Heart Association blood pressure categories in the second half of pregnancy - a systematic review of their association with adverse pregnancy outcomes. https://doi.org/10.1016/j.ajog.2023.01.013

In a pilot study, automated real-time systematic review updates were feasible, accurate, and work-saving Marshall, I. J., Trikalinos, T. A., Soboczenski, F., Yun, H. S., Kell, G., Marshall, R. & Wallace, B. C., Jan 2023, In: Journal of Clinical Epidemiology. 153, p. 26-33 https://doi.org/10.1016/j.jclinepi.2022.08.013

Bendayan, R. et al. (2022) ‘Mapping multimorbidity in individuals with schizophrenia and bipolar disorders: evidence from the South London and Maudsley NHS Foundation Trust Biomedical Research Centre (SLAM BRC) case register’, BMJ Open, 12(1), p. e054414. doi:10.1136/bmjopen-2021-054414.

Chaturvedi, J., Mascio, A., et al. (2021) ‘Development of a Lexicon for Pain’, Frontiers in Digital Health, 3, p. 778305. doi:10.3389/fdgth.2021.778305.

Chaturvedi, J., Sabbah, W., et al. (2021) ‘Hospital admissions for dental disorders in patients with severe mental illness in Southeast London: A register‐based cohort study’, European Journal of Oral Sciences, 129(1). doi:10.1111/eos.12752.

Dawood, T. et al. (2021) ‘Uncertainty-Aware Training for Cardiac Resynchronisation Therapy Response Prediction’, arXiv:2109.10641 [cs, eess] [Preprint]. Available at: http://arxiv.org/abs/2109.10641.

de Jong, V.M.T. et al. (2022) ‘Clinical prediction models for mortality in patients with covid-19: external validation and individual participant data meta-analysis’, BMJ, p. e069881. doi:doi.org/10.1136/bmj-2021-069881.

Francis, E.R. et al. (2021) ‘Incidence of suicidality in people with depression over a 10-year period treated by a large UK mental health service provider’, BJPsych Open, 7(6), p. e223. doi:10.1192/bjo.2021.1054.

Ferrari, D. et al.. (2022) Data–driven, AI–based clinical practice: experiences, challenges, and research directions. In 30th Italian Symposium on Advanced Database Systems, SEBD 2022.

Ferrari, D. et al. (2022) Multi-objective Symbolic Regression to Generate Data-driven, Non-fixed Structure and Intelligible Mortality Predictors using EHR: Binary Classification Methodology and Comparison with State-of-the-art. Accepted at AMIA Annual Symposium, November 2022, Washington DC.

Godfrey, T. (2021) ‘Domain-Specific Modelling Languages for Participatory Agent-Based Modelling in Healthcare’, in 2021 ACM/IEEE International Conference on Model Driven Engineering Languages and Systems Companion (MODELS-C). 2021 ACM/IEEE International Conference on Model Driven Engineering Languages and Systems Companion (MODELS-C), Fukuoka, Japan: IEEE, pp. 654–659. doi:10.1109/MODELS-C53483.2021.00105.

Martins, D. et al. (2021) ‘Imaging transcriptomics: Convergent cellular, transcriptomic, and molecular neuroimaging signatures in the healthy adult human brain’, Cell Reports, 37(13), p. 110173. doi:10.1016/j.celrep.2021.110173.

Merrick, B. et al. (2021) ‘Real-world deployment of lateral flow SARS-CoV-2 antigen detection in the emergency department to provide rapid, accurate and safe diagnosis of COVID-19’, Infection Prevention in Practice, 3(4), p. 100186. doi:10.1016/j.infpip.2021.100186.

Mirza, L. et al. (2021) ‘Investigating the association between physical health comorbidities and disability in individuals with severe mental illness’, European Psychiatry, 64(1), p. e77. doi:10.1192/j.eurpsy.2021.2255.

Norgaard, M. et al. (2021) PET-BIDS, an extension to the brain imaging data structure for positron emission tomography. preprint. Neuroscience. doi:10.1101/2021.06.16.448390.

Pontoriero, A.D. et al. (2021) ‘Automated Data Quality Control in FDOPA brain PET Imaging using Deep Learning’, Computer Methods and Programs in Biomedicine, 208, p. 106239. doi:10.1016/j.cmpb.2021.106239.

Wang, W. et al. (2022) Real-world effectiveness of steroids in severe COVID-19: longer courses associated with lower risk of death or ICU admission. preprint. In Review. Available at: https://doi.org/10.21203/rs.3.rs-1380901/v1.