Publications

Evaluation of sequence hybridization for respiratory viruses using the Twist Bioscience Respiratory Virus Research panel and the OneCodex Respiratory Virus sequence analysis workflow.

Kapel N. et al, (2023), Microbial genomics, 9

Algorithmic fairness and bias mitigation for clinical machine learning with deep reinforcement learning

Yang J. et al, (2023), Nature Machine Intelligence

Integrating at-scale health data into doctoral training (Preprint)

Nichols TE. et al, (2023)

Scalable federated learning for emergency care using low cost microcomputing: Real-world, privacy preserving development and evaluation of a COVID-19 screening test in UK hospitals

Soltan AAS. et al, (2023)

Protection against SARS-CoV-2 Omicron BA.4/5 variant following booster vaccination or breakthrough infection in the UK.

Wei J. et al, (2023), Nature communications, 14

Comparing genomic variant identification protocols for Candida auris.

Li X. et al, (2023), Microb Genom, 9

An adversarial training framework for mitigating algorithmic biases in clinical machine learning

Yang J. et al, (2023), npj Digital Medicine, 6

Performance of antigen lateral flow devices in the UK during the alpha, delta, and omicron waves of the SARS-CoV-2 pandemic: a diagnostic and observational study.

Eyre DW. et al, (2023), Lancet Infect Dis

The quality of vital signs measurements and value preferences in electronic medical records varies by hospital, specialty, and patient demographics

Jackson N. et al, (2023), Scientific reports, 13

Self-Aware SGD: Reliable Incremental Adaptation Framework For Clinical AI Models

Thakur A. et al, (2023), IEEE Journal of Biomedical and Health Informatics, 1 - 11

SARS-CoV-2 antibody responses post-vaccination in UK healthcare workers with pre-existing medical conditions: a cohort study.

Ward V. et al, (2022), BMJ open, 12

Treatment of enteric fever (typhoid and paratyphoid fever) with cephalosporins

Kuehn R. et al, (2022), Cochrane Database of Systematic Reviews, 2022

Benchmarking taxonomic classifiers with Illumina and Nanopore sequence data for clinical metagenomic diagnostic applications

Govender KN. and Eyre DW., (2022), Microbial Genomics, 8

RapiD_AI: A framework for Rapidly Deployable AI for novel disease & pandemic preparedness

Youssef A. et al, (2022)

Detecting changes in population trends in infection surveillance using community SARS-CoV-2 prevalence as an exemplar

Pritchard E. et al, (2022)

Combination therapy of infliximab and thiopurines, but not monotherapy with infliximab or vedolizumab, is associated with attenuated IgA and neutralisation responses to SARS-CoV-2 in inflammatory bowel disease.

Wellens J. et al, (2022), Gut, 71, 1919 - 1922

Increasing test specificity without impairing sensitivity: lessons learned from SARS-CoV-2 serology.

Perkmann T. et al, (2022), Journal of clinical pathology

Mortality risks associated with empirical antibiotic activity in Escherichia coli bacteraemia: an analysis of electronic health records

Yoon CH. et al, (2022), Journal of Antimicrobial Chemotherapy, 77, 2536 - 2545

Symptoms and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Positivity in the General Population in the United Kingdom

Vihta KD. et al, (2022), Clinical Infectious Diseases, 75, e329 - e337

RapiD_AI: A framework for Rapidly Deployable AI for novel disease & pandemic preparedness

Youssef A. et al, (2022)

Time-of-Day Variation in SARS-CoV-2 RNA Levels during the Second Wave of COVID-19

Zhuang X. et al, (2022), Viruses, 14, 1728 - 1728

Omicron-associated changes in SARS-CoV-2 symptoms in the United Kingdom

Vihta1 KD. et al, (2022), Clinical Infectious Diseases

Comparison of two T-cell assays to evaluate T-cell responses to SARS-CoV-2 following vaccination in naïve and convalescent healthcare workers

Phillips E. et al, (2022), Clinical and Experimental Immunology, 209, 90 - 98

Fatal COVID-19 outcomes are associated with an antibody response targeting epitopes shared with endemic coronaviruses

McNaughton AL. et al, (2022), JCI Insight, 7

Assessment of an institutional guideline for vancomycin dosing and identification of predictive factors associated with dose and drug trough levels

Gu Q. et al, (2022), Journal of Infection

SARS-CoV-2 antibody trajectories after a single COVID-19 vaccination with and without prior infection

Wei J. et al, (2022), Nature Communications, 13

Chest CT and Hospital Outcomes in Patients with Omicron Compared with Delta Variant SARS-CoV-2 Infection.

Tsakok MT. et al, (2022), Radiology

CO-CONNECT: A hybrid architecture to facilitate rapid discovery and access to UK wide data in the response to the COVID-19 pandemic (Preprint)

Jefferson E. et al, (2022), Journal of Medical Internet Research

Evolution of long-term vaccine induced and hybrid immunity in healthcare workers after different COVID-19 vaccination regimens: a longitudinal observational cohort study

Moore SC. et al, (2022)

Whole genome sequencing reveals hidden transmission of carbapenemase-producing Enterobacterales.

Marimuthu K. et al, (2022), Nature communications, 13

Penicillin Binding Protein Substitutions Co-occur with Fluoroquinolone Resistance in ‘Epidemic’ Lineages of Multi Drug-Resistant Clostridioides difficile

Dingle KE. et al, (2022)

Evaluation of metagenomic, 16S rRNA gene and ultra-plexed PCR-based sequencing approaches for profiling antimicrobial resistance gene and bacterial taxonomic composition of polymicrobial samples

Chau KK. et al, (2022)

Antibody responses and correlates of protection in the general population after two doses of the ChAdOx1 or BNT162b2 vaccines

Wei J. et al, (2022), Nature Medicine, 28, 1072 - 1082

BOTH VEDOLIZUMAB AND ANTI-TNF THERAPY ARE ASSOCIATED WITH ATTENUATION OF SEROLOGICAL AND NEUTRALIZING RESPONSES TO SARS-COV-2 INFECTION IN INFLAMMATORY BOWEL DISEASE

Wellens J. et al, (2022), GASTROENTEROLOGY, 162, S278 - S278

Molecular alterations due to Col5a1 haploinsufficiency in a mouse model of classic Ehlers–Danlos syndrome

Machol K. et al, (2022), Human Molecular Genetics, 31, 1325 - 1335

Clinical Metagenomic Sequencing for Species Identification and Antimicrobial Resistance Prediction in Orthopedic Device Infection.

Street TL. et al, (2022), Journal of clinical microbiology, 60

Real-world evaluation of rapid and laboratory-free COVID-19 triage for emergency care: external validation and pilot deployment of artificial intelligence driven screening.

Soltan AAS. et al, (2022), The Lancet. Digital health, 4, e266 - e278

Assessment of a vancomycin dosing guideline and identification of predictive factors associated with dose and drug trough levels

Gu Q. et al, (2022)

Casirivimab and imdevimab in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial

Abani O. et al, (2022), The Lancet, 399, 665 - 676

Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission.

Aggarwal D. et al, (2022), Nature communications, 13

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission.

Aggarwal D. et al, (2022), Nature communications, 13

Monitoring populations at increased risk for SARS-CoV-2 infection in the community using population-level demographic and behavioural surveillance

Pritchard E. et al, (2022), The Lancet Regional Health - Europe, 13, 100282 - 100282

Mortality risks associated with empirical antibiotic activity in E. coli bacteraemia: an analysis of electronic health records

Yoon CH. et al, (2022)

The quality of vital signs measurements in electronic medical records varies by hospital, specialty, and patient demographics

Jackson N. et al, (2022)

Omicron-associated changes in SARS-CoV-2 symptoms in the United Kingdom

Vihta K-D. et al, (2022)

Benchmarking taxonomic classifiers with Illumina and Nanopore sequence data for clinical metagenomic diagnostic applications

Govender KN. and Eyre DW., (2022)

Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study

Twohig KA. et al, (2022), The Lancet Infectious Diseases, 22, 35 - 42

T-cell and antibody responses to first BNT162b2 vaccine dose in previously infected and SARS-CoV-2-naive UK health-care workers: a multicentre prospective cohort study

Angyal A. et al, (2022), The Lancet Microbe, 3, e21 - e31

The challenge of limited vaccine supplies: impact of prior infection on anti-spike IgG antibody trajectories after a single COVID-19 vaccination

Wei J. et al, (2021)

Genomic epidemiology and longitudinal sampling of ward wastewater environments and patients reveals complexity of the transmission dynamics of blaKPC-carbapenemase-producing Enterobacterales in a hospital setting

Stoesser N. et al, (2021)

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Publications