Publications

SARS-CoV-2, influenza A/B and respiratory syncytial virus positivity and association with influenza-like illness and self-reported symptoms, over the 2022/23 winter season in the UK: a longitudinal surveillance cohort.

Dietz E. et al, (2024), BMC Med, 22

Target enrichment improves culture-independent detection of Neisseria gonorrhoeae and antimicrobial resistance determinants direct from clinical samples with Nanopore sequencing

Street TL. et al, (2024), Microbial Genomics, 10

System-wide approaches to antimicrobial therapy and antimicrobial resistance in the UK: the AMR-X framework.

AMR-X Collaborators None., (2024), The Lancet. Microbe

The burden of bacterial antimicrobial resistance in the WHO African region in 2019: a cross-country systematic analysis

Sartorius B. et al, (2024), The Lancet Global Health, 12, e201 - e216

Genomic epidemiology of Candida auris introduction and outbreaks in the United Kingdom

Kappel D. et al, (2024)

Target enrichment improves culture-independent detection ofNeisseria gonorrhoeaedirect from sample with Nanopore sequencing

Street TL. et al, (2024)

Persistence of SARS-CoV-2 antibodies over 18 months following infection: UK Biobank COVID-19 Serology Study.

Bešević J. et al, (2023), Journal of epidemiology and community health

The epidemiology of multidrug-resistant organisms in persons diagnosed with cancer in Norway, 2008-2018: expanding surveillance using existing laboratory and register data.

Danielsen AS. et al, (2023), European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology

The burden and dynamics of hospital-acquired SARS-CoV-2 in England.

Cooper BS. et al, (2023), Nature

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

The burden of antimicrobial resistance in the Americas in 2019: a cross-country systematic analysis

Aguilar GR. et al, (2023), The Lancet Regional Health - Americas, 25, 100561 - 100561

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), The Lancet. Infectious diseases, 23, 922 - 932

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

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

Risk of SARS-CoV-2 reinfection during multiple Omicron variant waves in the UK general population

Wei J. et al, (2023)

Temporal trends and clinical characteristics of acute hepatitis with unknown aetiology and human adenovirus infections in Oxfordshire from 2016 to 2022

Tan CCS. et al, (2023)

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

Nichols TE. 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

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)

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

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

Improving the representativeness of UK’s national COVID-19 Infection Survey through spatio-temporal regression and post-stratification

Pouwels KB. et al, (2023)

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

Thakur A. et al, (2023)

Defining normal inflammatory marker and vital sign responses to suspected bloodstream infection in adults with positive and negative blood cultures

Gu Q. et al, (2023)

Improving patient flow through hospitals with machine learning based discharge prediction

Zhou J. et al, (2023)

Interpretable Machine Learning-based Decision Support for Prediction of Antibiotic Resistance for Complicated Urinary Tract Infections

Yang J. et al, (2023)

Mode Connections For Clinical Incremental Learning: Lessons From The COVID-19 Pandemic

Thakur A. et al, (2023)

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

Correlates of protection against SARS-CoV-2 Omicron variant and anti-spike antibody responses after a third/booster vaccination or breakthrough infection in the UK general population

Wei J. et al, (2022)

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

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, 85, 382 - 389

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

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)

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Publications