Benjamin Wingfield's research while affiliated with Ulster University and other places
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Publications (11)
Background
Health organizations and countries around the world have found it difficult to control the spread of COVID-19. To minimize the future impact on the UK National Health Service and improve patient care, there is a pressing need to identify individuals who are at a higher risk of being hospitalized because of severe COVID-19. Early targeted...
BACKGROUND
Background - Health organisations and countries around the world have found it difficult to control the spread of the coronavirus disease 2019. To minimise the impact on the NHS and improve patient care, there is a drive for rapid tests capable of detecting individuals who are at high risk of contracting severe COVID-19. Early work focus...
Objective
The Covid Response Study (COVRES, NCT05548829) aims to carry out an integrated multi-omic analysis of factors contributing to host susceptibility to SARS-CoV-2 among a patient cohort of 1000 people from the geographically isolated island of Ireland.
Background
Health organisations and countries around the world have found it difficult to...
Quality control of genomic data is an essential but complicated multi-step procedure, often requiring separate installation and expert familiarity with a combination of different bioinformatics tools. Software incompatibilities, and inconsistencies across computing environments, are recurrent challenges, leading to poor reproducibility. Existing se...
A growing body of evidence supports an important role for alterations in the brain-gut-microbiome axis in the aetiology of depression and other psychiatric disorders. The potential role of the oral microbiome in mental health has received little attention, even though it is one of the most diverse microbiomes in the body and oral dysbiosis has been...
Quality control of genomic data is an essential but complicated multi-step procedure, often requiring separate installation and expert familiarity with a combination of different bioinformatics tools. Dependency hell and reproducibility are recurrent challenges. Existing semi-automated or automated solutions lack comprehensive quality checks, flexi...
Microbiota profiles measure the structure of microbial communities in a defined environment (known as microbiomes). In the past decade, microbiome research has focused on health applications as a result of which the gut microbiome has been implicated in the development of a broad range of diseases such as obesity, inflammatory bowel disease, and ma...
Motivation: Quality control of genomic data is an essential but complicated multi-step procedure, often requiring separate installation and expert familiarity with a combination of disparate bioinformatics tools. Results: To provide an automated solution that retains comprehensive quality checks and flexible workflow architecture, we have developed...
Autism spectrum disorder is an umbrella term for a group of neurodevelopmental disorders that is associated with impairments to social interaction, communication, and behaviour. Typically, autism spectrum disorder is first detected with a screening tool (e.g. modified checklist for autism in toddlers). However, the interpretation of autism spectrum...
Inflammatory Bowel Disease (IBD) is an umbrella term for a group of inflammatory diseases of the gastrointestinal tract, including Crohn's Disease and ulcerative colitis. Changes to the intestinal microbiome, the community of micro-organisms that resides in the human gut, have been shown to contribute to the pathogenesis of IBD. IBD diagnosis is of...
Citations
... By investigating the genetic, gene expression, and epigenetic profiles associated with COVID-19, it is possible to uncover essential information regarding the molecular signatures and regulatory processes involved in the progression and outcomes of the infection. Such comprehensive analyses have the potential to unveil novel biomarkers, therapeutic targets, and pathways that could enhance our understanding of COVID-19 pathophysiology and pave the way for more effective diagnostic and treatment strategies [71,72]. ...
... We used snpQT (v0.1.7) as the main software for quality control (QC), population stratification, association analysis, pre-imputation and post-imputation QC. snpQT is an automatic Nextflow software that ensures reproducibility and scalability, with an easy-touse design [118]. ...
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... On the other hand, both the above-mentioned gut microbiome study and the current salivary microbiome study showed a nonsignificant association with blood pressure and a significant association between beta diversity and depression. Furthermore, recent oral microbiome research focused on young adults showed that the composition of the oral microbiome differed significantly between participants with depressive disorder and those with no history of mental health problems 60 . ...
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... Interestingly, however, Caye et al. [18] used both logistic regressions and machine-learning approaches, and they found that machine learning did not outperform logistic regressions. Regarding ASD, some predictive models have been proposed based on neurobiological markers [14,19,20] or screening tests [21]. However, despite their potential utility, these models-especially those utilizing machine-learning techniques-suffer from a lack of transparency. ...
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... Proposed gut microbial species associated with CD In this study, 11 species were identi ed as being enriched in the CD group: Bi dobacterium dentium, Clostridium innocuum, Clostridium paraputri cum, Clostridium perfringens, Clostridium ramosum, F. umbilicata, Megamonas spp., Morganella morganii, O. splanchnicus, Parasutterella excrementihominis, and R. gnavus (Fig. 8). Besides F. umbilicata and O. splanchnicus, these bacteria have been reported as enriched in the gut of CD patients or are known gut pathobionts [50,52,[54][55][56][57][58][59]. F. umbilicata was signi cantly abundant in CD patients, with an LDA score > 4.0 (Fig. 7b). ...
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... The Micropheno framework predicted Crohn's disease using SVM and RF classifiers. In [17], SVM and MLP were used for classifying a given metagenomic sample into IBD or healthy class. The work combined two types of features such as the OTU abundances and gene group abundance and finally developed a hybrid classifier. ...
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