Anna Fowler
YOU?
Author Swipe
View article: BTN2A1 and BTN3A1 as Novel Coeliac Disease Risk Loci: An In Silico Analysis
BTN2A1 and BTN3A1 as Novel Coeliac Disease Risk Loci: An In Silico Analysis Open
Coeliac disease (CeD) is a gastrointestinal enteropathy triggered by the consumption of gluten in predisposed individuals. A recent study showed that individuals were at more than 10% risk of having CeD if a first-degree relative also had …
View article: <em>BTN2A1</em> and <em>BTN3A1</em> as Novel Coeliac Disease Risk Loci: An <em>in silico</em> Analysis
<em>BTN2A1</em> and <em>BTN3A1</em> as Novel Coeliac Disease Risk Loci: An <em>in silico</em> Analysis Open
Coeliac disease (CeD) is a gastrointestinal enteropathy triggered by the consumption of gluten in predisposed individuals. Only around 50% of CeD genetic risk is understood, with the majority of risk attributed to the HLA loci. We investig…
View article: Predicting High Confidence ctDNA Somatic Variants with Ensemble Machine Learning Models
Predicting High Confidence ctDNA Somatic Variants with Ensemble Machine Learning Models Open
Circulating tumour DNA (ctDNA) is a minimally invasive cancer biomarker that can be used to inform treatment of cancer patients. The utility of ctDNA as a cancer biomarker depends on the ability to accurately detect somatic variants associ…
View article: Evaluating the utility of amino acid similarity-aware kmers to represent TCR repertoires for classification
Evaluating the utility of amino acid similarity-aware kmers to represent TCR repertoires for classification Open
Insights gained through interpretation of models trained on the T-cell receptor (TCR) repertoire contribute to advances in understanding of immune-mediated disease. This has the potential to improve diagnostic tests and treatments, particu…
View article: Benchmarking UMI-aware and standard variant callers for low frequency ctDNA variant detection
Benchmarking UMI-aware and standard variant callers for low frequency ctDNA variant detection Open
Background Circulating tumour DNA (ctDNA) is a subset of cell free DNA (cfDNA) released by tumour cells into the bloodstream. Circulating tumour DNA has shown great potential as a biomarker to inform treatment in cancer patients. Collectin…
View article: An Interpretable Classification Model Using Gluten-Specific TCR Sequences Shows Diagnostic Potential in Coeliac Disease
An Interpretable Classification Model Using Gluten-Specific TCR Sequences Shows Diagnostic Potential in Coeliac Disease Open
Coeliac disease (CeD) is a T-cell mediated enteropathy triggered by dietary gluten which remains substantially under-diagnosed around the world. The diagnostic gold-standard requires histological assessment of intestinal biopsies taken at …
View article: Benchmarking UMI-aware and standard variant callers on synthetic and real ctDNA datasets
Benchmarking UMI-aware and standard variant callers on synthetic and real ctDNA datasets Open
Background Circulating tumour DNA (ctDNA) is a subset of cell free DNA (cfDNA) released by tumour cells into the bloodstream. Circulating tumour DNA has shown great potential as a biomarker to inform treatment in cancer patients. Collectin…
View article: Genomic profiling of idiopathic peri-hilar cholangiocarcinoma reveals new targets and mutational pathways
Genomic profiling of idiopathic peri-hilar cholangiocarcinoma reveals new targets and mutational pathways Open
Peri-hilar cholangiocarcinoma (pCCA) is chemorefractory and limited genomic analyses have been undertaken in Western idiopathic disease. We undertook comprehensive genomic analyses of a U.K. idiopathic pCCA cohort to characterize its mutat…
View article: College faculty experiences with online teaching during the COVID-19 pandemic
College faculty experiences with online teaching during the COVID-19 pandemic Open
Objective: The COVID-19 pandemic led to a rapid transition in operations for higher education institutions. The delivery of traditional teaching methods shifted to online instruction. Much of the research has explored student experiences d…
View article: Utility of Bulk T-Cell Receptor Repertoire Sequencing Analysis in Understanding Immune Responses to COVID-19
Utility of Bulk T-Cell Receptor Repertoire Sequencing Analysis in Understanding Immune Responses to COVID-19 Open
Measuring immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 19 (COVID-19), can rely on antibodies, reactive T cells and other factors, with T-cell-mediated responses appear…
View article: Predicting the animal hosts of coronaviruses from compositional biases of spike protein and whole genome sequences through machine learning
Predicting the animal hosts of coronaviruses from compositional biases of spike protein and whole genome sequences through machine learning Open
The COVID-19 pandemic has demonstrated the serious potential for novel zoonotic coronaviruses to emerge and cause major outbreaks. The immediate animal origin of the causative virus, SARS-CoV-2, remains unknown, a notoriously challenging t…
View article: Classification of intestinal <scp>T</scp>‐cell receptor repertoires using machine learning methods can identify patients with coeliac disease regardless of dietary gluten status
Classification of intestinal <span>T</span>‐cell receptor repertoires using machine learning methods can identify patients with coeliac disease regardless of dietary gluten status Open
In coeliac disease (CeD), immune‐mediated small intestinal damage is precipitated by gluten, leading to variable symptoms and complications, occasionally including aggressive T‐cell lymphoma. Diagnosis, based primarily on histopathological…
View article: Predicting the animal hosts of coronaviruses from compositional biases of spike protein and whole genome sequences through machine learning
Predicting the animal hosts of coronaviruses from compositional biases of spike protein and whole genome sequences through machine learning Open
The COVID-19 pandemic has demonstrated the serious potential for novel zoonotic coronaviruses to emerge and cause major outbreaks. The immediate animal origin of the causative virus, SARS-CoV-2, remains unknown, a notoriously challenging t…
View article: Classification of immune receptor repertoires using machine learning methods
Classification of immune receptor repertoires using machine learning methods Open
R code to generate k-mer counts from a set of CDR3 sequences, and to classify samples based on these counts. Contains 3 main functions: NonPos_Matrix: A function to generate a matrix of kmer counts from a matrix of CDR3 counts. input: Inpu…
View article: Inferring B cell specificity for vaccines using a mixture model
Inferring B cell specificity for vaccines using a mixture model Open
Vaccines have greatly reduced the burden of infectious disease, ranking in their impact on global health second only after clean water. Most vaccines confer protection by the production of antibodies with binding affinity for the antigen, …
View article: RahmanTeam/DECoN: v1.0.2
RahmanTeam/DECoN: v1.0.2 Open
No description provided.
View article: Accurate clinical detection of exon copy number variants in a targeted NGS panel using DECoN
Accurate clinical detection of exon copy number variants in a targeted NGS panel using DECoN Open
Background: Targeted next generation sequencing (NGS) panels are increasingly being used in clinical genomics to increase capacity, throughput and affordability of gene testing. Identifying whole exon deletions or duplications (termed exon…
View article: DECoN (Detection of Exon Copy Number)
DECoN (Detection of Exon Copy Number) Open
DECoN (Detection of Exon Copy Number) is a sensitive and specific tool for detection of exon copy number variants (exon CNVs) in targeted sequencing data.
View article: B-cell repertoire dynamics after sequential hepatitis B vaccination and evidence for cross-reactive B-cell activation
B-cell repertoire dynamics after sequential hepatitis B vaccination and evidence for cross-reactive B-cell activation Open
These results demonstrate the high-sensitivity of our vaccine-specific BCR analysis approach and suggest an alternative view of the B-cell response to novel antigens. In the response to the first vaccine dose, many vaccine-specific BCR clu…
View article: The Diversity and Molecular Evolution of B-Cell Receptors during Infection
The Diversity and Molecular Evolution of B-Cell Receptors during Infection Open
B-cell receptors (BCRs) are membrane-bound immunoglobulins that recognize and bind foreign proteins (antigens). BCRs are formed through random somatic changes of germline DNA, creating a vast repertoire of unique sequences that enable indi…
View article: The use of Transnasal Humidified Rapid‐Insufflation Ventilatory Exchange (THRIVE) to facilitate Tracheostomy under sedation
The use of Transnasal Humidified Rapid‐Insufflation Ventilatory Exchange (THRIVE) to facilitate Tracheostomy under sedation Open
Summary Transnasal Humidified Rapid‐Insufflation Ventilatory Exchange (THRIVE) is an apnoeic oxygenation technique which has also been observed to allow a degree of carbon dioxide clearance [1]. We present the case of a 61‐year‐old patient…
View article: In-Depth Assessment of Within-Individual and Inter-Individual Variation in the B Cell Receptor Repertoire
In-Depth Assessment of Within-Individual and Inter-Individual Variation in the B Cell Receptor Repertoire Open
High-throughput sequencing of the B cell receptor (BCR) repertoire can provide rapid characterization of the B cell response in a wide variety of applications in health, after vaccination and in infectious, inflammatory and immune-driven d…
View article: BCR repertoire sequencing: different patterns of B‐cell activation after two Meningococcal vaccines
BCR repertoire sequencing: different patterns of B‐cell activation after two Meningococcal vaccines Open
Next‐generation sequencing was used to investigate the B‐cell receptor heavy chain transcript repertoire of different B‐cell subsets (naive, marginal zone (MZ), immunoglobulin M (IgM) memory and IgG memory) at baseline, and of plasma cells…
View article: Long-term disability after lacunar stroke
Long-term disability after lacunar stroke Open
In lacunar stroke patients, older age was associated with worsening long-term disability, even without recurrence. Worse long-term function was associated with diabetes, cognitive status, and prior stroke, and regional differences may be a…