Steven J.M. Jones
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View article: Identification of Compound Heterozygous <i>CYP11A1</i> Variants via Reanalysis of Clinical Sequencing Data
Identification of Compound Heterozygous <i>CYP11A1</i> Variants via Reanalysis of Clinical Sequencing Data Open
A molecular diagnosis is currently achievable in approximately 50% of patients assessed by clinical geneticists at tertiary care centres. Next‐Generation Sequencing Panels contain a defined group of genes associated with a clinically defin…
View article: A nuclear TRiC/CCT chaperonin assembles meiotic HORMAD proteins into chromosome axes competent for crossing over
A nuclear TRiC/CCT chaperonin assembles meiotic HORMAD proteins into chromosome axes competent for crossing over Open
The meiotic chromosome axis organizes chromatin and sets the stage for homolog pairing and recombination. Meiotic HORMA domain proteins (mHORMADs) are conserved axis components that conformationally transform during target binding. In C. e…
View article: The Genome Sequence of the Hemlock Woolly Adelgid, <i>Adelges tsugae</i> Annand 1924
The Genome Sequence of the Hemlock Woolly Adelgid, <i>Adelges tsugae</i> Annand 1924 Open
The genome of the hemlock woolly adelgid (Adelges tsugae) is presented in 10 chromosomal pseudomolecules along with 132 unplaced scaffolds for a combined length of 216.56 Mb. The genome is highly contiguous with an N50 of 20.54 Mb and its …
View article: Evaluating Language Models for Biomedical Fact-Checking: A Benchmark Dataset for Cancer Variant Interpretation Verification
Evaluating Language Models for Biomedical Fact-Checking: A Benchmark Dataset for Cancer Variant Interpretation Verification Open
Accurate interpretation of genomic variants is critical for precision oncology but remains slow and dependent on specialized expertise. Public knowledgebases such as the Clinical Interpretation of Variants in Cancer (CIViC) help by curatin…
View article: Effect of maternal HIV status on the early neonatal microbiome
Effect of maternal HIV status on the early neonatal microbiome Open
Microbiome disruption is a proposed mechanism for the observed differences in child health outcomes by maternal HIV status, but the early neonatal microbiome of HIV-exposed (HE) newborns is not well-studied. We used 16S ribosomal ribonucle…
View article: Cross-Platform Methylation-Based Site of Origin Classification for Squamous Cell Carcinomas
Cross-Platform Methylation-Based Site of Origin Classification for Squamous Cell Carcinomas Open
Squamous cell carcinomas (SCCs) are one of the most common cancer types and can arise at nearly any anatomic site. Because SCCs are one of the most common metastases, do not have reliable site-specific morphologic or genomic features, and …
View article: Development and characterization of Novel Small Molecule Inhibitors Targeting LAG-3 Protein
Development and characterization of Novel Small Molecule Inhibitors Targeting LAG-3 Protein Open
Lymphocyte Activation Gene-3 (LAG-3) is a 503-amino acid transmembrane protein that modulates immune responses by negatively regulating the proliferation and activation of T cells - key effectors in adaptive immunity. The finely tuned expr…
View article: The peculiar hard state behaviour of the black hole X-ray binary Swift J1727.8−1613
The peculiar hard state behaviour of the black hole X-ray binary Swift J1727.8−1613 Open
Tracking the correlation between radio and X-ray luminosities during black hole X-ray binary outbursts is a key diagnostic of the coupling between accretion inflows (traced by X-rays) and relativistic jet outflows (traced by radio). We pre…
View article: Transcriptional patterns of cancer-related genes in primary and metastatic tumours revealed by machine learning
Transcriptional patterns of cancer-related genes in primary and metastatic tumours revealed by machine learning Open
Background A key to understanding cancer is to determine the impact on the cellular pathways caused by the repertoire of DNA changes accrued in a cancer cell. Exploring the interactions between genomic aberrations and the expressed transcr…
View article: Exploring Mass Public Transit Adoption for Road Traffic Decongestion and Sustainable Development in the Greater Kumasi Metropolis
Exploring Mass Public Transit Adoption for Road Traffic Decongestion and Sustainable Development in the Greater Kumasi Metropolis Open
This paper explores the adoption of mass public transit (MPT) as a solution to alleviate road traffic congestion for sustainable development in the Greater Kumasi Metropolis of Ghana. In this regard, the study explored (1) factors affectin…
View article: Social Care and Young Adults with Neuromuscular Conditions Diagnosed in Childhood: A Co-Produced Scoping Review
Social Care and Young Adults with Neuromuscular Conditions Diagnosed in Childhood: A Co-Produced Scoping Review Open
Context: The social care needs of young adults with neuromuscular conditions (NMCs) are poorly evidenced. To address the paucity in research, it is first necessary to consolidate current understanding of social care and its presence/absenc…
View article: Neutrophil extracellular trap gene expression signatures identify prognostic and targetable signaling axes for inhibiting pancreatic tumour metastasis
Neutrophil extracellular trap gene expression signatures identify prognostic and targetable signaling axes for inhibiting pancreatic tumour metastasis Open
Tumour associated neutrophils (TANs) promote metastasis through interactions of Neutrophil Extracellular Traps (NETs) with tumour cells. However, molecular details surrounding the interactions between NETs and Pancreatic Ductal Adenocarcin…
View article: Using long-read sequencing to detect and subtype a case with Temple syndrome
Using long-read sequencing to detect and subtype a case with Temple syndrome Open
Temple syndrome is an imprinting disorder resulting from abnormal genomic or epigenomic aberrations of chromosome 14 including maternal uniparental disomy (matUPD), paternal deletion of 14q32, or aberrant methylation of the imprinting cont…
View article: Nanopore direct RNA sequencing of human transcriptomes reveals the complexity of mRNA modifications and crosstalk between regulatory features
Nanopore direct RNA sequencing of human transcriptomes reveals the complexity of mRNA modifications and crosstalk between regulatory features Open
The identification and functional characterization of chemical modifications on an mRNA molecule, in particular N6-methyladenosine (m6A) modification, significantly broadened our understanding of RNA function and regulation. While interact…
View article: The genome sequence of the hemlock woolly adelgid, <i>Adelges tsugae</i> Annand 1924
The genome sequence of the hemlock woolly adelgid, <i>Adelges tsugae</i> Annand 1924 Open
The genome of the hemlock woolly adelgid ( Adelges tsugae ) is presented in 10 chromosomal pseudomolecules along with 132 unplaced scaffolds for a combined length of 216.56 Mb. The genome is highly contiguous, with a benchmarking universal…
View article: Protocol for assessing distances in pathway space for classifier feature sets from machine learning methods
Protocol for assessing distances in pathway space for classifier feature sets from machine learning methods Open
As genes tend to be co-regulated as gene modules, feature selection in machine learning (ML) on gene expression data can be challenged by the complexity of gene regulation. Here, we present a protocol for reconciling differences in classif…
View article: Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T
Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T Open
The complexities of cancer genomes are becoming more easily interpreted due to advancements in sequencing technologies and improved bioinformatic analysis. Structural variants (SVs) represent an important subset of somatic events in tumors…
View article: Investigating the alignment of teachers and admissions professionals on UCAS personal statements
Investigating the alignment of teachers and admissions professionals on UCAS personal statements Open
Teachers play a crucial role in supporting applicants with their UCAS personal statements, a key part of the undergraduate admissions process in the UK. This paper investigates the extent to which there is alignment between teachers and ad…
View article: Correction: Canadian COVID-19 host genetics cohort replicates known severity associations
Correction: Canadian COVID-19 host genetics cohort replicates known severity associations Open
[This corrects the article DOI: 10.1371/journal.pgen.1011192.].
View article: Whole-genome analysis of an aggressive metastatic pancreatic solid pseudopapillary neoplasm
Whole-genome analysis of an aggressive metastatic pancreatic solid pseudopapillary neoplasm Open
Pancreatic solid pseudopapillary neoplasms (SPNs) are uncommon tumors that rarely exhibit aggressive behavior. Given disease rarity, comprehensive studies to understand tumor biology, clinical course, and optimal management are limited. We…
View article: A nuclear TRiC/CCT chaperonin assembles meiotic HORMAD proteins into chromosome axes competent for crossing over
A nuclear TRiC/CCT chaperonin assembles meiotic HORMAD proteins into chromosome axes competent for crossing over Open
The meiotic chromosome axis organizes chromatin and sets the stage for homolog pairing and recombination. M eiotic HORMA d omain proteins (mHORMADs) are conserved axis components that conformationally transform during target binding. In C.…
View article: Uncovering the complexity of structural variants in four individuals with autism spectrum disorder
Uncovering the complexity of structural variants in four individuals with autism spectrum disorder Open
Autism spectrum disorder (ASD) is an increasingly recognized childhood developmental disorder. Despite extensive study, causal variants and molecular diagnosis remain elusive. There is both heterogeneity of the phenotype, as well as the ge…
View article: Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation
Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation Open
Human papillomavirus (HPV) integration has been implicated in transforming HPV infection into cancer. To resolve genome dysregulation associated with HPV integration, we performed Oxford Nanopore Technologies long-read sequencing on 72 cer…
View article: Adaptable and comprehensive approaches for long-read nanopore sequencing of polyadenylated and non-polyadenylated RNAs
Adaptable and comprehensive approaches for long-read nanopore sequencing of polyadenylated and non-polyadenylated RNAs Open
The advent of long-read (LR) sequencing technologies has provided a direct opportunity to determine the structure of transcripts with potential for end-to-end sequencing of full-length RNAs. LR methods that have been described to date incl…
View article: Neutrophil Extracellular Trap gene expression signatures identify prognostic and targetable signaling axes for inhibiting metastasis of pancreatic tumours
Neutrophil Extracellular Trap gene expression signatures identify prognostic and targetable signaling axes for inhibiting metastasis of pancreatic tumours Open
Tumour associated neutrophils (TANs) can promote metastasis through the interaction of Neutrophil Extracellular Traps (NETs) with tumour cells. Here, we examined the contribution of NETs in the progression of Pancreatic Ductal Adenocarcino…
View article: Correction: Titmuss et al. Immune Activation Following Irbesartan Treatment in a Colorectal Cancer Patient: A Case Study. Int. J. Mol. Sci. 2023, 24, 5869
Correction: Titmuss et al. Immune Activation Following Irbesartan Treatment in a Colorectal Cancer Patient: A Case Study. Int. J. Mol. Sci. 2023, 24, 5869 Open
The journal’s Editorial Office and Editorial Board are jointly issuing a resolution and removal of the Journal Notice linked to this article [...]