C. Jenkins

The Impact of Smoking Status on the Genomic Landscape of Lung Squamous Cell Carcinoma

This study shows that non-smokers or remote smokers with squamous cell lung cancer have high rates of actionable genomic alterations, supporting the use of comprehensive genomic profiling and targeted therapies.

Quantifying evidence for phenotypic specificity (PP4) for syndromic phenotypes: Large-scale integration of rare germline FH variants from diagnostic laboratory testing for HLRCC (Hereditary Leiomyomatosis and Renal Cell Cancer) and renal cancer

The paper quantifies phenotypic specificity of rare FH variants in HLRCC and renal cancer using likelihood ratios from clinical and population data.

Classification of Variants of Reduced Penetrance in High Penetrance Cancer Susceptibility Genes: Framework for Genetics Clinicians and Clinical Scientists by CanVIG-UK (Cancer Variant Interpretation Group-UK)

The paper develops a framework for classifying variants of reduced penetrance in cancer susceptibility genes to improve variant interpretation consistency.

Intracellular K+ limits T cell exhaustion and preserves antitumor function

This study shows that lowering intracellular K+ in T cells by disrupting Na+/K+ ATPase reduces T cell exhaustion and improves antitumor function by mitigating ROS accumulation.

Discovery of the gut microbial enzyme responsible for bilirubin reduction to urobilinogen

This study identifies BilR, a gut microbial enzyme that reduces bilirubin to urobilinogen, and shows its prevalence in healthy adults and decline in neonates and IBD patients.

Shigella serotypes associated with carriage in humans establish persistent infection in zebrafish

This paper shows that three Shigella serotypes associated with MSM transmission can establish persistent infection in zebrafish, failing to promote macrophage cell death.

Acquisition of a large virulence plasmid (pINV) promoted temperature-dependent virulence and global dispersal of O96:H19 enteroinvasive Escherichia coli

The paper shows that acquisition of the pINV plasmid in ST99 E. coli made its virulence temperature-dependent, aiding global dispersal.

Recent O-antigen diversification masks highly pathogenic STEC O104:H4

The paper identifies genomically similar, highly pathogenic STEC strains with diverse O-antigens, masking their potential risk due to rare serotypes.

Structural basis for potent antibody neutralization of SARS-CoV-2 variants including B.1.1.529

The paper identifies potent monoclonal antibodies that neutralize the B.1.1.529 SARS-CoV-2 variant and reveals structural mechanisms enabling their effectiveness.

A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among Shigella

This study compares two Shigella plasmids to identify plasmid features contributing to differences in their epidemiological success during outbreaks.

Severe fever with thrombocytopenia syndrome virus and parthenogenetic Asian longhorned tick Haemaphysalis longicornis (Acari: Ixodidae)

The paper investigates the role of parthenogenetic Asian longhorned ticks in spreading SFTSV, finding they contribute to rapid spread and long-range movement.

Heparin MicroIslands for Spontaneous Gradient Formation and Improved Diabetic Wound Healing Outcomes

This paper introduces heparin microislands to create chemotactic gradients for improved diabetic wound healing by enhancing cell migration and tissue regeneration.

Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei

The paper develops a genomic framework and genotyping scheme for Shigella sonnei to identify resistance determinants from WGS data, revealing common genotypes linked to antimicrobial resistance and global spread.

Accessory genome dynamics and structural variation of Shigella from persistent infections

This study examines accessory genome dynamics and structural variations in Shigella isolates from persistent infections in men who have sex with men, finding less variation in persistent carriage compared to reinfection and evidence of antimicrobial resistance acquisition.

In silico approach toward the identification of unique peptides from viral protein infection: Application to COVID-19

The paper develops an in silico method to identify unique peptides for diagnostic and vaccine targets in viral infections, applying it to SARS-CoV-2 and highlighting 24 peptides as the most diagnostic.

Standard Flow Multiplexed Proteomics (SFloMPro). An Accessible and Cost-Effective Alternative to NanoLC Workflows

This paper introduces SFloMPro, a cost-effective alternative to NanoLC for multiplexed proteomics, showing comparable results with higher reliability and lower cost.

BoxCar Assisted MS Fragmentation (BAMF)

This paper introduces BAMF, a method that improves MS/MS fragmentation by selecting ions directly from BoxCar scans, enabling detection of ions not visible in standard MS1 scans.

Yersinia canariae sp. nov., isolated from a human yersiniosis case

The paper describes the isolation and genomic characterization of a novel Yersinia species from a human yersiniosis case.

The First Publicly Available Annotated Genome for Cannabis plants

The paper describes the first publicly available annotated genome for Cannabis plants, enabling the use of genomic and proteomic tools for research.

The Cannabis Multi-Omics Draft Map Project

The paper constructs a comprehensive annotated Cannabis proteome draft map using combined DNA sequencing and shotgun proteomics data, identifying 13,000 proteins and highlighting post-translational modifications.

Comparison of single nucleotide variants identified by Illumina and Oxford Nanopore technologies in the context of a potential outbreak of Shiga Toxin Producing Escherichia coli.

The paper compares single nucleotide variants identified by Illumina and Oxford Nanopore sequencing in STEC O157:H7 isolates, finding discrepancies mainly due to methylation and suggesting both technologies can be used interchangeably for typing.

Application of Global Metabolomics to the Identification of Complex Counterfeit Medicinal Products

This study uses global metabolomics to identify complex counterfeit medicinal products by analyzing molecular profiles with UHPLC-HRAM-MS/MS and statistical tools.

Assessing a commercial capillary electrophoresis interface (ZipChip) for shotgun proteomic applications

This study evaluates the ZipChip CE-MS system for high-throughput shotgun proteomics, finding it capable of identifying up to 800 unique protein groups in 12 minutes.

Evaluation of whole genome sequencing for the identification and typing of Vibrio cholerae

This study evaluates whole genome sequencing for identifying and typing Vibrio cholerae isolates, finding high concordance with traditional methods and geographic clustering of ST69 isolates from UK travellers.

Salmonella enterica Serovar Typhimurium ST313 Responsible For Gastroenteritis In The UK Are Genetically Distinct From Isolates Causing Bloodstream Infections In Africa

This paper identifies genetically distinct ST313 Salmonella isolates causing gastroenteritis in the UK and invasive disease in Africa, highlighting their evolutionary divergence and adaptation to different environments.