Katherine J. Siddle

In vivo single-cell profiling of lncRNAs during Ebola virus infection

This study profiles lncRNA expression in single cells during Ebola virus infection in vivo, revealing cell-type specific changes and potential roles in immune response and viral hijacking.

DNA spike-ins enable confident interpretation of SARS-CoV-2 genomic data from amplicon-based sequencing

The paper introduces DNA spike-ins to detect contamination in SARS-CoV-2 amplicon-based sequencing and demonstrates their utility in a real-world outbreak investigation.

A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2

This study creates a single-cell and spatial atlas of autopsy tissues from COVID-19 patients, revealing altered cellular responses and potential therapeutic targets.

Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time

This paper develops CRISPR-Cas13a-based diagnostics for real-time detection of Ebola and Lassa viruses in field settings, demonstrating sensitivity and usability in clinical samples.

Population variation of miRNAs and isomiRs and their impact on human immunity to infection

The paper analyzes miRNA and isomiR variation in human monocytes across populations and infection, finding population differences driven by non-genetic factors and limited genetic control.

Real-time Metagenomic Analysis of Undiagnosed Fever Cases Unveils a Yellow Fever Outbreak in Edo State, Nigeria

The paper uses metagenomic sequencing to identify a yellow fever outbreak in Edo State, Nigeria, from undiagnosed fever cases.

Co-circulating mumps lineages at multiple geographic scales

The paper analyzes mumps virus circulation in the US using genomic data to show multiple co-circulating lineages and transmission patterns, but finds no evidence of vaccine escape variants.

Capturing diverse microbial sequence with comprehensive and scalable probe design

The paper introduces CATCH, a method for designing compact and scalable probe sets to enhance metagenomic sequencing sensitivity, demonstrating improved viral genome recovery and diversity preservation.