Joshua Quick

This study shows that library preparation methods significantly affect RNA virus detection in clinical metagenomics, with SISPA-based approaches outperforming others in most scenarios.

The paper provides Andes virus sequencing datasets and evaluates a tiling amplicon scheme for benchmarking and optimizing bioinformatic pipelines.

This paper introduces squirrel, a tool for analyzing MPXV genomes to detect outbreaks and classify APOBEC3 mutations, aiding public health responses.

The paper characterizes a laboratory contaminant, Noodlococcus, as a new species within the Kocuria genus, revealing two phylogenetically distinct clades with significant ANI differences.

The paper develops ARTIC HELP, an open-source alternative to ARTIC nanopore sequencing protocols using commercial enzymes, achieving comparable genome coverage for SARS-CoV-2 and Norovirus GII with reduced supply chain dependencies.

This paper presents a rapid, low-cost protocol for isolating pathogenic bacteria from human blood, achieving over 70% efficiency within 30 minutes.

PrimalScheme provides open-source tools for designing low-cost viral genome sequencing primers, generating over 67,000 schemes and enabling large-scale genomic surveillance.

FindingNemo improves ultra-long nanopore sequencing by optimizing DNA extraction and library preparation for higher yields and scalability.

V3 primer pools with 22 extra alternates improve coverage; revised library preps raise double-barcode demultiplexing from 42.15% to 74.5%, cut misassignment 35x and bring reagent cost near £10 per sample.

The paper uses nanopore sequencing to analyze poly(A) RNA from human cells, identifying long transcripts and modifications not captured by traditional methods.

The paper presents ultra-deep, long-read nanopore sequencing datasets from a mock microbial community to evaluate bioinformatics tools and pipelines for long-read metagenomics.

This paper describes a method to sequence Zika and other virus genomes directly from clinical samples using multiplex PCR and portable sequencing technologies, achieving complete genomes in 1-2 days.

This study analyzes 1600 Ebola virus genomes to show viral spread followed a gravity model, with cross-border transmission before border closures contributing to an international epidemic.

Base-by-base tests of raw nanopore current, native versus amplified DNA, detect 4mC, 5mC and 6mA without training data, recovering seven methylases' motifs (AUC 0.62–0.97).

The paper uses ZIKV genomes to estimate the origin and spread of Zika virus in Brazil and the Americas, providing a timeframe for baseline microcephaly rates.

This paper presents a method to assemble a complete bacterial genome using only nanopore sequencing data, achieving high accuracy without reference or other platforms.