Nicholas James Loman

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.

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.

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

MAJORA enables decentralized sequencing and integration of SARS-CoV-2 genomic data and metadata across the COG-UK network, supporting rapid genomic surveillance.

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 presents a gapless, telomere-to-telomere assembly of the human X chromosome using ultra-long-read nanopore sequencing and complementary technologies.

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.

Nanopore-only sequencing of GM12878 across 39 MinION flowcells (91.2 Gb) yielded an assembly with NG50 ∼3 Mb; adding 5× ultra-long reads raised NG50 to 6.4 Mbp.

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.

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.

CLIMB provides a cloud-based infrastructure for microbiologists to access computational resources and share bioinformatics methods and data.

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