Matthew Loose

The paper identifies an almost-complete Rickettsia africae chromosome in the genome of its arthropod vector, A. variegatum, demonstrating lateral gene transfer from the pathogen to the host.

This paper benchmarks 7 TR genotyping tools using Nanopore long-read data, finding that no single tool is best across all metrics, and that sequence-level accuracy is crucial for clinical and population studies.

This study introduces two novel amplicon sequencing schemes for RSV A and B, demonstrating their effectiveness in generating high-quality genomes globally and revealing minimal geographic clustering of RSV sequences.

The paper uses long-read sequencing on 100 samples from the 1000 Genomes Project to identify structural variants and improve understanding of human genetic variation.

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

This study creates a single-cell transcriptomic atlas of pig gastrulation, revealing conserved and divergent gene programs and fate dynamics across species.

Icarust simulates Oxford Nanopore sequencing runs to enable realistic testing of adaptive sampling software without using real sequencing consumables.

This paper introduces BOSS-RUNS, a framework for dynamic nanopore sequencing that adapts in real-time to maximize information gain and reduce coverage bias.

The paper shows that NANOG and NODAL interact with DPY30 to regulate H3K4me3 deposition in axolotl primitive ectoderm, conserved in humans, establishing a basal state of vertebrate pluripotency.

This paper analyzes SARS-CoV-2 whole-genome sequencing data from Indonesia, ASEAN, and East Asian countries to assess the impact of technology, resources, and demographics on sequencing efforts and variant spread.

This study shows that genetic variation in rDNA affects epigenetic states and rRNA expression in mice and humans, with species-specific patterns observed.

The paper introduces a barcode-aware adaptive sampling tool for nanopore sequencers, enabling targeted analysis of multiple genomes on a single flow cell.

MinoTour provides a LIMS system for real-time monitoring and analysis of Oxford Nanopore sequencers, enabling automated analysis during sequencing runs.

The paper demonstrates how real-time nanopore sequencing with minoTour can accelerate SARS-CoV-2 consensus generation and lineage assignment by predicting optimal sequencing completion points.

This study investigates epigenetic reprogramming in pig primordial germ cells, identifying similarities with human germline processes and potential for transgenerational epigenetic inheritance.

The paper introduces a method for targeted sequencing using nanopore adaptive sequencing, enabling efficient enrichment of specific genes and chromosomes from mixed samples.

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

Grass pea, a diploid legume with a 6.3 Gbp genome, gets two draft assemblies, one short-read and one Nanopore, plus 33,819 annotated genes.

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 analyzes pig embryos at single-cell resolution to study lineage segregation, pluripotency, and X-chromosome inactivation during early development, revealing conserved mechanisms with human embryos.

BulkVis visualizes Oxford Nanopore bulk fast5 files to inspect signal data and identify incorrectly split long reads.

The paper investigates the roles of foxc1a and foxc1b in regulating angiogenesis from arteries and veins in zebrafish by modulating VEGF and Dll4/Notch signaling.

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.

The paper introduces a method to generate gene models for the axolotl using low-coverage genomic reads, producing over 19,000 gene models.

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.

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 demonstrates real-time selective DNA sequencing using the MinION device by matching current traces to references and selecting specific DNA regions.