Lachlan Coin

This study uses CRISPR interference and Nanopore sequencing to investigate RNA modifications in E. coli, revealing their impact on growth and protein pathways.

The paper maps structural variation in the HLA locus across diverse populations, showing its role in haplotype diversity and gene expression differences.

This study uses long-read sequencing and genome graphs to analyze structural variation in Mycobacterium tuberculosis, identifying SVs linked to drug resistance and virulence.

LRGE estimates genome size from long read overlaps, outperforming k-mer-based methods and being more efficient than assembly-based approaches.

This study uses long-read RNA sequencing to analyze the transcriptomic response to interferon and influenza infection in ferrets, identifying ISGs and novel transcripts.

This study evaluates in vitro resistance development in MRSA to vancomycin, daptomycin, and linezolid, identifying mutations and mechanisms associated with resistance.

This study uses CRISPR-Cas9 to enrich specific transcripts for long-read sequencing, enabling efficient and accurate isoform discovery and low abundance transcript detection.

This paper introduces FS-PLS, a feature selection method that generates minimal disease signatures from omics data without requiring library size normalization, achieving smaller and comparable performance to existing methods.

The paper benchmarks poly(A) tail-length estimation tools using synthetic RNA standards, finding all tools accurate within 12% and recommending Dorado for its speed and ease of use.

The paper compares Nanopore direct RNA-seq and Illumina cDNA-seq in sepsis patients, finding strong correlation and identifying post- and co-transcriptional biomarkers.

This study benchmarks variant callers on bacterial nanopore data, finding deep learning tools outperform traditional methods and Illumina in accuracy and efficiency.

The paper benchmarks host removal and mycobacteria classification methods in metagenomic data, finding that custom databases improve accuracy and efficiency.

MERITS provides a comprehensive database of PE/PPE proteins from Mycobacterium, offering structural and functional information to aid in vaccine and diagnostic development.

This paper develops DrPRG, a tool for predicting drug resistance in Mycobacterium tuberculosis using reference graphs, showing improved sensitivity and specificity compared to existing methods.

This study introduces Sketchy, a genomic neighbor typing tool for bacterial outbreak surveillance, showing improved lineage prediction but limitations in clade-specific genotype resolution.

The paper identifies TSPAN8 variants associated with metabolomic regulation and metabolic diseases using CNV analysis and functional characterization in human induced pluripotent stem cells.

This paper uses nanopore sequencing and Random Forest models to estimate transmission dynamics of MRSA outbreaks, showing sustained transmission with Re > 1.

The paper identifies reduced host transcriptomic signatures for tuberculosis using microarray data and validates them with digital PCR, showing high accuracy in distinguishing TB from other conditions and latent TB.

This paper introduces npGraph, a streaming hybrid assembly tool that improves genome assembly accuracy using ONT long reads and an assembly graph, while maintaining low computational cost.

This study compares three long-read sequencing technologies for de novo assembly of the Macadamia jansenii genome, evaluating contiguity, accuracy, completeness, cost, and DNA requirements.

This paper develops a method to assemble whole-chromosome pseudomolecules for polyploid plant genomes using genotyping-by-sequencing and reference genome data, showing improved accuracy over existing tools.

This paper develops a targeted long-read sequencing method for high-throughput tandem repeat genotyping, achieving high accuracy and scalability.

The paper analyzes polyclonal vector integration sites using Nanopore sequencing to provide a scalable and cost-effective method for tracking gene-modified cells.

This study compares DNA and RNA nanopore sequencing for detecting drug resistance in XDR K. pneumoniae, finding RNA sequencing identifies more resistance genes and shows strong correlation with qRT-PCR.

scSplit demultiplexes pooled single-cell RNA-Seq samples using genetic differences inferred from the data, showing high accuracy and consistency with known truths.

The paper uses BioNano and nanopore data to analyze human chromosome ends, revealing heritable extensions and sequence duplications across primate lineages.

GtTR is a Bayesian method for estimating absolute tandem repeat copy numbers using targeted sequencing and reference data, achieving high accuracy in population-scale genotyping.

npInv detects and genotypes NAHR inversions using long read sub-alignment, identifying 30 inversions in NA12878 with 94% accuracy, including 15 novel ones.

This study uses dual transcriptome analysis to identify host and parasite gene expression associated with severe malaria in Gambian children, showing parasite load explains most human gene expression differences but only a third of parasite gene differences.

The paper assembles a complete genome of an XDR M. tuberculosis strain using Nanopore sequencing, identifies novel genetic variations in repetitive PE/PPE regions, and links these to drug resistance and virulence.