James M. Ferguson

Scientific computing in the age of agentic AI: an exploratory field report

This paper explores the use of LLM-based coding agents in scientific computing, presenting case studies in the life sciences and discussing their potential and challenges.

Integrative genomics of the siphonophore Physalia utriculus reveals the regulatory logic of colonial division of labour and the molecular basis of venom activity

This study presents a multi-omic atlas of the siphonophore Physalia utriculus, revealing the regulatory mechanisms of colonial division of labour and the molecular basis of venom activity.

The enduring advantages of the SLOW5 file format for raw nanopore sequencing data

This paper compares POD5 and SLOW5 file formats for nanopore sequencing data, finding SLOW5 offers better performance, lower cost, and easier management.

Nanopore- and AI-empowered microbial viability inference

This paper introduces a computational framework using nanopore sequencing and deep learning to infer microbial viability from raw signal data, showing high accuracy in controlled and real-world applications.

Repeat-rich regions cause false positive detection of NUMTs - a case study in amphibians using an improved cane toad reference genome

Squigulator: simulation of nanopore sequencing signal data with tunable noise parameters

Squigulator simulates nanopore sequencing signals with tunable noise parameters to test and improve analysis methods.

Interactive visualisation of raw nanopore signal data with Squigualiser

Squigualiser provides an interactive visualization tool for nanopore signal data, enabling alignment to reference genomes and comparison of multiple datasets.

Streamlining remote nanopore data access with slow5curl

slow5curl enables efficient retrieval of specific nanopore reads from large datasets, reducing storage and transfer costs for reanalysis.

Accelerated nanopore basecalling with SLOW5 data format

This paper introduces Buttery-eel, an open-source tool that accelerates nanopore basecalling by leveraging the SLOW5 data format for efficient data access on HPC and cloud environments.

Flexible and efficient handling of nanopore sequencing signal data with slow5tools

slow5tools converts and manipulates nanopore sequencing data in the SLOW5 format, offering efficient and flexible data handling with performance improvements over FAST5.

Comprehensive genetic diagnosis of tandem repeat expansion disorders with programmable targeted nanopore sequencing

This study develops a programmable nanopore sequencing assay for diagnosing all known pathogenic STRs in a single test, accurately diagnosing 27 patients with neurogenetic disorders.

InterARTIC: an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses

InterARTIC provides a web tool for analyzing whole-genome nanopore sequencing data of viruses, enabling users to reconstruct consensus sequences without bioinformatics expertise.

DNA methylation is required to maintain DNA replication timing precision and 3D genome integrity

This study shows DNA hypomethylation disrupts replication timing precision and 3D genome organisation in colorectal cancer DNMT1 and DNMT3B knockout cells.

SLOW5: a new file format enables massive acceleration of nanopore sequencing data analysis

The paper introduces SLOW5, a new file format for nanopore sequencing data that accelerates analysis on HPC systems by enabling efficient parallelization.

Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome

The paper presents two high-quality Basenji genome assemblies and compares structural variations across three dog breeds, highlighting the impact of reference genome choice on variant detection.

Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis

This study evaluates the analytical validity of nanopore sequencing for SARS-CoV-2 genome analysis, finding high accuracy for SNVs but limitations in detecting short indels and low-frequency variants.

Barcoding and demultiplexing Oxford Nanopore native RNA sequencing reads with deep residual learning

This paper introduces a deep learning method for barcoding and demultiplexing direct RNA sequencing reads without base-calling or additional library steps, achieving high specificity and read demultiplexing rates.

SquiggleKit: A toolkit for manipulating nanopore signal data

SquiggleKit simplifies nanopore signal data manipulation by providing tools for file handling, visualization, and signal processing.

High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes

This paper introduces RAGE-seq, a method combining long-read and short-read sequencing to analyze lymphocyte clonal and transcriptional features in breast cancer tissues.