Science unlocked: publication picks from December 2025

In this monthly series, we share a selection of recent publications that use Oxford Nanopore sequencing to unlock novel insights. Spanning human transcriptomics, cholera surveillance, and bioinformatics, these studies showcase the advances in scientific research made possible by Oxford Nanopore sequencing.

Featured in this edition:

1. Correcting the bias of human gene annotations

2. Oversharing on social media could save lives

3. Tracking cholera diversity and drug resistance in Africa

4. Decoding rearranged cancer genomes

Human genetics

1. Long-read transcriptomics of a diverse human cohort reveals ancestry bias in gene annotation (Nature Communications)

Current reference gene annotations are biased towards European ancestries so miss many population-specific isoforms from the rest of the world. Using Oxford Nanopore RNA sequencing, Clavell-Revelles and Reese et al.¹ profiled full-length transcripts from a genetically diverse human cohort. They revealed thousands of previously unannotated transcripts, underscoring the need for more inclusive, globally representative transcriptome annotations.

Key points:

• Using >800 million full-length nanopore RNA reads from 43 globally diverse lymphoblastoid cell lines, Clavell-Revelles and Reese et al. built PODER (population diversity-enhanced long-read), a cross-ancestry transcriptome annotation

• The authors identified >30,000 previously unannotated transcripts

• Non-European samples contributed disproportionately highly to novel transcripts and splice junctions, including ~2,400 population-specific transcripts, many of which would be missed without diverse sampling

• Incorporating these novel transcripts significantly improved detection of allele-specific transcript usage, with a larger gain in non-European individuals, highlighting how incomplete annotations can obscure genetic regulatory effects

• Their ultimate goal is to generate the human pantranscriptome: the set of all genes and transcripts found in the human species

Read our guide to transcriptomics with Oxford Nanopore.

Microbiology and infectious disease

2. Leveraging artificial intelligence community analytics and nanopore metagenomic surveillance to monitor early enteropathogen outbreaks (Frontiers in Public Health)

Foodborne illnesses are a burden on public health and the economy, but surveillance relies on active reporting by healthcare systems after diagnosis, which takes time and delays containment efforts. By analysing wastewater with Oxford Nanopore-based metagenomic sequencing and tracking social media mentions of symptoms, Gauthier et al.² found both methods indicated a salmonellosis outbreak over a month before a food recall was triggered. Together, wastewater sequencing and social media data mining could potentially fast-track outbreak responses.

Key points:

• Gauthier et al. used artificial intelligence (AI) to fill in a questionnaire based on participants’ public posts, engagements, and inferences on social media regarding gastrointestinal issues

• At the same time, wastewater was being collected from the community for metagenomic analysis using Oxford Nanopore sequencing

• Using these data sources, the authors were able to predict enteropathogen outbreaks sooner than waiting for case reports from hospitals

• AI predictions from social media were one week ahead of metagenomics peaks, but both methods detected a spike in cases over a month before a Salmonella-related food recall was initiated by the public health department

Read our white paper to find out how Oxford Nanopore technology overcomes common challenges with metagenomic sequencing.

3. Genomic diversity and antimicrobial resistance of Vibrio cholerae isolates from Africa: a PulseNet Africa initiative using nanopore sequencing to enhance genomic surveillance (Microbial Genomics)

Using Oxford Nanopore sequencing, PulseNet Africa researchers analysed Vibrio cholerae isolates from four African countries to map genomic diversity and antimicrobial resistance. The results revealed diverse strains and widespread antimicrobial resistance (AMR) to key antibiotics, while confirming the accuracy and practicality of Oxford Nanopore workflows for real-time surveillance and faster public health responses to cholera outbreaks.

Key points:

• Oxford Nanopore sequencing delivered complete, high-quality V. cholerae genomes

• Whole-genome analysis revealed active regional transmission, with expanding AFR12 and AFR15 pandemic lineages suggesting regional evolution

• Most clinical isolates were multi-drug resistant, particularly to trimethoprim and quinolones, raising treatment concerns

• Resistance to azithromycin and tetracycline remained uncommon, supporting their continued clinical use

• Nanopore-based workflows strengthened the genomic surveillance capacity of PulseNet Africa, enabling accurate pathogen identification, AMR tracking, and cross-border genomic collaboration

Check out our getting started guide for microbial sequencing with Oxford Nanopore.

Bioinformatics

4. Wakhan: reconstruction of chromosome-scale copy number profiles of tumour genomes with long-read sequencing (medRxiv)

In this study, Ahmad et al.⁴ present Wakhan, a new method for reconstructing haplotype-specific, chromosome-scale copy number alterations (CNA) in cancer genomes. By leveraging the long-read phasing and structural variant detection capabilities of Oxford Nanopore sequencing, Wakhan accurately resolves highly rearranged tumour karyotypes that short-read methods struggle with. The approach delivers robust results across cancer cell lines and shows strong agreement with clinical testing in paediatric tumours.

Key points:

• Benchmarking across multiple technologies showed Wakhan outperforms existing CNA callers, particularly for complex and highly rearranged cancer genomes

• Oxford Nanopore sequencing enables direct haplotype phasing, supporting chromosome-scale copy number reconstruction

• Integration with structural variant calling improves CNA boundary detection and biological interpretation

• The method is robust across sequencing depths, tumour purity levels, and tumour-only samples

• Wakhan showed strong agreement with current cytogenetic and microarray testing methods, highlighting its potential to support future clinical testing

• Wakhan CNA profiles also provide additional insights into mutational processes in breast cancer

Find out what rich insights Oxford Nanopore sequencing can provide to advance your cancer research.

Inspired? Apply Oxford Nanopore sequencing to your own research questions and you'll never see sequencing the same way again. Explore the nanopore sequencing solution.

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