Jonathan Göke

This paper introduces minimod, a tool for analyzing base modifications in long-read sequencing data, showing significant speed improvements over existing tools.

The paper presents a high-quality, gapless diploid reference genome for an Indian population, revealing extensive structural variation and improved performance for genomic analysis in South Asian samples.

This study benchmarks Nanopore long read RNA sequencing in human cell lines, showing improved isoform resolution compared to short reads.

Bambu-Clump improves transcript discovery and quantification from single-cell and spatial long-read RNA-seq data by leveraging cell and cluster information.

This paper introduces CFC-seq and SALA to sequence non-poly(A) RNAs, identifies 39,425 novel transcriptional units, and reveals a genomic code governing enhancer RNA fate based on promoter architecture.

This paper develops a lightweight k-mer model for RNA004 chemistry using basecaller move tables, achieving high alignment rates and comparable m6A detection performance to default models.

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

Flexiplex is a versatile sequence searching and demultiplexing tool for omics data that balances accuracy and efficiency, demonstrated on single cell RNA-seq and genotyping tasks.

Bambu improves transcript quantification from long-read RNA-Seq by using context-aware annotations, enhancing precision without sacrificing sensitivity.

This paper introduces m6Anet, a Multiple Instance Learning framework for detecting m6A methylation from direct RNA sequencing data, achieving performance comparable to experimental methods without retraining.

JAFFAL detects fusion genes from long-read transcriptome sequencing with high accuracy, outperforming existing methods and enabling single-cell resolution.

This paper introduces a new method to identify gene-specific regulatory elements by integrating epigenomics data and demonstrates its application in prioritizing doxorubicin-resistance genes.

This paper introduces xPore, a method to detect differential RNA modifications from direct RNA sequencing, showing it identifies m6A sites with single base resolution and quantifies modification rate differences across cell lines.

The paper identifies hundreds of genes deregulated by SVs in cancer, showing increased expression linked to SV breakpoints and enhancer elements.

AERON quantifies transcript expression and detects gene-fusions from long RNA reads, showing accuracy on simulated and real data.

This study identifies alternative promoters as key regulators in the cancer transcriptome using RNA-Seq data from 1,188 cancer samples.

The paper analyzes RNA alterations across 27 cancer types using whole-genome sequencing data, identifying gene expression associations with DNA variants and structural fusions.