Stuart Akeson

The paper uses in vitro transcribed RNA from genomic DNA to benchmark RNA modification detection by Nanopore direct RNA sequencing models.

tRNAZAP is a deep learning toolkit for analyzing nanopore tRNA sequencing data, achieving high accuracy in segmentation and classification tasks.

This paper develops a computational strategy for analyzing nanopore ionic current signals from synthetic proteins, achieving high accuracy in charge-based classification of amino acids.

This paper uses long-read sequencing to analyze haplotype-resolved DNA methylation at the APOE locus in brain samples, identifying allele-specific methylation patterns linked to Alzheimer's disease risk.

The paper introduces tRNAZAP, a deep learning method using nanopore ionic current signals to classify tRNA isodecoders, achieving better alignment results than BWA-MEM in E. coli and S. cerevisiae.

This paper evaluates updates to Nanopore direct RNA sequencing for detecting RNA modifications, showing improved accuracy in identifying pseudouridine and N6-methyladenosine.

This study shows that PUS7's cytoplasmic localization enhances stress tolerance by increasing pseudouridylation of mRNAs involved in metal and ROS homeostasis.

This study shows that pancreatic injury in axolotl leads to β-cell regeneration without blastema formation, through organ-wide proliferation that recovers β-cell mass.

The paper describes a comprehensive genomic dataset from a tumor-normal pair with broad consent, generated using multiple sequencing technologies for benchmarking somatic variant detection.

The paper generates and characterizes modification-free RNA transcripts from human cell lines for use as controls in nanopore direct RNA sequencing analysis.

This study uses direct RNA sequencing to examine pseudouridylation dynamics in neurons under healthy and unhealthy conditions, finding changes in psi writer expression and site occupancy.

This study compares 5mC detection accuracy between Nanopore R9 and R10 chemistries using human datasets, finding high concordance and strong correlation with Illumina bisulfite methods.