Jared T. Simpson

Decoding the naked mole-rat genome, telomere to telomere

The paper presents a telomere-to-telomere genome assembly of the naked mole-rat and compares it with a related species to identify gene losses and duplications associated with unique traits.

Multi-platform reassessment of human mitochondrial DNA methylation reveals signals consistent with technical artifacts

This study reassesses human mitochondrial DNA methylation using multiple platforms and finds signals likely due to technical artifacts rather than biological methylation.

A structure-selective endonuclease drives uniparental mitochondrial DNA inheritance

The paper identifies Hotaru, a testis-specific endonuclease, as essential for paternal mtDNA elimination in sperm, revealing its structural recognition of mtDNA cruciform DNA.

Write and Read: Harnessing Synthetic DNA Modifications for Nanopore Sequencing

This paper introduces a 'write-and-read' framework using synthetic DNA modifications to enable nanopore sequencing to detect chemically altered nucleotides and expand the sequence alphabet.

Detecting Protein-DNA Binding in Single Molecules using Antibody Guided Methylation

The paper introduces a method to detect protein-DNA binding in single molecules using antibody-guided methylation, generating identifiable methylation patterns near binding sites.

An updated reference genome sequence and annotation reveals gene losses and gains underlying naked mole-rat biology

The paper presents an updated reference genome for the naked mole-rat, identifying gene losses and gains linked to its unique physiological traits.

Detecting Somatic Mutations Without Matched Normal Samples Using Long Reads

This paper develops a method to detect somatic mutations in tumor samples without matched normal samples using long-read sequencing and demonstrates its application on cancer cell lines.

Somrit: The Somatic Retrotransposon Insertion Toolkit

Somrit improves the detection of rare somatic retrotransposon insertions by addressing mapping errors through consensus realignment.

Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing

This study introduces nanoNOMe, a method combining NOMe-seq and nanopore sequencing to profile chromatin accessibility and methylation in human cell lines, revealing phased methylation, large-scale patterns, and structural variations.

GPU Accelerated Adaptive Banded Event Alignment for Rapid Comparative Nanopore Signal Analysis

This paper introduces f5c, a GPU-optimized implementation of Adaptive Banded Event Alignment for faster nanopore signal analysis and DNA methylation detection.

Creating Standards for Evaluating Tumour Subclonal Reconstruction

This study develops quantitative metrics and simulated datasets to evaluate subclonal reconstruction methods in tumours.

Nanopore native RNA sequencing of a human poly(A) transcriptome

The paper uses nanopore sequencing to analyze poly(A) RNA from human cells, identifying long transcripts and modifications not captured by traditional methods.

Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads

This paper introduces a method to measure DNA replication dynamics on single molecules using nanopore sequencing and applies it to yeast to discover new replication origins.

Nanopore sequencing and assembly of a human genome with ultra-long reads

Nanopore-only sequencing of GM12878 across 39 MinION flowcells (91.2 Gb) yielded an assembly with NG50 ∼3 Mb; adding 5× ultra-long reads raised NG50 to 6.4 Mbp.

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

This paper describes a method to sequence Zika and other virus genomes directly from clinical samples using multiplex PCR and portable sequencing technologies, achieving complete genomes in 1-2 days.