Matthew T Parker

coelsch: Platform-agnostic single-cell analysis of meiotic recombination events

The paper benchmarks single-cell methods for meiotic recombination mapping in Arabidopsis thaliana and introduces tools to detect crossovers and haplotypes from sparse sequencing data.

Disruption of the mRNA m6A writer complex triggers autoimmunity in Arabidopsis

This study shows that disrupting the mRNA m6A writer complex in Arabidopsis triggers autoimmunity, with temperature-dependent effects on gene expression and pathogen resistance.

The mutational dynamics of the Arabidopsis centromeres

This study defines the mutation spectrum in Arabidopsis thaliana centromeres, showing higher point mutation rates and homology-directed repair-driven indels.

Generation of C9orf72h370 mice, an intron 1 humanised C9orf72 repeat-expansion knock-in model

The paper generates a mouse model with a humanised C9orf72 repeat expansion to study ALS and FTD, and demonstrates a method for creating such repeat expansions in genomic sequences.

Expression quantitative trait locus mapping in recombinant gametes using single nucleus RNA sequencing

This paper develops a method to map eQTLs using snRNA-seq of gametes from a small number of heterozygous individuals, uncovering cis- and trans-eQTLs in Arabidopsis pollen nuclei.

U6 snRNA m6A modification is required for accurate and efficient cis- and trans-splicing of C. elegans mRNAs

The paper shows that m6A modification of U6 snRNA by METT-10 is essential for accurate and efficient cis- and trans-splicing in C. elegans pre-mRNAs.

The evolution of splice site sequence preference is linked to the U6 snRNA m6A methyltransferase METTL16

The paper shows that variation in 5 splice site sequence preferences correlates with the presence of METTL16 and SNRNP27K, using inter-species association mapping in Saccharomycotina species.

m6A modification of U6 snRNA modulates usage of two major classes of pre-mRNA 5' splice site

The paper shows that m6A modification of U6 snRNA affects splicing accuracy and efficiency, revealing two major classes of 5' splice sites in eukaryotes.

Chromosome evolution and the genetic basis of agronomically important traits in greater yam

This paper presents a chromosome-scale genome assembly and genetic map for greater yam, identifies quantitative trait loci for disease and quality traits, and reveals domestication-related genetic patterns.

Yanocomp: robust prediction of m6A modifications in individual nanopore direct RNA reads.

Yanocomp predicts m6A modifications in Nanopore direct RNA reads by modeling adjacent kmers and accounting for outliers, enabling stoichiometry measurement and correlation with RNA processing events.

Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA

The paper shows that the FPA protein causes premature termination of NLR gene transcripts in Arabidopsis thaliana, regulating their expression and immune function.

Two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing

The paper improves intron detection in long-read RNA sequencing by filtering spurious splice junctions using machine learning and a two-pass alignment approach.

Nanopore direct RNA sequencing maps an Arabidopsis N6 methyladenosine epitranscriptome

This study uses nanopore direct RNA sequencing to map the m6A epitranscriptome in Arabidopsis, revealing its role in mRNA processing and circadian rhythms.