Christopher E. Mason

This paper demonstrates the detection of m6A RNA modifications in native RNA sequences using Oxford Nanopore Technologies with high accuracy.

Genome in a Bottle benchmark of 12745 sequence-resolved insertions and deletions of 50 bp or more, integrating 19 calling methods, scores false negatives and false positives alike.

The paper analyzes single-cell sperm RNA-seq data from fathers of autistic and healthy children to identify mutation clusters and expression differences associated with ASD risk.

The paper develops standardized tools and best practices for benchmarking germline small variant calls in human genomes using truth sets and performance metrics.

The paper uses metagenomics to analyze urban beach and sewage waters in Montevideo, finding distinct bacterial communities and antibiotic resistance genes in sewage.

KrakenLinked improves taxonomic classification of metagenomic linked-reads by combining tree pruning and taxa promotion algorithms, reducing false identifications compared to short reads.

This study improves the detection of m6A in bacterial DNA using nanopore sequencing with a binary classifier, highlighting the importance of read quality and comparing results to PacBio methylation calls.

Minerva deconvolves barcoded reads in metagenomics to improve taxonomic assignments and sequence clustering without a reference genome.

The paper identifies YTHDC2 as essential for meiotic progression in mice, showing its role in gene expression transitions and its evolutionary conservation.

The paper investigates factors affecting transcriptome assembly quality, finding that input RNA-Seq data quality and base-calling accuracy are more critical than coverage.

This study benchmarks eleven metagenomic classifiers using 846 species and evaluates strategies to reduce false positives in taxonomic classification.

The paper identifies Dnmt3c as a fifth DNA methyltransferase paralog essential for retrotransposon methylation and male germline function in mice, revealing its role in meiosis and transposon repression.

The paper tests nanopore sequencing in microgravity using a parabolic flight simulator and proposes new computational methods to address sequencing challenges in reduced gravity.