Andrew D. Smith

The paper examines DNA methylation dynamics in marsupial embryos, finding global demethylation in the trophectoderm but not the embryonic lineage, suggesting 5mC erasure in extraembryonic tissue is ancestral in therian mammals.

PrimalScheme provides open-source tools for designing low-cost viral genome sequencing primers, generating over 67,000 schemes and enabling large-scale genomic surveillance.

The paper examines age-related changes in the human sperm methylome, finding that donor variability outweighs age effects, but age-dependent changes exist and vary by genomic location.

The paper identifies PRC2 low-methylated regions as a universal biomarker of aging and rejuvenation, showing they account for most age-related DNA methylation gain across tissues.

The paper introduces a new bisulfite sequencing read mapping algorithm that uses a two-letter DNA encoding to improve speed and memory efficiency while maintaining accuracy.

V3 primer pools with 22 extra alternates improve coverage; revised library preps raise double-barcode demultiplexing from 42.15% to 74.5%, cut misassignment 35x and bring reagent cost near £10 per sample.

This paper develops a DNA methylation age prediction model for human sperm, achieving high accuracy and repeatability, and identifies smoking as a subtle factor affecting sperm aging.

SMURF-seq enables fast, multiplexed copy number profiling using long-read sequencers by ligating short DNA molecules into long reads.

This paper introduces ROP to identify the source of unmapped RNA-Seq reads across diverse tissues, showing it can account for 99.9% of 1 trillion reads and reveals immune and microbial correlations.

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.