Matthew J. Collins

The paper reconstructs 3,500 years of sheeppox virus evolution using ancient genomes from archaeological and medieval parchment sources, showing divergence events and gene inactivation.

The paper investigates discrepancies between input food composition and recovered protein signals in experimental foodcrusts, highlighting biases in residue analysis.

The paper provides a 5000-year-old dental calculus metagenomic dataset from 174 UK archaeological samples to study ancient human oral microbiomes and related topics like diet and antimicrobial resistance.

The paper benchmarks sequencing tools for identifying degraded proteins in ancient samples, finding optimal strategies for peptide and PTM detection.

Orthrus improves metaproteomics analysis by combining de novo sequencing and database searching, outperforming existing tools in peptide output and taxonomic diversity.

Anubis authenticates ancient proteins using deamidation patterns and random forest classification, demonstrating reliability with ancient and degraded beta-lactoglobulin.

The paper investigates how sequence variation in β-lactoglobulin peptides affects their preservation in the archaeological record by analyzing their conformational stability and hydrolysis vulnerability in bulk water.

This study investigates how cooking and burial affect protein preservation in foodcrusts and ceramics using experimental analogues of Mesolithic ingredients.

The paper introduces a method to estimate glutamine deamidation levels in parchment collagen using low-resolution MALDI-TOF data, finding it useful for archaeological and industrial applications.

This study uses a dry non-invasive method to extract and analyze palaeoproteomic evidence from a medieval parchment birth girdle, revealing biomolecular traces of use during childbirth.

The paper sequences a 5,700-year-old human genome and oral microbiome from Stone Age chewing gum, revealing genetic and microbial insights.

The paper reports the first use of a non-invasive DNA sampling technique on the York Gospels to uncover a biological palimpsest spanning over 1,000 years.

This study analyzes 185 paleogenomic datasets to model ancient DNA decay, finding cytosine deamination follows a thermal age model but DNA fragmentation does not correlate with age.