Peter Wad Sackett

EnZight identifies and prioritizes substitution hotspots in enzymes using structural alignment, demonstrating effectiveness in improving catalytic activity and thermostability.

This paper presents a computational framework to reconstruct ancient protein structures from degraded metagenomic data, successfully recovering methane metabolism proteins from 2-million-year-old Greenlandic samples.

CHARON estimates the number of individuals and drift time in eDNA samples using statistical methods, validated with simulations and synthetic data.

MAVISp provides a modular structural framework for analyzing protein variant effects, offering over eight million variants across 1000 proteins with curated data and a web server for accessibility.

SAFARI improves ancient DNA alignment by using RYmer indices to handle chemical damage patterns, resulting in more accurate alignments and better damage rate estimation.

AdDeam estimates and clusters DNA damage profiles from ancient DNA fragments to identify contaminants and outliers efficiently.

This study shows that analyzing genetic variants at the isoform level reveals significant associations with human phenotypes and rare variants, highlighting the importance of isoform-resolved analysis in genetics.

soibean improves species-level classification of ancient environmental DNA using mitochondrial pangenome graphs, revealing new insights from archaeological datasets.

CarpeDeam improves de novo assembly of ancient metagenomic datasets by incorporating damage-aware models, recovering longer sequences and proteins better than existing tools.

The paper benchmarks adapter trimming and read merging tools for ancient DNA sequencing, finding significant differences in quality score calculation but not in population genetics analysis.

This paper evaluates the Li and Stephens haplotype-copying model's performance on ancient DNA by using forward-simulated data and a constant-sized population model, finding it robust for haplotypes up to 900,000 years old.

HaploCart classifies human mtDNA haplogroups using a pangenomic reference graph and Bayesian inference, outperforming existing tools with more accurate and unbiased confidence scores.

The paper introduces HLAAssoc-1.0 to infer HLA-DRB3/4/5 alleles from HLA-DRB1 data, improving allele and motif deconvolutions in immunopetidomics and training of binding prediction models.

euka improves taxonomic identification and abundance estimation in ancient eDNA by using pangenomic graphs and maximum-likelihood methods, outperforming existing tools.

NetAllergen improves allergenicity prediction by integrating MHC-II presentation propensity, outperforming existing methods when sequence similarity to known allergens is low.

RosettaDDGPrediction enables high-throughput calculation of free energy changes from amino acid substitutions using Rosetta, with tools for data aggregation and visualization.