Louis Kraft

Ancient Reconstructed Proteins: A Framework for Resurrecting Protein Structures from Million-Year-Old Metagenomes

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.

SAFARI: Pangenome Alignment of Ancient DNA Using Purine/Pyrimidine Encodings

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: A Fast and Scalable Tool for Estimating and Clustering Reference-Level Damage Profiles

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

CarpeDeam: A De Novo Metagenome Assembler for Heavily Damaged Ancient Datasets

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

Benchmarking software tools for trimming adapters and merging next-generation sequencing data for ancient DNA

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.