Nikolay Oskolkov

This study demonstrates the feasibility of recovering genomic and transcriptomic profiles from decades-old FFPE brain tissues, showing improved data quality through optimized library preparation strategies.

DNAharvester is a Nextflow pipeline designed to process highly degraded DNA from ancient specimens, improving authentic data recovery through modular workflows and contamination mitigation.

This study analyzes ancient sediment DNA to identify plant-microbe association signals in a 2-million-year-old Arctic ecosystem, finding rhizosphere-like microbial taxa and functional traits.

This study benchmarks filtering strategies for ancient metagenomic data to improve taxonomic classification accuracy by optimizing thresholding based on sequencing depth.

The paper presents a method to identify and mask microbial-like sequences in eukaryotic reference genomes to improve taxonomic inference from ancient environmental metagenomic data.

This study detects ancient fungal DNA in Otzi's gut, identifying Pseudogymnoascus species and proposing a bioinformatic pipeline for analyzing fungal aDNA in historical samples.

The paper shows that IDH2, a mitochondrial enzyme, acts as a major antioxidant defense in cardiomyocytes, with its activity compensating for reduced expression in heart failure, and identifies an epigenetic mechanism linking oxidative stress to cardiac function.

aMeta is a metagenomic profiling workflow that improves accuracy and reduces memory usage in ancient microbiome analysis.

The paper investigates how genetic variants affect gene expression in human pancreatic islets and identifies candidate genes linked to type 2 diabetes.

This study identifies TCF7L2-target genes and their regulatory network in insulin secretion, showing TCF7L2 regulates proinsulin synthesis, processing, and clearance in rodents and human islets.