Netanel Loyfer

This paper detects neuronal DNA in cfDNA using non-CpG methylation patterns, finding elevated levels in neurological conditions and brain-dead donors.

The paper introduces FLEXseq, a methylation sequencing method that enriches and sequences DNA fragments flanking the CCGG motif, showing strong correlation with WGBS and potential for diagnostic applications.

The paper identifies genetic variants influencing DNA methylation across tissues and development in mice and humans, revealing two distinct epigenetic programming periods and linking methylation to regulatory elements and disease variants.

The paper identifies a systematic over-conversion error in EM-seq that introduces false-positive methylation signals in cfDNA analysis.

Pleiades, a whole-genome epigenetic model, detects Alzheimer's and Parkinson's disease from plasma cell-free DNA with high accuracy.

The paper shows that DNA methylation changes at clustered CpG sites encode chronological age with high accuracy using deep learning on blood samples.

The paper creates a comprehensive atlas of allele-specific DNA methylation across 39 human cell types, identifying 325k genomic regions and 460 novel imprinted loci with cell-type-specific patterns.

wgbstools provides a computational suite for DNA methylation sequencing data representation, visualization, and analysis, enabling fragment-level analysis and integration with genetic data.

The paper constructs a human DNA methylation atlas using whole-genome bisulfite sequencing of 39 cell types, revealing cell type-specific methylation patterns and regulatory elements.

This study compares the reprogramming dynamics of pluripotent and trophoblast stem cell states using multi-omics analysis, revealing distinct trajectories and reprogramming markers.

The paper uses immune cell type-specific methylation patterns in circulating cell-free DNA to monitor immune dynamics and find that immune-derived cfDNA levels reflect immune homeostasis and predict immune responses to perturbations.

The paper develops a method to determine the tissue origins of circulating cell-free DNA using a methylation atlas and validates it in healthy and disease states.