Amir Eden

Improved deconvolution of circulating tumor DNA from ultra-low-pass whole-genome methylation sequencing using CelFiE-ISH

This study improves ctDNA deconvolution in ULP-WGS data using CelFiE-ISH, achieving lower cancer fraction detection limits than CNA benchmarks.

Systematic errors in enzymatic conversion limit cell-free DNA methylation specificity

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

DNA Methylation-Based Deconvolution Sheds Light on Glioblastoma Heterogeneity and Cell-Type Composition Associated with Patient Survival

This paper uses DNA methylation-based deconvolution to analyze glioblastoma cellular composition and identifies astrocyte-to-oligodendrocyte ratios as prognostic markers for patient survival.

A local sequence signature defines a subset of heterochromatin-associated CpGs with minimal loss of methylation in healthy tissues but extensive loss in cancer

The paper identifies a sequence signature that predicts CpG methylation loss in healthy tissues and cancer, revealing slow-loss CpGs with minimal methylation loss in health but significant loss in cancer.

Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing

This study demonstrates the ability to detect cell-of-origin and cancer-specific methylation features from cell-free DNA using Oxford Nanopore sequencing.

A Novel Role for Nucleolin in Splice Site Selection

This study identifies nucleolin as a novel regulator of splice site selection by directly interacting with initiator-tRNA, preventing latent splicing that would generate defective mRNAs.