Assaf Grunwald

Beyond Bisulfite Sequencing: Resolving 5-hmC with Nanopore Sequencing Unmasks the True-5mC Methylation Entropy Landscape

The paper compares True-5mC methylation entropy analysis using nanopore sequencing to bisulfite sequencing in kidney cancer and mouse brain, showing bisulfite introduces systematic biases affecting biological interpretation.

Write and Read: Harnessing Synthetic DNA Modifications for Nanopore Sequencing

This paper introduces a 'write-and-read' framework using synthetic DNA modifications to enable nanopore sequencing to detect chemically altered nucleotides and expand the sequence alphabet.

Optical Genome and Epigenome Mapping of Clear Cell Renal Cell Carcinoma

The paper uses optical genome and epigenome mapping to identify somatic alterations in early-stage clear cell renal cell carcinoma, revealing both known and novel genomic and epigenomic changes.

Long-Read Structural and Epigenetic Profiling of a Kidney Tumor-Matched Sample with Nanopore Sequencing and Optical Genome Mapping

The paper compares optical genome mapping and nanopore sequencing for structural and epigenetic analysis of a kidney tumor, highlighting their strengths in variant detection and epigenetic profiling.

Towards accesible brain-tumor classification at the point of care Nanopore methylation sequencing from Formalin Fixed Paraffin Embedded (FFPE) pathology samples

This paper develops a validated protocol for using Oxford Nanopore methylation sequencing on FFPE samples to classify brain tumors, enabling point-of-care diagnosis.

Reduced representation optical methylation mapping (R2OM2).

R2OM2 creates fluorescent optical methylation profiles along chromosomal DNA for epigenetic profiling, comparable to WGBS with single-molecule resolution.

Reduced representation optical methylation mapping (R2OM2).

The paper introduces R2OM2, a method combining optical methylation profiling with genome mapping to analyze epigenetic variation in single cells and large structural aberrations.