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.

bioRxiv · Aug 7, 2026 · PreprintBioinformatics

Write and Read: Harnessing Synthetic DNA Modifications for Nanopore Sequencing

Uri Bertocchi, Assaf Grunwald, Gal Goldner, Eliran Eitan, Sigal Avraham, Shani Dvir, Jasline Deek, Yael Michaeli, Brian Yao, Jennifer Listgarten, Jared T. Simpson, Winston Timp, Yuval Ebenstein

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.

ACS Nano · Nov 3, 2025Peer-reviewedBioengineering

Optical Genome and Epigenome Mapping of Clear Cell Renal Cell Carcinoma

Sapir Margalit, Zuzana Tulpová, Yael Michaeli, Tahir Detinis Zur, Jasline Deek, Sivan Louzoun Zada, Gil Nifker, Assaf Grunwald, Yuval Scher, Leonie Schütz, Elmar G. Weinhold, Yehudit Gnatek, Dorit Omer, Benjamin Dekel, Eitan Friedman, Yuval Ebenstein

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.

NAR Cancer · Jan 15, 2025Peer-reviewedGenomics

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

Sapir Margalit, Zuzana Tulpová, Tahir Detinis Zur, Yael Michaeli, Jasline Deek, Gil Nifker, Rita Haldar, Yehudit Gnatek, Dorit Omer, Benjamin Dekel, Hagit Baris Feldman, Assaf Grunwald, Yuval Ebenstein

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.

NAR Genomics and Bioinformatics · Jan 7, 2025Peer-reviewedGenomics