Yael Michaeli

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.

Simultaneous global labeling (SiGL) of 5-methylcytosine and 5-hydroxymethylcytosine by DNA alkylation with a synthetic cofactor and engineered methyltransferase

The paper introduces a method to simultaneously analyze 5-methylcytosine and 5-hydroxymethylcytosine in clinical samples, showing reduced 5-hydroxymethylcytosine in colorectal cancer and chronic lymphocytic leukaemia.

Chemoenzymatic labeling of DNA methylation patterns for single-molecule epigenetic mapping

This paper develops a chemoenzymatic method to label non-methylated CpGs in DNA, enabling single-molecule epigenetic profiling in human and plant genomes.

Nanopore callers for epigenetics from limited supervised data

The paper demonstrates that a hybrid HMM-DNN approach outperforms both pure HMM and DNN methods for 5mC calling with incomplete training data.

Genome wide mapping of DNA lesions by Repair Assisted Damage Detection sequencing - RADD-Seq

The paper introduces RADD-Seq, a method to map DNA damage and repair sites genome-wide, showing oxidative damage distribution and repair prioritization in human cells.

Genome-wide epigenetic profiling of 5-hydroxymethylcytosine by long-read optical mapping

This paper introduces a long-read optical mapping technology to profile 5-hydroxymethylcytosine (5-hmC) across the genome, revealing long-range epigenetic correlations and cell-to-cell variation.

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.

Cas9-Assisted Targeting of CHromosome segments (CATCH) for targeted nanopore sequencing and optical genome mapping

The paper introduces a method to isolate and enrich large genomic regions for targeted analysis using Cas9 excision and pulsed field gel electrophoresis, enabling cost-effective detection of mutations and structural variants.