Hila Sharim

A ML-framework for the discovery of next-generation IBD targets using a harmonized single-cell atlas of patient tissue

The paper develops a machine learning framework to identify cell type-specific gene targets for IBD using a harmonized single-cell atlas and validates them experimentally.

Long Reads Capture Simultaneous Enhancer-Promoter Methylation Status for Cell-type Deconvolution

The paper develops a method to deconvolve cell-type mixtures using enhancer-promoter methylation profiles from long-read data, achieving higher accuracy than promoter-based approaches.

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.