Sapir Margalit

Single cell transcriptomics reveals enrichment of aggregation-prone alpha-synuclein isoforms across synucleinopathies

The paper uses long-read and single nucleus RNA-seq to identify novel SNCA transcript isoforms and their association with Parkinson's and Lewy body dementia.

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.

DeepOM: Single-molecule optical genome mapping via deep learning

DeepOM uses deep learning to improve alignment of single-molecule optical genome mapping images to genomic references, showing better performance for shorter DNA molecules.

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.

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.