Zohar Yakhini B

NinjaSeq replaces conventional end-repair/dA-tailing with restriction enzymes for nanopore sequencing, enabling random access and improved decoding accuracy.

The paper identifies context-dependent factors affecting CRISPR-Cas9 editing efficiency across species using endogenous editing data and shows that repair outcomes are conserved.

HIPI predicts cell marker expression from H&E images to infer spatial protein expression in tumors.

This paper develops a model to determine sequencing coverage for DNA-based data storage, using coupon collector and Markov Chain methods to analyze decoding probability and error correction.

This paper introduces a combinatorial DNA encoding method for data storage, achieving 6.5x higher density and near-zero reconstruction error through shortmer-based alphabets and error correction.

SPIRAL identifies significant biological processes in single cell RNA-seq or spatial transcriptomics data by detecting sub-matrices of genes and cells.

The paper investigates how intronic sequence features influence splicing efficiency and mRNA expression in yeast, revealing evolutionary adaptations and mechanisms of alternative splicing.

The paper introduces the HTA index to assess heterogeneity in spatial data, demonstrating its application in spatial transcriptomics, imaging, and GIS.

The paper uses high-throughput oligo libraries and machine learning to design non-repetitive RNA binding cassettes for gene editing and RNA tracking, demonstrating their functionality in mammalian cells.

The paper develops deep learning methods to infer spatial gene expression from pathology whole-slide images and links tumor heterogeneity to survival in breast and lung cancer.

SOLQC is a tool for analyzing synthetic oligo libraries using NGS data, providing statistical and graphical insights into quality and error rates.

The paper develops a deep-sequencing platform to refine DNA triplex binding rules and creates a synthetic regulatory tool for in vivo applications.

The paper shows that synthetic 5 UTRs can be up- or down-regulated by RBP binding, revealing RNA-RBP interactions that control translation.

The paper introduces a deep learning model with attention mechanisms to predict DNA methylation from gene expression and sequence data, achieving high correlation and identifying potential methylation-related genes.

The paper develops an in vivo method to quantify RNA-binding protein-RNA interactions using a reporter gene repression assay and SHAPE-seq in bacteria.

This paper introduces composite DNA alphabets to improve DNA storage capacity and fidelity by leveraging synthesis redundancy, achieving a 25% increase in storage capacity.

The paper identifies haplotypes and LD patterns in 80 genes that differ between breast cancer patients and controls, and finds negative correlations in LD patterns for some genes.

The paper identifies an insulation mechanism in bacterial σ54 promoters using a synthetic oligo library and sequencing, showing CT-rich motifs reduce downstream gene expression.