Nir Friedman

Hepatobiliary Progenitor-like Reprogramming in Liver Metastases

This study identifies hepatobiliary progenitor-like reprogramming in liver metastases, driven by TGF-β and hypoxia, and shows its association with poor survival.

Urine cf-Nucleosomes: A Non-invasive Window into Human Physiology and Disease

The paper demonstrates that urine contains cell-free nucleosomes that retain histone modifications and can reflect tissue-specific and pathological changes.

ChIP-seq of plasma cell-free nucleosomes identifies cell-of-origin gene expression programs

The paper introduces cfChIP-seq to analyze cell-free nucleosomes and shows it can detect disease-related transcriptional changes and patient-specific features in cancer.

Flexibility and constraint in preimplantation gene regulation in mouse

The paper examines how different fertilization methods affect preimplantation gene regulation in mouse embryos, identifying stable and flexible gene expression patterns and the role of sperm RNAs in development.

Deciphering eukaryotic cis-regulatory logic with 100 million random promoters

The paper uses random yeast promoters to model cis-regulatory logic, achieving high prediction accuracy for gene expression.

Charting a tissue from single-cell transcriptomes

The paper introduces a method to reconstruct spatial positions of cells from single-cell transcriptomes without reference imaging data, leveraging expression space distances.

A synthetic biology approach to probing nucleosome symmetry

The paper introduces a synthetic biology approach to study nucleosome symmetry by creating asymmetric H3 heterodimers and demonstrates their utility in analyzing histone modification crosstalk.

Elucidating Combinatorial Chromatin States by Co-ImmunoPrecipitation (comb-ChIP)

The paper introduces comb-ChIP, a method to determine genome-wide co-occurrence of histone marks at single nucleosome resolution, revealing differences in chromatin pathways and responses to genetic perturbation.

Genome-wide histone modification patterns in Kluyveromyces Lactis reveal evolutionary adaptation of a heterochromatin-associated mark

The paper maps H3K9 methylation and other histone modifications in Kluyveromyces lactis, revealing its presence in highly transcribed regions and a disconnect between mark localization and function.