Aviezer Lifshitz

Circulating hematopoietic stem and progenitor cells in myeloproliferative neoplasms

This study profiles circulating hematopoietic stem and progenitor cells in MPN patients, identifying transcriptional signatures and quantitative readouts to distinguish MF from other MPNs and predict progression.

A weak-interaction model defines the cell-autonomous function of DNA methylation in gastrulation

The paper introduces a weak-interaction model showing DNA methylation moderates, but does not block, trans-acting regulatory machineries during mouse gastrulation.

Neural stem cell epigenomes and fate bias are temporally coordinated during corticogenesis

The paper integrates single-cell transcriptomics and epigenomics to show how neural stem cells shift lineage bias and epigenetic states during mouse corticogenesis.

Natural and age-related variation in circulating human hematopoietic stem cells

The paper characterizes age-related and inter-individual variation in circulating hematopoietic stem cells and establishes a normal reference to identify hematological disorders.

Metacell projection for interpretable and quantitative use of transcriptional atlases

MCProj projects query scRNA-seq data onto reference atlases to identify consistent and novel cell states while correcting for technical biases.

A divide and conquer metacell algorithm for scalable scRNA-seq analysis

The paper introduces Metacell-2, a scalable algorithm for scRNA-seq analysis that improves efficiency and quality in decomposing datasets into cohesive groups.

MetaCell: analysis of single cell RNA-seq data using k-NN graph partitions

MetaCell partitions scRNA-seq data into homogeneous metacells to address sparsity, enabling clustering and gene expression analysis without enforcing global structure.

Single cell analysis reveals dynamics of transposable element transcription following epigenetic de-repression

The paper analyzes single-cell transcription of transposable elements in epigenetically relaxed cancer cells, revealing cell cycle and transcription factor-dependent variation in TE activity.

Cnidarian cell type diversity revealed by whole-organism single-cell RNA-seq analysis

The paper uses whole-organism single-cell RNA-seq to analyze cell type diversity in Nematostella vectensis, identifying 35% of genes and 51% of TFs as cell type-specific.

SHAMAN: bin-free randomization, normalization and screening of Hi-C matrices

SHAMAN provides a method for analyzing Hi-C data without predefined resolution, minimizing biases by randomizing contact matrices and assessing enrichment.