Amos Tanay

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.

This study reconstructs mouse vasculogenesis using single-cell and spatial analyses, revealing a transient vascular-primed state and the role of VEGF in endothelial specification.

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

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

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

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

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

This study uses TATTOO-seq to identify spatial and cell type-specific regulatory programs during limb development and shows how perturbations affect cell fate and spatial organization.

The paper analyzes health records to show seasonal patterns in human hormones, finding that effector hormones peak in winter-spring while upstream pituitary hormones peak in summer, suggesting a circannual clock mechanism.

The paper identifies microhomology-mediated end joining (MMEJ) as the mechanism behind recurrent deletions in myeloid malignancies and shows that these deletions occur in multipotent hematopoietic stem cells.

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

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.

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

This study uses single-cell Hi-C to analyze chromosomal organization dynamics across the cell cycle, revealing distinct cell cycle-dependent changes in chromosomal compartments, TADs, and loops.