Elad Chomsky

The paper evaluates deconvolution methods for bulk RNA-Seq using scnRNA-Seq data, identifies biases, and introduces SQUID, a method that outperforms others in predicting cell mixtures and identifying cancer subclones.

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.

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.

This study identifies the Gatad2a-Chd4-Mbd3 subcomplex of the NuRD complex as a key inhibitor of naive pluripotency, showing that its disruption enables deterministic reprogramming of somatic cells to iPSCs.

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.

This paper maps high-resolution epigenetic and biosynthetic changes during reprogramming of fibroblasts to iPSCs, identifying two gene modules regulated by different mechanisms.