Priyojit Das

Rearrangement of 3D genome organization in breast cancer epithelial - mesenchymal transition and metastasis organotropism

This study identifies 3D genome compartment changes associated with epithelial-mesenchymal transition and organotropism in breast cancer metastasis.

Dosage compensation of transposable elements in mammals

The paper investigates whether transposable elements (TEs) on the X chromosome undergo XCI or Xa-hyperactivation, finding TEs are only silenced during XCI and not activated during Xa-hyperactivation.

Re-analysis of CLAP data affirms PRC2 as an RNA binding protein

This paper re-analyzes CLAP data and finds PRC2 is an RNA binding protein, contradicting previous conclusions due to issues in the original analysis pipeline.

Differential contributions of nuclear lamina association and genome compartmentalization to gene regulation

The paper examines how nuclear lamina association and genome compartmentalization influence gene regulation across different cell types and treatments.

Transcriptional profiling of Hutchinson-Gilford Progeria syndrome fibroblasts reveals deficits in mesenchymal stem cell commitment to differentiation related to early events in endochondral ossification.

This study identifies transcriptional deficits in HGPS fibroblasts related to mesenchymal differentiation and endochondral ossification, with age-dependent gene expression changes.

Constricted migration is associated with stable 3D genome structure differences in cancer cells

This study shows that constricted migration in cancer cells leads to stable 3D genome structure changes associated with increased migration efficiency and altered gene expression.

Characterizing the variation in chromosome structure ensembles in the context of the nuclear microenvironment

The paper analyzes single-cell chromosome imaging data to reveal cell-type and region-specific structural variations in chromatin ensembles, linking these variations to epigenetic states.

SMILE: Mutual Information Learning for Integration of Single Cell Omics Data

SMILE integrates single-cell omics data by learning discriminative representations through mutual information maximization, effectively removing batch effects and aligning diverse data types.

Inferring Chromosome Radial Organization from Hi-CData

The paper infers chromosome radial organization from Hi-C data using PCA and force-directed layout algorithms, showing high correlation with microscopy data across different cell types.