Aleksandra A. Galitsyna

The paper temporally maps nuclear reorganization during human stem cell differentiation and identifies three temporally ordered transitions in nuclear structure and function.

The paper identifies 'fountains' as enhancer-specific chromosome organization elements emerging during zygotic genome activation in zebrafish and mouse.

This study shows cohesin-mediated chromatin remodeling is essential for dendritic cell differentiation and function, particularly antigen cross-presentation and IL-12 secretion.

This paper introduces Chimaera, a CNN that predicts Hi-C maps from DNA sequences, revealing chromatin structure features and evolutionary relationships across species.

The paper investigates chromatin looping in Dictyostelium discoideum, finding that convergent gene pairs act as directional barriers for chromatin extrusion during development.

Pairtools processes sequencing data into contact pairs for 3C+ analysis, offering high-performance and flexible tools for various protocols.

Cooltools provides scalable and flexible analysis tools for high-resolution Hi-C data, addressing challenges in storage, memory, and customization.

Bioframe provides a Python library for efficient genomic interval operations using pandas dataframes, extending the data science stack for computational genomics.

The paper introduces Red-C, a method to study RNA-DNA interactions, identifies ncRNAs associated with repressed chromatin, and traces mRNA production kinetics in K562 cells.