I am a computational biologist inspired by the complexity of the data.
At MIT, I am a Postdoctoral Researcher in the Leonid Mirny Group, where I specialize in exploring the three-dimensional organization of genomes across various experimental systems. My work focuses on understanding how spatial genome architecture influences biological function and regulation.
Below, you’ll find a brief summary of my experiences and research projects.
My interest in various branches of biology revolves around a unifying theme: chromatin organization.
In the new work published today in NAR, Aleksei Shkolikov and I explore what we can see in Hi-C — with convolutional autoencoder — across the tree of life in 22 species, ranging from amoeba and dinoflagellate to vertebrates and insects. With our approach called Chimaera, we learn the rules
In this update, I show that chromatin “fountains” form at enhancers not only in early zebrafish embryos but also during mitotic exit in mouse embryonic stem cells (mESCs). This is exciting because fountains appear to be a universal early feature of genome folding and likely reflect cohesin loading at enhancers.
I’m pleased to share the results of a project I started during my graduate studies, now beautifully completed by my colleagues.
The study applies a sophisticated method to construct joint embeddings of DNA sequences and Hi-C chromatin organization maps within a shared space. This framework allows for the exploration of
The recording of my January 2025 NGS Webinar Series talk is now available. I cover my recent work on chromatin in dendritic cells. Thanks to the West German Genome Center for organizing the series and supporting open scientific discussion.
The second week of December 2024, I have attended 2024 4DN Annual Meeting in San Diego. I presented my work on the chromatin of the dendritic cells to the chromatin biology community. My poster:
Does chromatin organization shape immune responses? Our recent study with Nick Adams led by Reizis Lab and Leonid Mirny explores how cohesin, a key player in chromatin loop extrusion, controls the chromatin architecture essential for conventional dendritic cells (cDC). DCs bridge innate and adaptive immunity. Surprisingly, strictly required factor for
A very curious part of my PhD work on Dictyostelium discoideum chromatin has been published in Nucleic Acid Research this week. My part was designing a 1D extrusion and polymer model to explain why the “bright dots” are happening at the convergent gene positions (CGPs).
Dictyostelium discoideum is a social amoeba famous for its pseudo-multicellularity: to multiply, its cells aggregate into fruiting body that produces spores. We call this fascinating organism simply as “Dicty”.
It turns out this organism has pretty unique genome organization into loops that coincide with the convergent genes positions.
Aleksandra Galitsyna, 2025