Publications in 2025

Wed, 29 Apr 2026 05:27:42 +0400

In 2025, I lead a bioinformatics and NGS data analytics department. Over the year, our team supported 26 abstracts and 4 papers — we processed data, formulated and tested hypotheses, ran statistics, created figures, and wrote results and methods. Most of the abstracts were collaborations with clinics and universities, along with a few fully in-house studies. Participating in conferences helps us demonstrate our expertise, build new connections, and start new projects. Below are some of the most interesting examples.

Paper “Breast Cancer Classifier...”

There is a well-known breast cancer classification called “PAM50” — it was developed about thirty years ago and describes molecular-level differences and their relationship to patient prognosis. Everyone knows and uses it, but due to legal restrictions, we could not apply it directly. Our goal was to redesign a similar classification — conceptually close, no worse, and ideally better.

I led the project: defined the problem, structured the narrative, broke it down into key blocks, selected the figures, grouped them into panels, and estimated the scope of work. The full analysis, writing, and final visualization were done by Polina Turova, the first author.

We redesigned the classifier, showed that it performs on par with the original, introduced a new HER2-low subtype, and removed the Normal-like subtype. In 2023, this work was presented at the SABCS conference as an abstract and poster, and in 2025 it was published in a solid journal.

To design the figures, I printed relevant papers and plots, arranged them physically on paper, then recreated them in Figma, describing what problem each figure and chart solves. After that, Polina filled the drafts with real data and finalized them. Images 5 and 6 are the final versions published in the journal.

Paper ”Validation of combined DNA and RNA analysis in oncology...”

This paper describes how BostonGene analyzes patient data. I contributed to one of the sections — proposing a methodology for analyzing genetic events in patients and how to visualize them.

Only clinically significant genetic events were included in the analysis, as defined by a dedicated BostonGene team. The visualization is an adaptation of “Panorama of driver events” from another paper.

American Association for Cancer Research

A large oncology conference in the US, with a strong focus on translational medicine.

“Pan-cancer analysis of TRIM37 copy-number and development of fit-for-screening in situ hybridization tools”. AACR abstract book.

American Society of Clinical Oncology

The main clinical oncology conference in the US.

“Molecular subtyping and insights into sarcoma biology and prognosis”. ASCO abstract book.

American Society of Hematology

The largest conference on lymphomas and blood disorders in the world.

“Refining diffuse large B-cell lymphoma subtyping using lymphly, an evidence-based classifier”. BostonGene news. ASH conference site.

San-Antonio Breast Cancer Symposium

The largest conference on breast cancer in the world.

“Tumor-associated macrophage (TAMs) and cancer-associated fibroblasts (CAFs) profiles in invasive lobular carcinoma (ILC) vs no special type (NST)”. BostonGene news.