Maria S. Poptsova

The paper analyzes miRNA tissue specificity in normal and tumor tissues, identifies dysregulated miRNAs, and links them to oncogenic pathways.

This study identifies pericyte-derived cancer-associated fibroblasts (CAFs) in glioblastoma, showing their association with poor survival and increased abundance after chemoradiotherapy.

OmiXAI is an ensemble XAI pipeline for deep learning in omics data that reduces feature sets and benchmarks XAI methods on Z-DNA prediction.

The paper uses AI-driven protein design to discover that ADAR1 interacts with YTHDC1, linking m6A modification to dsRNA editing and suggesting a mechanism for RNA editing regulation.

The paper introduces a framework that integrates DNA sequences with omics data using a pretrained model, enabling reconstruction and unified representation of genomic and functional information.

This paper tests linear and convolutional Kolmogorov-Arnold Networks (KANs) as alternatives to MLPs in genomic sequence classification and generation, showing LKANs outperform CKANs and baselines on benchmark datasets.

The paper evaluates generative models for improving non-B DNA structure prediction through data augmentation, finding diffusion models perform best for Z-DNA and H-DNA while WGAN excels for G-quadruplexes.

The paper identifies conserved Z-flipons between human and mouse that are linked to increased transcription initiation rates in CpG-promoters.

The paper uses G4-DNABERT to map G-quadruplexes to enhancer and promoter regions, supporting their role in chromatin looping and gene regulation.

The paper identifies Z-flipon variants' roles in health and disease by analyzing Z-DNA and Z-RNA effects across multiple genomic features and disease associations.

This study applies graph neural networks to predict Z-DNA in genomes, showing improved performance over previous methods using sequence and omics data.

The paper explores the role of flipons and miRNAs in promoter specification during development, suggesting a connection between RNA and DNA mechanisms in establishing cell identity.