Tatiana Shashkova

Cell type-specific interpretation of noncoding variants using deep learning-based methods

The paper introduces DeepCT, a deep learning model that predicts cell type-specific effects of noncoding variants by learning from sparse epigenetic data.

PROSTATA: Protein Stability Assessment using Transformers

PROSTATA predicts protein stability changes from point mutations using a transformer-based model, outperforming existing neural network approaches.

SEMA: Antigen B-cell conformational epitope prediction using deep transfer learning

SEMA predicts conformational B-cell epitopes using transfer learning on antigen sequences and structures, achieving ROC AUC of 0.76 on an independent test set.

Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR

The paper introduces MAGAR, a framework to identify methylation quantitative trait loci (methQTLs) and distinguish common from cell-type-specific effects using DNA methylation and genotyping data.

Varicose veins of lower extremities: insights from the first large-scale genetic study

This study identifies 7 genetic loci associated with varicose veins and finds genetic overlaps with traits like intelligence and smoking.

Knomics-Biota - a system for exploratory analysis of human gut microbiota data

Knomics-Biota provides a web-based tool for exploratory analysis of human gut metagenomic data, enabling users to generate reports and visualize microbiota composition in relation to experimental factors and public datasets.