Elizaveta M. Solovyeva

Specificity and exon target space of splicing modifying compounds

This study investigates the specificity of splicing modulators by analyzing their interactions with RNA structures and demonstrates reprogramming of their specificity through genetic manipulation of the spliceosome.

Single Cell Foundation Models Evaluation (scFME) for In-Silico Perturbation

The paper introduces scFME, a framework to evaluate fine-tuned foundation models for in-silico perturbation, showing its effectiveness in characterizing model performance.

Evaluating Foundation Models for In-Silico Perturbation

This paper evaluates foundation models for in-silico perturbation using a novel framework, revealing differences in their performance across biological contexts and gene categories.

Integrative proteogenomics for differential expression and splicing variation in a DM1 mouse model

The paper uses an integrative proteogenomics approach to analyze splicing variation and differential expression in a DM1 mouse model, identifying both known and novel aberrant splicing events.

Massive proteogenomic reanalysis of publicly available proteomic datasets of human tissues in search for protein recoding via adenosine-to-inosine RNA editing

The paper reanalyzes proteomic datasets to identify ADAR-mediated RNA editing events and finds 18 core recoded protein sites across human tissues.

DirectMS1Quant: ultrafast quantitative proteomics with MS/MS-free mass spectrometry

This study compares DirectMS1Quant, an MS1-only quantitation method, with MS/MS-based methods like LFQ, TMT, and DIA, showing comparable efficiency despite shorter runtime.

A proteomics sample metadata representation for multiomics integration, and big data analysis.

The paper introduces a standardized metadata format for proteomics datasets to improve reusability and integration across public repositories.