Nadezhda T. Doncheva

ProteoBench provides a centralized platform for comparing proteomics data analysis workflows, enabling benchmarking and community collaboration.

PathwayPilot is a web tool for visualizing and comparing metabolic pathways using metaproteomic data, demonstrating its effectiveness in analyzing enzyme expression shifts in gut microbiota under caloric restriction.

The paper develops a proteomics method to identify drug targets across the proteome, revealing organ-specific interactions and global drug effects.

The paper identifies 14,056 citrullination sites across 4,008 proteins using mass spectrometry, revealing widespread citrullination and its functional roles in histone marks and autoantigens.

The paper identifies Golgi fragmentation as an early AD phenotype in neurons using stem cell and mouse models, showing its link to SORL1 variants and glycosylation changes.

Arena3Dweb provides an interactive 3D visualization tool for multi-layered networks with clustering, directional connections, and integration capabilities.

The paper identifies 51 differentially regulated genes in UC colon and blood by comparing a DSS-UC mouse model with human UC data, suggesting biomarkers and therapeutic targets.

stringApp, a Cytoscape app, imports STRING and STITCH networks with disease, tissue, localization and drug-target annotations, enabling GUI-based enrichment, clustering and visualization of proteomics data.

The paper introduces Viruses.STRING, a database of virus-host protein-protein interactions combining experimental and text-mining evidence.