NetworkPrioritizer: a versatile tool for network-based prioritization of candidate disease genes or other molecules. - Tim Kacprowski; Nadezhda T. Doncheva; Mario Albrecht (Bioinform., 2013)

setsApp: Set operations for Cytoscape Nodes and Edges. - John H. Morris; Allan Wu; Nadezhda T. Doncheva; Mario Albrecht; Thomas E. Ferrin (F1000Research, 2014)

Network biology methods for functional characterization and integrative prioritization of disease ge. - Nadezhda T. Doncheva (2016)

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. - Damian Szklarczyk; John H. Morris; Helen Cook; Michael Kuhn 004; Stefan Wyder; Milan Simonovic; Alberto Santos; Nadezhda T. Doncheva; Alexander Roth 001; Peer Bork; Lars Juhl Jensen; Christian von Mering (Nucleic Acids Res., 2017)

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. - Damian Szklarczyk; Annika L. Gable; David Lyon; Alexander Junge; Stefan Wyder; Jaime Huerta-Cepas; Milan Simonovic; Nadezhda T. Doncheva; John H. Morris; Peer Bork; Lars Juhl Jensen; Christian von Mering (Nucleic Acids Res., 2019)

Visualize omics data on networks with Omics Visualizer, a Cytoscape App. - Marc Legeay; Nadezhda T. Doncheva; John H. Morris; Lars Juhl Jensen (F1000Research, 2020)

The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. - Damian Szklarczyk; Annika L. Gable; Katerina C. Nastou; David Lyon; Rebecca Kirsch; Sampo Pyysalo; Nadezhda T. Doncheva; Marc Legeay; Tao Fang; Peer Bork; Lars Juhl Jensen; Christian von Mering (Nucleic Acids Res., 2021)

The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. - Damian Szklarczyk; Rebecca Kirsch; Mikaela Koutrouli; Katerina C. Nastou; Farrokh Mehryary; Radja Hachilif; Annika L. Gable; Tao Fang; Nadezhda T. Doncheva; Sampo Pyysalo; Peer Bork; Lars Juhl Jensen; et al. (Nucleic Acids Res., 2023)