M
Milan Simonovic
Researcher at Swiss Institute of Bioinformatics
Publications - 10
Citations - 35093
Milan Simonovic is an academic researcher from Swiss Institute of Bioinformatics. The author has contributed to research in topics: String (computer science) & Interaction information. The author has an hindex of 9, co-authored 9 publications receiving 26185 citations. Previous affiliations of Milan Simonovic include University of Lausanne & University of Zurich.
Papers
More filters
Journal ArticleDOI
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 Tsankova Doncheva,John H. Morris,Peer Bork,Lars Juhl Jensen,Christian von Mering +11 more
TL;DR: The latest version of STRING more than doubles the number of organisms it covers, and offers an option to upload entire, genome-wide datasets as input, allowing users to visualize subsets as interaction networks and to perform gene-set enrichment analysis on the entire input.
Journal ArticleDOI
STRING v10: protein–protein interaction networks, integrated over the tree of life
Damian Szklarczyk,Andrea Franceschini,Stefan Wyder,Kristoffer Forslund,Davide Heller,Jaime Huerta-Cepas,Milan Simonovic,Alexander Roth,Alberto Santos,Kalliopi Tsafou,Michael Kuhn,Peer Bork,Lars Juhl Jensen,Christian von Mering +13 more
TL;DR: H hierarchical and self-consistent orthology annotations are introduced for all interacting proteins, grouping the proteins into families at various levels of phylogenetic resolution in the STRING database.
Journal ArticleDOI
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.
Damian Szklarczyk,John H. Morris,Helen Cook,Michael Kuhn,Stefan Wyder,Milan Simonovic,Alberto Santos,Nadezhda Tsankova Doncheva,Alexander Roth,Peer Bork,Lars Juhl Jensen,Christian von Mering +11 more
TL;DR: In the latest version 10.5 of STRING, the biggest changes are concerned with data dissemination: the web frontend has been completely redesigned to reduce dependency on outdated browser technologies, and the database can now also be queried from inside the popular Cytoscape software framework.
Journal ArticleDOI
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
Andrea Franceschini,Damian Szklarczyk,Sune Frankild,Michael Kuhn,Milan Simonovic,Alexander Roth,Jianyi Lin,Pablo Minguez,Peer Bork,Christian von Mering,Lars Juhl Jensen +10 more
TL;DR: The update to version 9.1 of STRING is described, introducing several improvements, including extending the automated mining of scientific texts for interaction information, to now also include full-text articles, and providing users with statistical information on any functional enrichment observed in their networks.
Journal ArticleDOI
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
Damian Szklarczyk,Andrea Franceschini,Michael Kuhn,Milan Simonovic,Alexander Roth,Pablo Minguez,Tobias Doerks,Manuel Stark,Jean Muller,Peer Bork,Lars Juhl Jensen,Christian von Mering +11 more
TL;DR: An update on the online database resource Search Tool for the Retrieval of Interacting Genes (STRING), which provides uniquely comprehensive coverage and ease of access to both experimental as well as predicted interaction information.