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Alexander Junge
Researcher at University of Copenhagen
Publications - 12
Citations - 10940
Alexander Junge is an academic researcher from University of Copenhagen. The author has contributed to research in topics: Relationship extraction & Information extraction. The author has an hindex of 8, co-authored 11 publications receiving 5772 citations. Previous affiliations of Alexander Junge include Saarland University & Max Planck Society.
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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
RAIN: RNA-protein Association and Interaction Networks.
Alexander Junge,Jan C. Refsgaard,Christian Garde,Christian Garde,Xiaoyong Pan,Alberto Santos,Ferhat Alkan,Christian Anthon,Christian von Mering,Christopher T. Workman,Christopher T. Workman,Lars Juhl Jensen,Jan Gorodkin +12 more
TL;DR: It is demonstrated that RAIN outperforms the underlying microRNA-target predictions in inferring ncRNA interactions and its integration with the STRING database of protein–protein interactions.
Journal ArticleDOI
Transcriptome and metabolite changes during hydrogen cyanamide-induced floral bud break in sweet cherry
Irina Alexandra Ionescu,Gregorio López-Ortega,Meike Burow,Almudena Bayo-Canha,Alexander Junge,Oliver Gericke,Birger Lindberg Møller,Raquel Sánchez-Pérez +7 more
TL;DR: This work identified the most up-regulated pathways: the cytokinin pathway, as well as the jasmonate and the hydrogen cyanide pathway, which strongly suggest an inductive effect of these metabolites in bud dormancy release and provide a stepping stone for the characterization of key genes in bud roommancy release.
Journal ArticleDOI
KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape
Nicolas Alcaraz,Nicolas Alcaraz,Josch K. Pauling,Richa Batra,Eudes Barbosa,Eudes Barbosa,Alexander Junge,Alexander Junge,Alexander Junge,Anne Geske Lindhard Christensen,Vasco Azevedo,Henrik J. Ditzel,Henrik J. Ditzel,Jan Baumbach,Jan Baumbach,Jan Baumbach +15 more
TL;DR: KeyPathwayMiner 4.0 can further integrate existing knowledge by adding a search bias towards sub-networks that contain (avoid) genes provided in a positive (negative) list and has been implemented as an app for the standard bioinformatics network analysis tool: Cytoscape.
Journal ArticleDOI
RNAscClust: clustering RNA sequences using structure conservation and graph based motifs.
Milad Miladi,Alexander Junge,Fabrizio Costa,Stefan E. Seemann,Jakob Hull Havgaard,Jan Gorodkin,Rolf Backofen,Rolf Backofen +7 more
TL;DR: This work presents RNAscClust, the implementation of a new algorithm to cluster a set of structured RNAs taking their respective structural conservation into account, and shows that the clustering accuracy clearly benefits from an increasing degree of compensatory base pair changes in the alignments.