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Rebecca Kirsch
Researcher at University of Copenhagen
Publications - 9
Citations - 3427
Rebecca Kirsch is an academic researcher from University of Copenhagen. The author has contributed to research in topics: Biology & Computer science. The author has an hindex of 3, co-authored 4 publications receiving 184 citations. Previous affiliations of Rebecca Kirsch include Leipzig University.
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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 Tsankova Doncheva,Marc Legeay,Tao Fang,Peer Bork,Lars Juhl Jensen,Christian von Mering +11 more
TL;DR: Changes to the text-mining system, a new scoring-mode for physical interactions, as well as extensive user interface features for customizing, extending and sharing protein networks are described.
Journal ArticleDOI
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 Tsankova Doncheva,Sampo Pyysalo,Peer Bork,Lars Juhl Jensen,Christian von Mering +12 more
TL;DR: STRING as mentioned in this paper collects and integrates protein-protein interactions, both physical interactions as well as functional associations, from a number of sources: automated text mining of the scientific literature, computational interaction predictions from co-expression, conserved genomic context, databases of interaction experiments and known complexes/pathways from curated sources.
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Mapping the RNA-Seq trash bin: Unusual transcripts in prokaryotic transcriptome sequencing data
Gero Doose,Maria Alexis,Rebecca Kirsch,Sven Findeiß,David Langenberger,Rainer Machné,Mario Mörl,Steve Hoffmann,Peter F. Stadler +8 more
TL;DR: This work reanalyzes a series of published RNA-seq data sets, screening them specifically for non-contiguously mapping reads, and recovers most of the known cases together with several novel archaeal ncRNAs associated with circularized products.
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eggNOG 6.0: enabling comparative genomics across 12 535 organisms
Ana Hernández-Plaza,Damian Szklarczyk,J. Botas,Carlos Pérez Cantalapiedra,Joaquín Giner-Lamia,Daniel R. Mende,Rebecca Kirsch,Thomas Rattei,Ivica Letunic,Lars Juhl Jensen,Peer Bork,Christian von Mering,Jaime Huerta-Cepas +12 more
TL;DR: The eggNOG 6.0 as discussed by the authors database provides a hierarchy of over 17M orthologous groups (OGs) computed at 1601 taxonomic levels, spanning 10 756 bacterial, 457 archaeal and 1322 eukaryotic organisms.
Journal ArticleDOI
Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks.
Nadezhda Tsankova Doncheva,John H. Morris,Henrietta Holze,Rebecca Kirsch,Katerina C. Nastou,Yesid Cuesta-Astroz,Thomas Rattei,Damian Szklarczyk,Christian von Mering,Lars Juhl Jensen +9 more
TL;DR: The stringApp 2.0 as mentioned in this paper improves the support for heterogeneous networks and provides new functionality that makes it possible to create networks that contain proteins and interactions from STRING as well as other biological entities and associations from other sources.