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000255490 037__ $$aDZNE-2023-00291
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000255490 1001_ $$aLiebhoff, Anna-Maria$$b0
000255490 245__ $$aPathogen detection in RNA-seq data with Pathonoia.
000255490 260__ $$aHeidelberg$$bSpringer$$c2023
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000255490 520__ $$aBacterial and viral infections may cause or exacerbate various human diseases and to detect microbes in tissue, one method of choice is RNA sequencing. The detection of specific microbes using RNA sequencing offers good sensitivity and specificity, but untargeted approaches suffer from high false positive rates and a lack of sensitivity for lowly abundant organisms.We introduce Pathonoia, an algorithm that detects viruses and bacteria in RNA sequencing data with high precision and recall. Pathonoia first applies an established k-mer based method for species identification and then aggregates this evidence over all reads in a sample. In addition, we provide an easy-to-use analysis framework that highlights potential microbe-host interactions by correlating the microbial to the host gene expression. Pathonoia outperforms state-of-the-art methods in microbial detection specificity, both on in silico and real datasets.Two case studies in human liver and brain show how Pathonoia can support novel hypotheses on microbial infection exacerbating disease. The Python package for Pathonoia sample analysis and a guided analysis Jupyter notebook for bulk RNAseq datasets are available on GitHub.
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000255490 650_7 $$2Other$$aMetagenomics
000255490 650_7 $$2Other$$aPathogen detection
000255490 650_7 $$2Other$$aRNA sequencing
000255490 650_2 $$2MeSH$$aHumans
000255490 650_2 $$2MeSH$$aRNA-Seq
000255490 650_2 $$2MeSH$$aAlgorithms
000255490 650_2 $$2MeSH$$aSequence Analysis, RNA: methods
000255490 650_2 $$2MeSH$$aBase Sequence
000255490 650_2 $$2MeSH$$aBacteria: genetics
000255490 650_2 $$2MeSH$$aMetagenomics: methods
000255490 650_2 $$2MeSH$$aHigh-Throughput Nucleotide Sequencing: methods
000255490 7001_ $$0P:(DE-2719)2812499$$aMenden, Kevin$$b1$$udzne
000255490 7001_ $$aLaschtowitz, Alena$$b2
000255490 7001_ $$0P:(DE-HGF)0$$aFranke, Andre$$b3
000255490 7001_ $$aSchramm, Christoph$$b4
000255490 7001_ $$0P:(DE-2719)2810547$$aBonn, Stefan$$b5$$udzne
000255490 773__ $$0PERI:(DE-600)2041484-5$$a10.1186/s12859-023-05144-z$$gVol. 24, no. 1, p. 53$$n1$$p53$$tBMC bioinformatics$$v24$$x1471-2105$$y2023
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