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Survey of metaproteomics software tools for functional microbiome analysis.
PLoS One. 2020 Nov 10;15(11):e0241503. doi: 10.1371/journal.pone.0241503. eCollection 2020.
PLoS One. 2020.
PMID: 33170893
Free PMC article.
Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis.
Schiebenhoefer H, Van Den Bossche T, Fuchs S, Renard BY, Muth T, Martens L.
Schiebenhoefer H, et al.
Expert Rev Proteomics. 2019 May;16(5):375-390. doi: 10.1080/14789450.2019.1609944. Epub 2019 Apr 30.
Expert Rev Proteomics. 2019.
PMID: 31002542
Review.
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A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane.
Schiebenhoefer H, Schallert K, Renard BY, Trappe K, Schmid E, Benndorf D, Riedel K, Muth T, Fuchs S.
Schiebenhoefer H, et al.
Nat Protoc. 2020 Oct;15(10):3212-3239. doi: 10.1038/s41596-020-0368-7. Epub 2020 Aug 28.
Nat Protoc. 2020.
PMID: 32859984
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Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows.
Van Den Bossche T, Kunath BJ, Schallert K, Schäpe SS, Abraham PE, Armengaud J, Arntzen MØ, Bassignani A, Benndorf D, Fuchs S, Giannone RJ, Griffin TJ, Hagen LH, Halder R, Henry C, Hettich RL, Heyer R, Jagtap P, Jehmlich N, Jensen M, Juste C, Kleiner M, Langella O, Lehmann T, Leith E, May P, Mesuere B, Miotello G, Peters SL, Pible O, Queiros PT, Reichl U, Renard BY, Schiebenhoefer H, Sczyrba A, Tanca A, Trappe K, Trezzi JP, Uzzau S, Verschaffelt P, von Bergen M, Wilmes P, Wolf M, Martens L, Muth T.
Van Den Bossche T, et al. Among authors: schiebenhoefer h.
Nat Commun. 2021 Dec 15;12(1):7305. doi: 10.1038/s41467-021-27542-8.
Nat Commun. 2021.
PMID: 34911965
Free PMC article.
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MegaGO: A Fast Yet Powerful Approach to Assess Functional Gene Ontology Similarity across Meta-Omics Data Sets.
Verschaffelt P, Van Den Bossche T, Gabriel W, Burdukiewicz M, Soggiu A, Martens L, Renard BY, Schiebenhoefer H, Mesuere B.
Verschaffelt P, et al. Among authors: schiebenhoefer h.
J Proteome Res. 2021 Apr 2;20(4):2083-2088. doi: 10.1021/acs.jproteome.0c00926. Epub 2021 Mar 4.
J Proteome Res. 2021.
PMID: 33661648
Free article.
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CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance.
Wittig A, Miranda F, Hölzer M, Altenburg T, Bartoszewicz JM, Beyvers S, Dieckmann MA, Genske U, Giese SH, Nowicka M, Richard H, Schiebenhoefer H, Schmachtenberg AJ, Sieben P, Tang M, Tembrockhaus J, Renard BY, Fuchs S.
Wittig A, et al. Among authors: schiebenhoefer h.
Bioinformatics. 2022 Sep 2;38(17):4223-4225. doi: 10.1093/bioinformatics/btac411.
Bioinformatics. 2022.
PMID: 35799354
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