Michael Kuhn - Publications

BIOTEC Technische Universität Dresden, Dresden, Sachsen, Germany 
computational biology

45 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Li Y, Kuhn M, Zukowska-Kasprzyk J, Hennrich ML, Kastritis PL, O'Reilly FJ, Phapale P, Beck M, Gavin AC, Bork P. Coupling proteomics and metabolomics for the unsupervised identification of protein-metabolite interactions in Chaetomium thermophilum. Plos One. 16: e0254429. PMID 34242379 DOI: 10.1371/journal.pone.0254429  1
2021 Hildebrand F, Gossmann TI, Frioux C, Özkurt E, Myers PN, Ferretti P, Kuhn M, Bahram M, Nielsen HB, Bork P. Dispersal strategies shape persistence and evolution of human gut bacteria. Cell Host & Microbe. PMID 34111423 DOI: 10.1016/j.chom.2021.05.008  1
2019 Li Y, Kuhn M, Gavin AC, Bork P. Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features. Bioinformatics (Oxford, England). PMID 31605112 DOI: 10.1093/Bioinformatics/Btz736  1
2019 Romanov N, Kuhn M, Aebersold R, Ori A, Beck M, Bork P. Disentangling Genetic and Environmental Effects on the Proteotypes of Individuals. Cell. PMID 31031010 DOI: 10.1016/J.Cell.2019.03.015  1
2018 Tramontano M, Andrejev S, Pruteanu M, Klünemann M, Kuhn M, Galardini M, Jouhten P, Zelezniak A, Zeller G, Bork P, Typas A, Patil KR. Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies. Nature Microbiology. 3: 514-522. PMID 29556107 DOI: 10.1038/S41564-018-0123-9  1
2018 Maier L, Pruteanu M, Kuhn M, Zeller G, Telzerow A, Anderson EE, Brochado AR, Fernandez KC, Dose H, Mori H, Patil KR, Bork P, Typas A. Extensive impact of non-antibiotic drugs on human gut bacteria. Nature. PMID 29555994 DOI: 10.1038/Nature25979  1
2016 Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva NT, Roth A, Bork P, Jensen LJ, von Mering C. The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Research. PMID 27924014 DOI: 10.1093/Nar/Gkw937  1
2015 Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P, Kuhn M. STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. Nucleic Acids Research. PMID 26590256 DOI: 10.1093/Nar/Gkv1277  1
2015 Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C, Bork P. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Research. PMID 26582926 DOI: 10.1093/Nar/Gkv1248  1
2015 Kuhn M, Letunic I, Jensen LJ, Bork P. The SIDER database of drugs and side effects. Nucleic Acids Research. PMID 26481350 DOI: 10.1093/Nar/Gkv1075  1
2015 Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Research. 43: D447-52. PMID 25352553 DOI: 10.1093/Nar/Gku1003  1
2014 Kuhn M, Hyman AA, Beyer A. Coiled-coil proteins facilitated the functional expansion of the centrosome. Plos Computational Biology. 10: e1003657. PMID 24901223 DOI: 10.1371/Journal.Pcbi.1003657  1
2014 Esner M, Meyenhofer F, Kuhn M, Thomas M, Kalaidzidis Y, Bickle M. Development of a Kinetic Assay for Late Endosome Movement. Journal of Biomolecular Screening. 19: 1070-1078. PMID 24556389 DOI: 10.1177/1087057114524278  1
2014 Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldón T, Rattei T, Creevey C, Kuhn M, Jensen LJ, von Mering C, Bork P. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Research. 42: D231-9. PMID 24297252 DOI: 10.1093/Nar/Gkt1253  1
2014 Kuhn M, Szklarczyk D, Pletscher-Frankild S, Blicher TH, von Mering C, Jensen LJ, Bork P. STITCH 4: integration of protein-chemical interactions with user data. Nucleic Acids Research. 42: D401-7. PMID 24293645 DOI: 10.1093/Nar/Gkt1207  1
2013 Kuhn M, Al Banchaabouchi M, Campillos M, Jensen LJ, Gross C, Gavin AC, Bork P. Systematic identification of proteins that elicit drug side effects. Molecular Systems Biology. 9: 663. PMID 23632385 DOI: 10.1038/Msb.2013.10  1
2013 Iskar M, Zeller G, Blattmann P, Campillos M, Kuhn M, Kaminska KH, Runz H, Gavin AC, Pepperkok R, van Noort V, Bork P. Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding. Molecular Systems Biology. 9: 662. PMID 23632384 DOI: 10.1038/Msb.2013.20  1
2013 Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Research. 41: D808-15. PMID 23203871 DOI: 10.1093/Nar/Gks1094  1
2012 Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T, Jensen LJ, von Mering C, Bork P. eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Research. 40: D284-9. PMID 22096231 DOI: 10.1093/Nar/Gkr1060  1
2012 Kuhn M, Szklarczyk D, Franceschini A, von Mering C, Jensen LJ, Bork P. STITCH 3: zooming in on protein-chemical interactions. Nucleic Acids Research. 40: D876-80. PMID 22075997 DOI: 10.1093/Nar/Gkr1011  1
2011 Zhao XM, Iskar M, Zeller G, Kuhn M, van Noort V, Bork P. Prediction of drug combinations by integrating molecular and pharmacological data. Plos Computational Biology. 7: e1002323. PMID 22219721 DOI: 10.1371/Journal.Pcbi.1002323  1
2011 Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, von Mering C. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Research. 39: D561-8. PMID 21045058 DOI: 10.1093/Nar/Gkq973  1
2010 Gallego O, Betts MJ, Gvozdenovic-Jeremic J, Maeda K, Matetzki C, Aguilar-Gurrieri C, Beltran-Alvarez P, Bonn S, Fernández-Tornero C, Jensen LJ, Kuhn M, Trott J, Rybin V, Müller CW, Bork P, et al. A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae. Molecular Systems Biology. 6: 430. PMID 21119626 DOI: 10.1038/Msb.2010.87  1
2010 Iskar M, Campillos M, Kuhn M, Jensen LJ, van Noort V, Bork P. Drug-induced regulation of target expression. Plos Computational Biology. 6. PMID 20838579 DOI: 10.1371/Journal.Pcbi.1000925  1
2010 Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita KF, Yamamoto Y, Yamaguchi A, Kawashima S, Chun HW, Aerts J, Aranda B, Barboza LH, Bonnal RJ, Bruskiewich R, Bryne JC, ... ... Kuhn M, et al. The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*. Journal of Biomedical Semantics. 1: 8. PMID 20727200 DOI: 10.1186/2041-1480-1-8  1
2010 Lister AL, Datta RS, Hofmann O, Krause R, Kuhn M, Roth B, Schneider R. Live coverage of scientific conferences using web technologies. Plos Computational Biology. 6: e1000563. PMID 20126525 DOI: 10.1371/Journal.Pcbi.1000563  1
2010 Lister AL, Datta RS, Hofmann O, Krause R, Kuhn M, Roth B, Schneider R. Live Coverage of Intelligent Systems for Molecular Biology/European Conference on computational biology (ISMB/ECCB) 2009. Plos Computational Biology. 6: e1000640. PMID 20126524 DOI: 10.1371/Journal.Pcbi.1000640  1
2010 Kuhn M, Campillos M, Letunic I, Jensen LJ, Bork P. A side effect resource to capture phenotypic effects of drugs. Molecular Systems Biology. 6: 343. PMID 20087340 DOI: 10.1038/Msb.2009.98  1
2010 Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Research. 38: D190-5. PMID 19900971 DOI: 10.1093/Nar/Gkp951  1
2010 Kuhn M, Szklarczyk D, Franceschini A, Campillos M, von Mering C, Jensen LJ, Beyer A, Bork P. STITCH 2: an interaction network database for small molecules and proteins. Nucleic Acids Research. 38: D552-6. PMID 19897548 DOI: 10.1093/Nar/Gkp937  1
2010 O'Donoghue SI, Horn H, Pafilis E, Haag S, Kuhn M, Satagopam VP, Schneider R, Jensen LJ. Reflect: A practical approach to web semantics Journal of Web Semantics. 8: 182-189. DOI: 10.1016/J.Websem.2010.03.003  1
2009 Pafilis E, O'Donoghue SI, Jensen LJ, Horn H, Kuhn M, Brown NP, Schneider R. Reflect: augmented browsing for the life scientist. Nature Biotechnology. 27: 508-10. PMID 19513049 DOI: 10.1038/Nbt0609-508  1
2009 Pavlopoulos GA, Pafilis E, Kuhn M, Hooper SD, Schneider R. OnTheFly: a tool for automated document-based text annotation, data linking and network generation. Bioinformatics (Oxford, England). 25: 977-8. PMID 19223449 DOI: 10.1093/Bioinformatics/Btp081  1
2009 Saunders N, Beltrão P, Jensen L, Jurczak D, Krause R, Kuhn M, Wu S. Microblogging the ISMB: a new approach to conference reporting. Plos Computational Biology. 5: e1000263. PMID 19180175 DOI: 10.1371/Journal.Pcbi.1000263  1
2009 Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C. STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Research. 37: D412-6. PMID 18940858 DOI: 10.1093/Nar/Gkn760  1
2008 Campillos M, Kuhn M, Gavin AC, Jensen LJ, Bork P. Drug target identification using side-effect similarity. Science (New York, N.Y.). 321: 263-6. PMID 18621671 DOI: 10.1126/Science.1158140  1
2008 Kuhn M, Campillos M, González P, Jensen LJ, Bork P. Large-scale prediction of drug-target relationships. Febs Letters. 582: 1283-90. PMID 18291108 DOI: 10.1016/J.Febslet.2008.02.024  1
2008 Kuhn M, von Mering C, Campillos M, Jensen LJ, Bork P. STITCH: interaction networks of chemicals and proteins. Nucleic Acids Research. 36: D684-8. PMID 18084021 DOI: 10.1093/Nar/Gkm795  1
2008 Günther S, Kuhn M, Dunkel M, Campillos M, Senger C, Petsalaki E, Ahmed J, Urdiales EG, Gewiess A, Jensen LJ, Schneider R, Skoblo R, Russell RB, Bourne PE, Bork P, et al. SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Research. 36: D919-22. PMID 17942422 DOI: 10.1093/Nar/Gkm862  1
2008 Jensen LJ, Julien P, Kuhn M, von Mering C, Muller J, Doerks T, Bork P. eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Research. 36: D250-4. PMID 17942413 DOI: 10.1093/Nar/Gkm796  1
2007 von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Krüger B, Snel B, Bork P. STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Research. 35: D358-62. PMID 17098935 DOI: 10.1093/Nar/Gkl825  1
2005 Kuhn M, Janovjak H, Hubain M, Müller DJ. Automated alignment and pattern recognition of single-molecule force spectroscopy data Journal of Microscopy. 218: 125-132. PMID 15857374 DOI: 10.1111/j.1365-2818.2005.01478.x  1
2005 Kuhn M, Janovjak H, Hubain M, Labudde D, Müller DJ. Pattern recognition of single-molecule force spectroscopy data Biophotonics International. 12: 50-51.  1
2004 Kuhn M, Meiler J, Baker D. Strand-loop-strand motifs: prediction of hairpins and diverging turns in proteins. Proteins. 54: 282-8. PMID 14696190 DOI: 10.1002/Prot.10589  1
1994 Chistoserdova L, Kuhn M, Lidstrom ME. Identification of a promoter region for mxaF (moxF) from the type I methanotroph, Methylobacter albus BG8 Fems Microbiology Letters. 121: 343-348. PMID 7926691 DOI: 10.1111/J.1574-6968.1994.Tb07124.X  1
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