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Michael Kuhn - Publications

Affiliations: 
BIOTEC Technische Universität Dresden, Dresden, Sachsen, Germany 
Area:
computational biology
Website:
http://www.mckuhn.de/
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47 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
2024 Mücke MM, Hernández-Tejero M, Gu W, Kuhn M, Janz M, Keller MI, Fullam A, Altepeter L, Mücke VT, Finkelmeier F, Schwarzkopf KM, Cremonese C, Hunyady PM, Heilani MW, Uschner FE, et al. Terlipressin therapy is associated with increased risk of colonisation with multidrug-resistant bacteria in patients with decompensated cirrhosis. Alimentary Pharmacology & Therapeutics. PMID 38414095 DOI: 10.1111/apt.17899  0.302
2023 Müller P, de la Cuesta-Zuluaga J, Kuhn M, Baghai Arassi M, Treis T, Blasche S, Zimmermann M, Bork P, Patil KR, Typas A, Garcia-Santamarina S, Maier L. High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities. Nature Protocols. PMID 38092943 DOI: 10.1038/s41596-023-00926-4  0.436
2023 Schmidt TSB, Fullam A, Ferretti P, Orakov A, Maistrenko OM, Ruscheweyh HJ, Letunic I, Duan Y, Van Rossum T, Sunagawa S, Mende DR, Finn RD, Kuhn M, Pedro Coelho L, Bork P. SPIRE: a Searchable, Planetary-scale mIcrobiome REsource. Nucleic Acids Research. PMID 37897342 DOI: 10.1093/nar/gkad943  0.795
2023 Wuyts S, Alves R, Zimmermann-Kogadeeva M, Nishijima S, Blasche S, Driessen M, Geyer PE, Hercog R, Kartal E, Maier L, Müller JB, Garcia Santamarina S, Schmidt TSB, Sevin DC, Telzerow A, ... ... Kuhn M, et al. Consistency across multi-omics layers in a drug-perturbed gut microbial community. Molecular Systems Biology. e11525. PMID 37485738 DOI: 10.15252/msb.202311525  0.464
2022 Fullam A, Letunic I, Schmidt TSB, Ducarmon QR, Karcher N, Khedkar S, Kuhn M, Larralde M, Maistrenko OM, Malfertheiner L, Milanese A, Rodrigues JFM, Sanchis-López C, Schudoma C, Szklarczyk D, et al. proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes. Nucleic Acids Research. PMID 36408900 DOI: 10.1093/nar/gkac1078  0.786
2021 Forslund SK, Chakaroun R, Zimmermann-Kogadeeva M, Markó L, Aron-Wisnewsky J, Nielsen T, Moitinho-Silva L, Schmidt TSB, Falony G, Vieira-Silva S, Adriouch S, Alves RJ, Assmann K, Bastard JP, Birkner T, ... ... Kuhn M, et al. Combinatorial, additive and dose-dependent drug-microbiome associations. Nature. 600: 500-505. PMID 34880489 DOI: 10.1038/s41586-021-04177-9  0.785
2021 Van Espen L, Bak EG, Beller L, Close L, Deboutte W, Juel HB, Nielsen T, Sinar D, De Coninck L, Frithioff-Bøjsøe C, Fonvig CE, Jacobsen S, Kjærgaard M, Thiele M, Fullam A, ... Kuhn M, et al. A Previously Undescribed Highly Prevalent Phage Identified in a Danish Enteric Virome Catalog. Msystems. 6: e0038221. PMID 34665009 DOI: 10.1128/mSystems.00382-21  0.404
2021 Maier L, Goemans CV, Wirbel J, Kuhn M, Eberl C, Pruteanu M, Müller P, Garcia-Santamarina S, Cacace E, Zhang B, Gekeler C, Banerjee T, Anderson EE, Milanese A, Löber U, et al. Unravelling the collateral damage of antibiotics on gut bacteria. Nature. PMID 34646011 DOI: 10.1038/s41586-021-03986-2  0.72
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  0.477
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  0.347
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  0.403
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  0.471
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  0.615
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  0.666
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  0.787
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  0.765
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  0.814
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  0.778
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  0.778
2014 Rückert F, Kuhn M, Scharm R, Endig H, Kersting S, Klein F, Bahra M, Rückert W, Wilhelm TJ, Niedergethmann M, Grützmann R. Evaluation of POSSUM for patients undergoing pancreatoduodenectomy. Journal of Investigative Surgery : the Official Journal of the Academy of Surgical Research. 27: 338-48. PMID 25029109 DOI: 10.3109/08941939.2014.932475  0.408
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  0.511
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  0.784
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  0.767
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  0.817
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  0.787
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  0.781
2012 Edelmann J, Holzmann K, Miller F, Winkler D, Bühler A, Zenz T, Bullinger L, Kühn MW, Gerhardinger A, Bloehdorn J, Radtke I, Su X, Ma J, Pounds S, Hallek M, et al. High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations. Blood. 120: 4783-94. PMID 23047824 DOI: 10.1182/Blood-2012-04-423517  0.452
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  0.762
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  0.767
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  0.802
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  0.818
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  0.637
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  0.781
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  0.798
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  0.803
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  0.815
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  0.476
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  0.681
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  0.727
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  0.463
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  0.807
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  0.801
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  0.821
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  0.822
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  0.819
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  0.798
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  0.818
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