Michael Kuhn

This is the homepage of Michael Kuhn (né Müller). I am from Leipzig and/or Dresden and lived in Pasadena, CA, for three years while studying at Caltech. I did my PhD in the lab of Peer Bork at the EMBL Heidelberg, working on integrating protein-chemical interactions with phenotypic data to predict drug targets and to find the molecular basis of side effects.

Between 2009 and 2016, I worked as a post doc in the labs of Andreas Beyer (first Biotec, TU Dresden, now University of Cologne), Tony Hyman and Marino Zerial (MPI-CBG). My main topics of research were: the evolutionary analysis of the centrosome, the conservation of tissue-specific gene expression patterns between distant species, and the analysis of large-scale screening data. Since 2016, I have been a research staff scientist in the lab of Peer Bork, partially managing the lab and also performing research on the gut microbiota and the effects of medications on humans.

eMail: mkuhn@embl.de

Elsewhere: FediScience Mastodon account, bioCS, a blog

Scientific Interests

I enjoy working at the intersection of wet-lab and computational biology. During my post-doc, this mainly concerned cell biology questions, while now I am more working with microbiological data.

Underlying tools that I built together with others are: STITCH, SIDER, and MATADOR.

Scientific Vita

An affair with chemistry in high school led me twice to the International Chemistry Olympiad. However, I learned from hands-on experience in organic chemistry labs that I did not want to pursue a wet-lab career. Therefore I decided to study computer science at Caltech, where it was also possible to put an emphasis on biochemistry. Caltech's Summer Undergraduate Research Fellowship (SURF) provided me with the opportunity to work in David Baker's lab in Seattle. During a year-long study term in Dresden, I worked on automatically analyzing single molecule force spectroscopy spectra with Daniel J. Müller. Later, I worked in Michael Schroeder's lab on protein-protein interfaces, again with SURF funding. I received my PhD (Dr. rer. nat.) from the University of Heidelberg with summa cum laude after research in the lab of Peer Bork at the EMBL in Heidelberg. The topic of my PhD thesis was: "Integrating chemical and protein interactions: From interaction networks to human phenotypes."


See list below, my Google Scholar and ResearcherID profiles, or try this PubMed search which retrieves most of the listed publications. (* - These authors contributed equally. Underlined if corresponding author.)
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, Schierwagen R, Brol MJ, Fischer J, Klein S, Peiffer KH, Hogardt M, Shoaie S, Coenraad MJ, Bojunga J, Arroyo V, Zeuzem S, Kempf VAJ, Welsch C, Laleman W, Bork P, Fernandez J, Trebicka J; MICROB-PREDICT and PREDICT Study Group of the EASL-CLIF Consortium.
Terlipressin therapy is associated with increased risk of colonisation with multidrug-resistant bacteria in patients with decompensated cirrhosis.
Aliment Pharmacol Ther. 2024 Feb 27.
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.
Nat Protoc. 2023 Dec 13.
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 Res. 2024 Jan 5;52(D1):D777-D783.
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, Treit PV, Wenzel T, Typas A, Patil KR, Mann M, Kuhn M, Bork P.
Consistency across multi-omics layers in a drug-perturbed gut microbial community
Mol Syst Biol. 2023 Jul 24:e11525.
Thiele M, Suvitaival T, Trošt K, Kim M, de Zawadzki A, Kjaergaard M, Rasmussen DN, Lindvig KP, Israelsen M, Detlefsen S, Andersen P, Juel HB, Nielsen T, Georgiou S, Filippa V, Kuhn M, Nishijima S, Moitinho-Silva L, Rossing P, Trebicka J, Anastasiadou E, Bork P, Hansen T, Legido-Quigley C, Krag A; MicrobLiver Consortium; GALAXY Consortium.
Sphingolipids Are Depleted in Alcohol-Related Liver Fibrosis.
Gastroenterology. 2023 Jun;164(7):1248-1260.
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, Sunagawa S, Zeller G, Huerta-Cepas J, von Mering C, Bork P, Mende DR.
proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes
Nucleic Acids Res. 2023 Jan 6;51(D1):D760-D766.
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, Caesar R, Chilloux J, Coelho LP, Fezeu L, Galleron N, Helft G, Isnard R, Ji B, Kuhn M, Le Chatelier E, Myridakis A, Olsson L, Pons N, Prifti E, Quinquis B, Roume H, Salem JE, Sokolovska N, Tremaroli V, Valles-Colomer M, Lewinter C, Søndertoft NB, Pedersen HK, Hansen TH; MetaCardis Consortium*; Gøtze JP, Køber L, Vestergaard H, Hansen T, Zucker JD, Hercberg S, Oppert JM, Letunic I, Nielsen J, Bäckhed F, Ehrlich SD, Dumas ME, Raes J, Pedersen O, Clément K, Stumvoll M, Bork P.
Combinatorial, additive and dose-dependent drug-microbiome associations.
Nature. 2021 Dec;600(7889):500-505.
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, Holm JC, Bork P, Krag A, Hansen T, Arumugam M, Matthijnssens J.
A Previously Undescribed Highly Prevalent Phage Identified in a Danish Enteric Virome Catalog.
mSystems. 2021 Oct 26;6(5):e0038221.
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, Forslund SK, Patil KR, Zimmermann M, Stecher B, Zeller G, Bork P, Typas A.
Unravelling the collateral damage of antibiotics on gut bacteria.
Nature. 2021 Oct 13. doi: 10.1038/s41586-021-03986-2.
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. 2021 Jul 9;16(7):e0254429.
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. 2021 Jun 2:S1931-3128(21)00236-5.
Li Y, Kuhn M, Gavin AC, Bork P.
Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features.
Bioinformatics. 2019 Oct 12.
Romanov N, Kuhn M, Aebersold R, Ori A, Beck M, Bork P.
Disentangling Genetic and Environmental Effects on the Proteotypes of Individuals.
Cell. 2019 May 16;177(5):1308-1318.e10.
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.
Nat Microbiol. 2018 Mar 19.
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. 2018 Mar 19
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 Res. 2017 Jan 4;45(D1):D362-D368.
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 Res. 2016 Jan 4;44(D1):D380-4.
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 Res. 2016 Jan 4;44(D1):D286-93.
Kuhn M, Letunic I, Jensen LJ, Bork P.
The SIDER database of drugs and side effects.
Nucleic Acids Res. 2016 Jan 4;44(D1):D1075-9.
Eduati F et al.; NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration.
Prediction of human population responses to toxic compounds by a collaborative competition.
Nat Biotechnol. 2015 Aug 10.
Kuhn M, Beyer A.
Preprint: Conservation of expression regulation throughout the animal kingdom.
bioRxiv, doi: http://dx.doi.org/10.1101/007252
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 Res. 2015 Jan;43(Database issue):D447-52
Kuhn M, Hyman AA, Beyer A.
Coiled-coil proteins facilitated the functional expansion of the centrosome.
PLoS Comput Biol. 2014 Jun 5;10(6):e1003657
Esner M, Meyenhofer F, Kuhn M, Thomas M, Kalaidzidis Y, Bickle M.
Development of a Kinetic Assay for Late Endosome Movement.
J Biomol Screen. 2014 Feb 20.
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 Res. 2014 Jan;42(Database issue):D231-9.
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 Res. 2014 Jan;42(Database issue):D401-7.
Kuhn M, Al Banchaabouchi M, Campillos M, Jensen LJ, Gross C, Gavin AC, Bork P.
Systematic identification of proteins that elicit drug side effects.
Mol Syst Biol. 2013 Apr 30;9:663.
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.
Mol Syst Biol. 2013 Apr 30;9:662
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 Res. 2013 Jan;41(Database issue):D808-15.
Zhao XM, Iskar M, Zeller G, Kuhn M, van Noort V, Bork P.
Prediction of drug combinations by integrating molecular and pharmacological data.
PLoS Comput Biol. 2011 Dec;7(12):e1002323.
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 Res. 2012 Jan;40(Database issue):D284-9.
Kuhn M*, Szklarczyk D*, Franceschini A, von Mering C, Jensen LJ, Bork P.
STITCH 3: zooming in on protein-chemical interactions.
Nucleic Acids Res. 2012 Jan;40(Database issue):D876-80.
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, Kaksonen M, Russell RB, Gavin AC.
A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae.
Mol Syst Biol. 2010 Nov 30;6:430.
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 Res. 2011 Jan;39(Database issue):D561-8.
Iskar M, Campillos M, Kuhn M, Jensen LJ, van Noort V, Bork P.
Drug-Induced Regulation of Target Expression.
PLoS Comput Biol. 2010 Sep 9;6(9). pii: e1000925.
Katayama T et al.
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows
Journal of Biomedical Semantics 2010, 1:8
O'Donoghue SI, Horn H, Pafilis E, Haag S, Kuhn M, Satagopam VP, Schneider R, Jensen LJ.
Reflect: A practical approach to web semantics
Web Semantics: Science, Services and Agents on the World Wide Web, Volume 8, Issues 2-3, July 2010, Pages 182-189
Lister AL, Datta RS, Hofmann O, Krause R, Kuhn M, Roth B, Schneider R.
Live coverage of scientific conferences using web technologies.
PLoS Comput Biol. 2010 Jan 29;6(1):e1000563.
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 Comput Biol. 2010 Jan 29;6(1):e1000640.
Kuhn M, Campillos M, Letunic I, Jensen LJ, Bork P.
A side effect resource to capture phenotypic effects of drugs.
Mol Syst Biol. 2010;6:343.
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 Res. 2010 Jan;38(Database issue):D190-5.
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 Res. 2010 Jan;38(Database issue):D552-6.
Pafilis E, O'Donoghue SI, Jensen LJ, Horn H, Kuhn M, Brown NP, Schneider R.
Reflect: augmented browsing for the life scientist.
Nat Biotechnol. 2009 Jun;27(6):508-10.
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. 2009 Apr 1;25(7):977-8.
Saunders N, Beltrão P, Jensen LJ, Jurczak D, Krause R, Kuhn M, Wu S.
Microblogging the ISMB: A New Approach to Conference Reporting.
PLoS Comput Biol. 2009 Jan;5(1):e1000263.
Jensen LJ*, Kuhn M*, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, Mering CV.
STRING 8—a global view on proteins and their functional interactions in 630 organisms.
Nucleic Acids Res. 2009 Jan;37(Database issue):D412-6.
Campillos M*, Kuhn M*, Gavin AC, Jensen LJ, Bork P.
Drug target identification using side-effect similarity.
Science. 2008 Jul 11;321(5886):263-6.
Kuhn M*, Campillos M*, González P*, Jensen LJ*, Bork P*.
Large-scale prediction of drug-target relationships.
FEBS Lett. 2008 Apr 9;582(8):1283-90.
Kuhn M, von Mering C, Campillos M, Jensen LJ, Bork P.
STITCH: interaction networks of chemicals and proteins.
Nucleic Acids Res. 2008 Jan;36(Database issue):D684-8.
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, Preissner R.
SuperTarget and Matador: resources for exploring drug-target relationships.
Nucleic Acids Res. 2008 Jan;36(Database issue):D919-22.
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 Res. 2008 Jan;36(Database issue):D250-4.
von Mering C*, Jensen LJ*, Kuhn M, Chaffron S, Doerks T, Kruger B, Snel B, Bork P.
STRING 7--recent developments in the integration and prediction of protein interactions.
Nucleic Acids Res. 2007 Jan;35(Database issue):D358-62.
Kuhn M, Janovjak H, Hubain M, Muller DJ.
Automated alignment and pattern recognition of single-molecule force spectroscopy data.
J Microsc. 2005 May;218(Pt 2):125-32.
Kuhn M, Meiler J, Baker D.
Strand-loop-strand motifs: prediction of hairpins and diverging turns in proteins.
Proteins. 2004 Feb 1;54(2):282-8.
Meiler J, Müller M, Zeidler A, Schmäschke F
Generation and evaluation of dimension-reduced amino acid parameter representations by artificial neural networks.
J. Mol. Model. 7 (2001), 360-369

Arabic numerals: peer reviewed papers. Roman numerals: meeting reports etc.