Michael Kuhn

This is the homepage of Michael Kuhn. 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, BlueSky account, bioCS, a (dormant) 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 and SIDER. Unfortunately, due to lack of funding in this area, we have not been able to update these ressources.

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."

Publications

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.)
56.
Nishijima S, Stankevic E, Aasmets O, Schmidt TSB, Nagata N, Keller MI, Ferretti P, Juel HB, Fullam A, Robbani SM, Schudoma C, Hansen JK, Holm LA, Israelsen M, Schierwagen R, Torp N, Telzerow A, Hercog R, Kandels S, Hazenbrink DHM, Arumugam M, Bendtsen F, Brøns C, Fonvig CE, Holm JC, Nielsen T, Pedersen JS, Thiele MS, Trebicka J, Org E, Krag A, Hansen T, Kuhn M, Bork P; GALAXY and MicrobLiver Consortia.
Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations
Cell. 2024 Nov 4:S0092-8674(24)01204-2
55.
Garcia-Santamarina S*, Kuhn M*, Devendran S, Maier L, Driessen M, Mateus A, Mastrorilli E, Brochado AR, Savitski MM, Patil KR, Zimmermann M, Bork P, Typas A.
Emergence of community behaviors in the gut microbiota upon drug treatment
Cell. 2024 Oct 31;187(22):6346-6357.e20
54.
Duan Y, Santos-Júnior CD, Schmidt TS, Fullam A, de Almeida BLS, Zhu C, Kuhn M, Zhao XM, Bork P, Coelho LP.
A catalog of small proteins from the global microbiome
Nat Commun. 2024 Aug 31;15(1):7563
53.
Santos-Júnior CD, Torres MDT, Duan Y, Rodríguez Del Río Á, Schmidt TSB, Chong H, Fullam A, Kuhn M, Zhu C, Houseman A, Somborski J, Vines A, Zhao XM, Bork P, Huerta-Cepas J, de la Fuente-Nunez C, Coelho LP.
Discovery of antimicrobial peptides in the global microbiome with machine learning
Cell. 2024 Jul 11;187(14):3761-3778.e16.
52.
Thiele M, Villesen IF, Niu L, Johansen S, Sulek K, Nishijima S, Espen LV, Keller M, Israelsen M, Suvitaival T, Zawadzki A, Juel HB, Brol MJ, Stinson SE, Huang Y, Silva MCA, Kuhn M, Anastasiadou E, Leeming DJ, Karsdal M, Matthijnssens J, Arumugam M, Dalgaard LT, Legido-Quigley C, Mann M, Trebicka J, Bork P, Jensen LJ, Hansen T, Krag A; MicrobLiver consortium; GALAXY consortium.
Opportunities and barriers in omics-based biomarker discovery for steatotic liver diseases
J Hepatol. 2024 Aug;81(2):345-359
51.
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.
50.
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.
49.
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.
48.
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.
47.
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.
46.
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.
45.
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.
44.
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.
43.
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.
42.
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.
41.
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.
40.
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.
39.
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.
38.
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.
37.
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
36.
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.
35.
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.
34.
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.
33.
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.
iv.
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.
32.
Kuhn M, Beyer A.
Preprint: Conservation of expression regulation throughout the animal kingdom
bioRxiv, doi: http://dx.doi.org/10.1101/007252
31.
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
30.
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
29.
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.
28.
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.
27.
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.
26.
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.
25.
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
24.
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.
23.
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.
22.
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.
21.
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.
20.
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.
19.
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.
18.
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.
17.
Katayama T et al.
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows
Journal of Biomedical Semantics 2010, 1:8
16.
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
iii.
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.
ii.
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.
15.
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.
14.
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.
13.
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.
12.
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.
11.
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.
i.
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.
10.
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.
9.
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.
8.
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.
7.
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.
6.
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.
5.
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.
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.
3.
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.
2.
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.
1.
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.