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.
Elsewhere: Twitter, bioCS, a blog, Tumblr, Biology StackExchange
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.
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.)
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.
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.
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.
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
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.
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.
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.
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.
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
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.
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.
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.
Arabic numerals: peer reviewed papers. Roman numerals: meeting reports etc.