Curation of Human Disease Networks

Dr. Andreas Ruepp
Deputy Director (acting), Group Leader Curation of Human Disease Networks

Phone: +49 89 3187-3189
Building/Room: 56/153

Group Leader: Curation of Human Disease Networks

Curriculum Vitae

  • 1986-1992 study of biology at the Ludwig Maximilians University Munich
  • 1992-1996 PhD at the Max-Planck Institute for Biochemistry in Martinsried
  • 1996-2001 PostDoc at the Max-Planck Institute for Biochemistry in the department of Wolfgang Baumeister
  • Project1: Sequencing the genome of Thermoplasma acidophilum
  • Project2: Analysis of the proteome of Thermoplasma acidophilum
  • 2001-2002 Senior Scientist at the EPIDAUROS Biotechnologie AG in Bernried
  • Project: Sequencing the genome of Desulfotalea psychrophila.
  • Since December 2002: Head of Annotation at MIPS


Allebrandt KV, Teder-Laving M, Cusumano P, Frishman G, Levandovski R, Ruepp A, Hidalgo MPL, Costa R, Metspalu A, Roenneberg T, De Pittà C. Identifying pathways modulating sleep duration: from genomics to transcriptomics. Sci Rep. (Jul 2017)

Ward-Caviness CK, Xu T, Aspelund T, Thorand B, Montrone C, Meisinger C, Dunger-Kaltenbach I, Zierer A, Yu Z, Helgadottir IR, Harris TB, Launer LJ, Ganna A, Lind L, Eiriksdottir G, Waldenberger M, Prehn C, Suhre K, Illig T, Adamski J, Ruepp A, Koenig W, Gudnason V, Emilsson V, Wang-Sattler R, Peters A. Improvement of myocardial infarction risk prediction via inflammation-associated metabolite biomarkers. Heart (Mar 2017)

Kostareva, A., Kiselev, A., Gudkova, A., Frishman, G., Ruepp, A., Frishman, D., Smolina, N., Tarnovskaya, S., Nilsson, D., Zlotina, A., Khodyuchenko, T., Vershinina, T., Pervunina, T., Klyushina, A., Kozlenok, A., Sjoberg, G., Golovljova, I., Sejersen, T., Shlyakhto, E. Genetic spectrum of idiopathic restrictive cardiomyopathy uncovered by next-generation sequencing. PLoS ONE 11:e0163362 (2016)

Liu, X., Baarsma, H.A., Thiam, C.H., Montrone, C., Brauner, B., Fobo, G., Heier, J.S., Duscha, S., Königshoff, M., Angeli, V., Ruepp, A., Campillos, M.J. Systematic identification of pharmacological targets from small-molecule phenotypic screens. Cell Chem. Bio. 23, 1302-1313 (2016)

Arloth, J., Bogdan, R., Weber, P., Frishman, G., Menke, A., Wagner, K.V., Balsevich, G., Schmidt, M.V., Karbalai, N., Czamara, D., Altmann, A., Trümbach, D., Wurst, W., Mehta, D., Uhr, M., Klengel, T., Erhardt, A., Carey, C.E., Conley, E.D., Ruepp, A., Müller-Myhsok, B., Hariri, A.R., Binder, E.B. Genetic differences in the immediate transcriptome response to stress predict risk-related brain function and psychiatric disorders. Neuron 86, 1189-1202 (2015)

Xu, T., Brandmaier, S., Messias, A.C., Herder, C., Draisma, H.H., Demirkan, A., Yu, Z., Ried, J.S., Haller, T., Heier, M., Campillos, M., Fobo, G., Stark, R.G., Holzapfel, C., Adam, J., Chi, S., Rotter, M., Panni, T., Quante, A.S., He, Y., Prehn, C., Römisch-Margl, W., Kastenmüller, G., Willemsen, G., Pool, R., Kasa, K., van Dijk, K.W., Hankemeier, T., Meisinger, C., Thorand, B., Ruepp, A., Hrabě de Angelis, M., Li, Y., Wichmann, H.-E., Stratmann, B., Strauch, K., Metspalu, A., Gieger, C., Suhre, K., Adamski, J., Illig, T., Rathmann, W., Roden, M., Peters, A., van Duijn, C.M., Boomsma, D.I., Meitinger, T., Wang-Sattler, R. Effects of metformin on metabolite profiles and LDL cholesterol in patients with type 2 diabetes. Diabetes Care 38, 1858-1867 (2015)

Altmaier, E., Fobo, G., Heier, M., Thorand, B., Meisinger, C., Römisch-Margl, W., Waldenberger, M., Gieger, C., Illig, T., Adamski, J., Suhre, K., Kastenmüller, G. Metabolomics approach reveals effects of antihypertensives and lipid-lowering drugs on the human metabolism. Eur. J. Epidemiol. 29, 325-336 (2014)

Bleves, S., Dunger, I., Walter, M.C., Frangoulidis, D., Kastenmüller, G., Voulhoux, R., Ruepp, A. HoPaCI-DB: Host-Pseudomonas and Coxiella interaction database. Nucleic Acids Res. 42, D671-D676 (2014)

Blohm, P., Frishman, G., Smialowski, P., Goebels, F., Wachinger, B., Ruepp, A., Frishman, D. Negatome 2.0: A database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis. Nucleic Acids Res. 42, D396-D400 (2014)

Mehta, D., Newport, D.J., Frishman, G., Kraus, L., Rex-Haffner, M., Ritchie, J.C., Lori, A., Knight, B.T., Stagnaro, E., Ruepp, A., Stowe, Z.N., Binder, E.B. Early predictive biomarkers for postpartum depression point to a role for estrogen receptor signaling. Psychol. Med. 44, 2309-2322 (2014)

Montrone, C., Kokkaliaris, K.D., Loeffler, D., Lechner, M., Kastenmüller, G., Schroeder, T., Ruepp, A. HSC-Explorer: A curated database for hematopoietic stem cells. PLoS ONE 8:e70348 (2013)

Lechner, M., Höhn, V., Brauner, B., Dunger, I., Fobo, G., Frishman, G., Montrone, C., Kastenmüller, G., Wägele, B., Ruepp, A. CIDeR: Multifactorial interaction networks in human diseases. Genome Biol. 13:R62 (2012)

Ruepp, A., Kowarsch, A., Theis, F.J. PhenomiR: MicroRNAs in human diseases and biological processes. Methods Mol. Biol. 822, 249-260 (2012)

Sass, S., Dietmann, S., Burk, U.C., Brabletz, S., Lutter, D., Kowarsch, A., Mayer, K.F.X., Brabletz, T., Ruepp, A., Theis, F.J., Wang, Y. MicroRNAs coordinately regulate protein complexes. BMC Syst. Biol. 5:136 (2011)

Ruepp A, Kowarsch A, Schmidl D, Bruggenthin F, Brauner B, Dunger I, Fobo G, Frishman G, Montrone C, Theis FJ. PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes. Genome Biol. 2010 Jan 20;11(1):R6. PMID: 20089154

Smialowski P, Pagel P, Wong P, Brauner B, Dunger I, Fobo G, Frishman G, Montrone C, Rattei T, Frishman D, Ruepp A. The Negatome database: a reference set of non-interacting protein pairs. Nucleic Acids Res. 2010 Jan;38(Database issue):D540-4. 

Ruepp A, Waegele B, Lechner M, Brauner B, Dunger-Kaltenbach I, Fobo G, Frishman G, Montrone C, Mewes HW. CORUM: the comprehensive resource of mammalian protein complexes--2009. Nucleic Acids Res. 2010 Jan;38(Database issue):D497-501.

Wong P, Althammer S, Hildebrand A, Kirschner A, Pagel P, Geissler B, Smialowski P, Blöchl F, Oesterheld M, Schmidt T, Strack N, Theis FJ, Ruepp A, Frishman D. An evolutionary and structural characterization of mammalian protein complex organization. BMC Genomics. 2008 Dec 23;9:629.

Waegele B, Dunger-Kaltenbach I, Fobo G, Montrone C, Mewes HW, Ruepp A. CRONOS: the cross-reference navigation server. Bioinformatics. 2009 Jan 1;25(1):141-3.

Antranikian G, Ruepp A, Gordon PM, Ballschmiter M, Zibat A, Stark M, Sensen CW, Frishman D, Liebl W, Klenk HP. Rapid access to genes of biotechnologically useful enzymes by partial genome sequencing: the thermoalkaliphile Anaerobranca gottschalkii. J Mol Microbiol Biotechnol. 2009;16(1-2):81-90.

Waegele B, Schmidt T, Mewes HW, Ruepp A. OREST: the online resource for EST analysis. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W140-4.

Pfeiffer F, Schuster SC, Broicher A, Falb M, Palm P, Rodewald K, Ruepp A, Soppa J, Tittor J, Oesterhelt D. Evolution in the laboratory: the genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1. Genomics. 2008 Apr;91(4):335-46.

Grimm M, Stephan R, Iversen C, Manzardo GG, Rattei T, Riedel K, Ruepp A, Frishman D, Lehner A. Cellulose as an extracellular matrix component present in Enterobacter sakazakii biofilms. J Food Prot. 2008 Jan;71(1):13-8.

Mewes HW, Dietmann S, Frishman D, Gregory R, Mannhaupt G, Mayer KF, Münsterkötter M, Ruepp A, Spannagl M, Stümpflen V, Rattei T. MIPS: analysis and annotation of genome information in 2007. Nucleic Acids Res. 2008 Jan;36(Database issue):D196-201.

Ruepp A, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Stransky M, Waegele B, Schmidt T, Doudieu ON, Stümpflen V, Mewes HW. CORUM: the comprehensive resource of mammalian protein complexes. Nucleic Acids Res. 2008 Jan;36(Database issue):D646-50.

Datson NA, Morsink MC, Atanasova S, Armstrong VW, Zischler H, Schlumbohm C, Dutilh BE, Huynen MA, Waegele B, Ruepp A, de Kloet ER, Fuchs E. Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate. BMC Genomics. 2007 Jun 25;8:190.

Brügger K, Chen L, Stark M, Zibat A, Redder P, Ruepp A, Awayez M, She Q, Garrett RA, Klenk HP. The genome of Hyperthermus butylicus: a sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 degrees C. Archaea. 2007 May;2(2):127-35.

Dietmann S, Aguilar D, Mader M, Oesterheld M, Ruepp A, Stuempflen V, Mewes HW. Resources and tools for investigating biomolecular networks in mammals. Curr Pharm Des. 2006;12(29):3723-34.

Lehner A, Grimm M, Rattei T, Ruepp A, Frishman D, Manzardo GG, Stephan R. Cloning and characterization of Enterobacter sakazakii pigment genes and in situ spectroscopic analysis of the pigment. FEMS Microbiol Lett. 2006 Dec;265(2):244-8.

Lehner A, Riedel K, Rattei T, Ruepp A, Frishman D, Breeuwer P, Diep B, Eberl L, Stephan R. Molecular characterization of the alpha-glucosidase activity in Enterobacter sakazakii reveals the presence of a putative gene cluster for palatinose metabolism. Syst Appl Microbiol. 2006 Dec;29(8):609-25.

Prokisch H, Andreoli C, Ahting U, Heiss K, Ruepp A, Scharfe C, Meitinger T. MitoP2: the mitochondrial proteome database--now including mouse data. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D705-11.

Ruepp A, Doudieu ON, van den Oever J, Brauner B, Dunger-Kaltenbach I, Fobo G, Frishman G, Montrone C, Skornia C, Wanka S, Rattei T, Pagel P, Riley L, Frishman D, Surmeli D, Tetko IV, Oesterheld M, Stümpflen V, Mewes HW. The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D568-71.

Güldener U, Münsterkötter M, Oesterheld M, Pagel P, Ruepp A, Mewes HW, Stümpflen V. MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D436-41.

Mewes HW, Frishman D, Mayer KF, Münsterkötter M, Noubibou O, Pagel P, Rattei T, Oesterheld M, Ruepp A, Stümpflen V. MIPS: analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D169-72.

Tetko IV, Facius A, Ruepp A, Mewes HW. Super paramagnetic clustering of protein sequences. BMC Bioinformatics. 2005 Apr 1;6:82.

Tetko IV, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Fobo G, Ruepp A, Antonov AV, Surmeli D, Mewes HW. MIPS bacterial genomes functional annotation benchmark dataset. Bioinformatics. 2005 May 15;21(10):2520-1.

Pagel P, Kovac S, Oesterheld M, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Mark P, Stümpflen V, Mewes HW, Ruepp A, Frishman D. The MIPS mammalian protein-protein interaction database. Bioinformatics. 2005 Mar;21(6):832-4.

Ruepp A, Zollner A, Maier D, Albermann K, Hani J, Mokrejs M, Tetko I, Güldener U, Mannhaupt G, Münsterkötter M, Mewes HW. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res. 2004 Oct 14;32(18):5539-45.

Rabus R, Ruepp A, Frickey T, Rattei T, Fartmann B, Stark M, Bauer M, Zibat A, Lombardot T, Becker I, Amann J, Gellner K, Teeling H, Leuschner WD, Glöckner FO, Lupas AN, Amann R, Klenk HP. The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments. Environ Microbiol. 2004 Sep;6(9):887-902.

Mewes HW, Amid C, Arnold R, Frishman D, Güldener U, Mannhaupt G, Münsterkötter M, Pagel P, Strack N, Stümpflen V, Warfsmann J, Ruepp A. MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D41-4.

Ruepp A, Rockel B, Gutsche I, Baumeister W, Lupas AN. The Chaperones of the archaeon Thermoplasma acidophilum. J Struct Biol. 2001 Aug;135(2):126-38.

Ruepp A, Graml W, Santos-Martinez ML, Koretke KK, Volker C, Mewes HW, Frishman D, Stocker S, Lupas AN, Baumeister W. The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum. Nature. 2000 Sep 28;407(6803):508-13.

Ruepp A, Eckerskorn C, Bogyo M, Baumeister W. Proteasome function is dispensable under normal but not under heat shock conditions in Thermoplasma acidophilum. FEBS Lett. 1998 Mar 20;425(1):87-90.

Ruepp A, Wanner G, Soppa J. A 71-kDa protein from Halobacterium salinarium belongs to a ubiquitous P-loop ATPase superfamily with head-rod-tail structure. Arch Microbiol. 1998 Jan;169(1):1-9.

Ruepp A, Soppa J. Fermentative arginine degradation in Halobacterium salinarium (formerly Halobacterium halobium): genes, gene products, and transcripts of the arcRACB gene cluster. J Bacteriol. 1996 Aug;178(16):4942-7.

Ruepp A, Müller HN, Lottspeich F, Soppa J. Catabolic ornithine transcarbamylase of Halobacterium halobium (salinarium): purification, characterization, sequence determination, and evolution. J Bacteriol. 1995 Mar;177(5):1129-36.