Curation of Human Disease Networks





  • 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)


  • Kowarsch, A., Marr, C., Schmidl, D., Ruepp, A., Theis, F.J. Tissue-specific target analysis of disease-associated microRNAs in human signaling pathways. PLoS ONE 5:e11154 (2010)
  • Mewes, H.-W., Ruepp, A., Theis, F.J., Rattei, T., Walter, M.C., Frishman, D., Suhre, K., Spannagl, M., Mayer, K.F.X., Stuempflen, V., Antonov, A. MIPS: Curated databases and comprehensive secondary data resources in 2010. Nucleic Acids Res. 39, 1, D220-D224 (2010)


  • Ruepp, A., Wägele, B., Lechner, M., Brauner, B., Dunger-Kaltenbach, I., Fobo, G., Frishman, G., Montrone, C., Mewes, H.-W. CORUM: The comprehensive resource of mammalian protein complexes - 2009. Nucleic Acids Res. 38, 1, D497-D501 (2010)
  • Ruepp, A., Kowarsch, A., Schmidl, D., Buggenthin, F., Brauner, B., Dunger, I., Fobo, G., Frishman, G., Montrone, C., Theis, F.J. PhenomiR: A knowledgebase for microRNA expression in diseases and biological processes. Genome Biol. 11:R6 (2010)
  • 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. 38, 1, D540-D544 (2010)
  • Antranikian, G., Ruepp, A., Gordon, P.M., Ballschmiter, M., Zibat, A., Stark, M., Sensen, C.W., Frishman, D., Liebl, W., Klenk, H.P. Rapid access to genes of biotechnologically useful enzymes by partial genome sequencing: The thermoalkaliphile Anaerobranca gottschalkii. J. Mol. Microbiol. Biotechnol. 16, 81-90 (2009)
    Wägele, B., Dunger-Kaltenbach, I., Fobo, G., Montrone, C., Mewes, H.-W., Ruepp, A. CRONOS: The cross-reference navigation server. Bioinformatics 25, 141-143 (2009)


  • Grimm, M., Stephan, R., Iversen, C., Manzardo, G.G., Rattei, T., Riedel, K., Ruepp, A., Frishman, D., Lehner, A. Cellulose as an extracellular matrix component present in Enterobacter sakazakii biofilms. J. Food Prot. 71, 13-18 (2008)
  • Mewes, H.-W., Dietmann, S., Frishman, D., Gregory, R., Mannhaupt, G., Mayer, K.F.X., Münsterkötter, M., Ruepp, A., Spannagl, M., Stuempflen, V., Rattei, T. MIPS: Analysis and annotation of genome information in 2007. Nucleic Acids Res. 36, D196-D201 (2008)
  • Pfeiffer, F., Schuster, S.C., Broicher, A., Falb, M., Palm, P., Rodewald, K., Ruepp, A., Soppa, J., Tittor, J., Oesterhelt, D. Genome sequences of Halobacterium salinarum: A reply. Genomics 91, 553-554 (2008)
  • Pfeiffer, F., Schuster, S.C., 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 91, 335-346 (2008)
  • Ruepp, A., Brauner, B., Dunger-Kaltenbach, I., Frishman, G., Montrone, C., Stransky, M., Wägele, B., Schmidt, T., Doudieu, O.N., Stuempflen, V., Mewes, H.-W. CORUM: The comprehensive resource of mammalian protein complexes. Nucleic Acids Res. 36, D646-D650 (2008)
  • Wägele, B., Schmidt, T., Mewes, H.-W., Ruepp, A. OREST: The online resource for EST analysis. Nucleic Acids Res. 36, W140-W144 (2008)
  • Wong, P., Althammer, S., Hildebrand, A., Kirschner, A., Pagel, P., Geissler, B., Smialowski, P., Blöchl, F., Oesterheld, M., Schmidt, T., Strack, N., Theis, F.J., Ruepp, A., Frishman, D. An evolutionary and structural characterization of mammalian protein complex organization. BMC Genomics 9:629 (2008)

2007 and earlier

  • Artamonova, I.I., Frishman, G., Frishman, D. Applying negative rule mining to improve genome annotation. BMC Bioinformatics 8:261 (2007)
  • Brügger, K., Chen, L., Stark, M., Zibat, A., Redder, P., Ruepp, A., Awayez, M., She, Q., Garrett, R.A., Klenk, H.P. The genome of Hyperthermus butylicus: A sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 °C. Archaea 2, 127-135 (2007)
  • Datson, N.A., Morsink, M.C., Atanasova, S., Armstrong, V.W., Zischler, H., Schlumbohm, C., Dutilh, B.E., Huynen, M.A., Wägele, B., Ruepp, A., de Kloet, E.R., 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 8:190 (2007)
  • Dietmann, S., Aguilar, D., Mader, M.T., Oesterheld, M., Ruepp, A., Stuempflen, V., Mewes, H.-W. Resources and tools for investigating biomolecular networks in mammals. Curr. Pharm. Des. 12, 3723-3734 (2006)
  • Güldener, U., Münsterkötter, M., Oesterheld, M., Pagel, P., Ruepp, A., Mewes, H.-W., Stuempflen, V. MPact: The MIPS protein interaction resource on yeast. Nucleic Acids Res. 34, 436-441 (2006)
  • 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. 29, 609-625 (2006)
  • Lehner, A., Grimm, M., Rattei, T., Ruepp, A., Frishman, D., Manzardo, G.G.G., Stephan, R. Cloning and characterization of Enterobacter sakazakii pigment genes and in situ spectroscopic analysis of the pigment. FEMS Microbiol. Lett. 265, 244-248 (2006)
  • Mewes, H.-W., Frishman, D., Mayer, K.F.X., Münsterkötter, M., Noubibou, O., Pagel, P., Rattei, T., Oesterheld, M., Ruepp, A., Stuempflen, V. MIPS: Analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res. 34, D169-D172 (2006)
  • 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. 34, D705-D711 (2006)
  • Ruepp, A., Mewes, H.-W. Prediction and classification of protein functions. Drug Discov. To. Techn. 3, 145-151 (2006)
  • Ruepp, A., Doudieu, O.N., van den Oever, J., Brauner, B., Dunger-Kaltenbach, I., Fobo, G., Frishman, G., Montrone, C., Skornia, C., Wanka, S., Rattei, T., Pagel, P., Riley, M.L., Frishman, D., Surmeli, D., Tetko, I.V., Oesterheld, M., Stuempflen, V., Mewes, H.-W. The mouse functional genome database (MfunGD) :Functional annotation of proteins in the light of their cellular context. Nucleic Acids Res. 34, D568–D571 (2006)
  • Artamonova, I.I., Frishman, G., Gelfand, M.S., Frishman, D. Mining sequence annotation databanks for association patterns. Bioinformatics 21, 3, 49-57 (2005)
  • Pagel, P., Kovac, S., Oesterheld, M., Brauner, B., Dunger-Kaltenbach, I., Frishman, G., Montrone, C., Mark, P., Stuempflen, V., Mewes, H.-W., Ruepp, A. The MIPS mammalian protein-protein interaction database. Bioinformatics 21, 832-834 (2005)
  • Tetko, I.V., Brauner, B., Dunger-Kaltenbach, I., Frishman, G., Montrone, C., Fobo, G., Ruepp, A., Antonov, A.V. MIPS bacterial genomes functional annotation benchmark dataset. Bioinformatics 21, 2520-2521 (2005)
  • Tetko, I.V., Facius, A., Ruepp, A., Mewes, H.-W. Super paramagnetic clustering of protein sequences. BMC Bioinformatics 6:82 (2005)
  • Mewes, H.-W., Amid, C., Arnold, R., Frishman, D., Güldener, U., Mannhaupt, G., Münsterkötter, M., Pagel, P., Strack, N., Stuempflen, V., Warfsmann, J., Ruepp, A. MIPS : analysis and annotation of proteins from whole genomes. Nucleic Acids Res. 32, D41-D44 (2004)
  • Ruepp, A., Zollner, A., Maier, D., Albermann, K., Hani, J., Mokrejs, M., Tetko, I.V., Güldener, U., Mannhaupt, G., Münsterkötter, M., Mewes, H.-W. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res. 32, 5539-5545 (2004)

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