All Publications of the Group Biocuration for Digital Health

2023 Scientific Article in Cardiovascular Diabetology Cardiovasc. Diabetol. 22:141 (2023)

Shi, M. ; Han, S. ; Klier, K. ; Fobo, G. ; Montrone, C. ; Yu, S. ; Harada, M. ; Henning, A.K. ; Friedrich, N. ; ... ; Prehn, C. ; Adamski, J. ; Ruepp, A. ; Peters, A. ; Wang-Sattler, R.

Identification of candidate metabolite biomarkers for metabolic syndrome and its five components in population-based human cohorts.

2022 Nature Cardiovascular Research Nat. Cardio. Res. 1, 529-531 (2022)

Spielmann, N. ; Miller, G. ; Oprea, T.I. ; Hsu, C.W. ; Fobo, G. ; Frishman, G. ; Montrone, C. ; Haseli Mashhadi, H. ; ... ; Leuchtenberger, S. ; Ruepp, A. ; Sanz-Moreno, A. ; Cho, Y.-L. ; Teperino, R. ; Brandmaier, S. ; Sharma, S. ; Galter, I. ; Östereicher, M.A. ; Zapf, L. ; Mayer-Kuckuk, P. ; Gilly, A. ; Rayner, N.W. ; Aguilar-Pimentel, J.A. ; Becker, L. ; Garrett, L. ; Hölter, S.M. ; Amarie, O.V. ; Calzada-Wack, J. ; Klein-Rodewald, T. ; da Silva Buttkus, P. ; Lengger, C. ; Stoeger, C. ; Gerlini, R. ; Rathkolb, B. ; Mayr, D. ; Mckay, M.

Publisher Correction: Extensive identification of genes involved in congenital and structural heart disorders and cardiomyopathy (Nature Cardiovascular Research, (2022), 1, 2, (157-173), 10.1038/s44161-022-00018-8).

2022 Scientific Article in Nucleic Acids Research Nucleic Acids Res. 51, D539-D545 (2022)

Tsitsiridis, G. ; Steinkamp, R. ; Giurgiu, M. ; Brauner, B. ; Fobo, G. ; Frishman, G. ; Montrone, C. ; Ruepp, A.

CORUM: The comprehensive resource of mammalian protein complexes-2022.

2022 Scientific Article in Viruses Viruses 14:1591 (2022)

Liu, H. ; Bergant, V. ; Frishman, G. ; Ruepp, A. ; Pichlmair, A. ; Vincendeau, M. ; Frishman, D.

Influenza A virus infection reactivates human endogenous retroviruses associated with modulation of antiviral immunity.

2022 Scientific Article in Nature Cardiovascular Research Nat. Cardio. Res. 1, 157-173 (2022)

Spielmann, N. ; Miller, G. ; Oprea, T.I. ; Hsu, C.-W. ; Fobo, G. ; Frishman, G. ; Montrone, C. ; Hasel Mashhadi, H. ; ... ; Leuchtenberger, S. ; Ruepp, A. ; Sanz-Moreno, A. ; Cho, Y.-L. ; Teperino, R. ; Brandmaier, S. ; Sharma, S. ; Galter, I. ; Östereicher, M.A. ; Zapf, L. ; Mayer-Kuckuk, P. ; Gilly, A. ; Rayner, N.W. ; Zeggini, E. ; Grallert, H. ; Wurst, W. ; Marschall, S. ; Fuchs, H. ; Gailus-Durner, V. ; Hrabě de Angelis, M. ; IMPC Consortium (Aguilar-Pimentel, J.A. ; Becker, L. ; Garrett, L. ; Hölter, S.M. ; Amarie, O.V. ; Calzada-Wack, J. ; Klein-Rodewald, T. ; Lengger, C. ; Stoeger, C. ; Gerlini, R. ; Rathkolb, B. ; Seisenberger, C. ; Bürger, A. ; Giesert, F.)

Extensive identification of genes involved in congenital and structural heart disorders and cardiomyopathy.

2021 Molecular Systems Biology Mol. Syst. Biol. 17:e10851 (2021)

Ostaszewski, M. ; Niarakis, A. ; Mazein, A. ; Kuperstein, I. ; ... ; Ruepp, A. ; Fobo, G. ; Montrone, C. ; Brauner, B. ; Frishman, G. ; Schmiester, L. ; Hasenauer, J. ; Schneider, R.

COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms (vol 17, e10387, 2021).

2021 Scientific Article in Molecular Systems Biology Mol. Syst. Biol. 17:e10387 (2021)

Ostaszewski, M. ; Niarakis, A. ; Mazein, A. ; Kuperstein, I. ; ... ; Ruepp, A. ; Fobo, G. ; Montrone, C. ; Brauner, B. ; Frishman, G. ; Hasenauer, J. ; Schneider, R.

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms.

2021 Scientific Article in Cell Stem Cell Cell Stem Cell 28, 1566-1581.e8 (2021)

Padmanabhan Nair, V. ; Liu, H. ; Ciceri, G. ; Jungverdorben, J. ; Frishman, G. ; ... ; Rothenaigner, I. ; Schorpp, K.K. ; Klepper, L. ; Ruepp, A. ; Hadian, K. ; Vincendeau, M.

Activation of HERV-K(HML-2) disrupts cortical patterning and neuronal differentiation by increasing NTRK3.

2021 Scientific Reports Sci. Rep. 11:3582 (2021)

Kataka, E. ; Zaucha, J. ; Frishman, G. ; Ruepp, A. ; Frishman, D.

Author Correction: Edgetic perturbation signatures represent known and novel cancer biomarkers (Scientific Reports, (2020), 10, 1, (4350), 10.1038/s41598-020-61422-3).

2020 Scientific Article in Nature Communications Nat. Commun. 11:1148 (2020)

Arnold, M. ; Nho, K. ; Kueider-Paisley, A. ; Massaro, T. ; Huynh, K. ; Brauner, B. ; ... ; Kastenmüller, G.

Sex and APOE ε4 genotype modify the Alzheimer’s disease serum metabolome.

2020 Scientific Article in Scientific Reports Sci. Rep. 10:4350 (2020)

Kataka, E. ; Zaucha, J. ; Frishman, G. ; Ruepp, A. ; Frishman, D.

Edgetic perturbation signatures represent known and novel cancer biomarkers.

2019 Scientific Article in Nucleic Acids Research Nucleic Acids Res. 47, D559-D563 (2019)

Giurgiu, M. ; Reinhard, J. ; Brauner, B. ; Dunger-Kaltenbach, I. ; Fobo, G. ; Frishman, D. ; Montrone, C. ; Ruepp, A.

CORUM: The comprehensive resource of mammalian protein complexes2019.

2018 Scientific Article in Orphanet Journal of Rare Diseases : OJRD Orphanet J. Rare Dis. 13:22 (2018)

Adler, A. ; Kirchmeier, P. ; Reinhard, J. ; Brauner, B. ; Dunger, I. ; Fobo, G. ; Frishman, G. ; Montrone, C. ; Mewes, H.-W. ; Arnold, M. ; Ruepp, A.

PhenoDis: A comprehensive database for phenotypic characterization of rare cardiac diseases.

2017 Scientific Article in Scientific Reports Sci. Rep. 7:4555 (2017)

Allebrandt, K.V. ; Teder-Laving, M. ; Cusumano, P. ; Frishman, G. ; Levandovski, R. ; Ruepp, A. ; ... ; De Pittà, C.

Identifying pathways modulating sleep duration: From genomics to transcriptomics.

2017 Scientific Article in Heart Heart 103, 1278-1285 (2017)

Ward-Caviness, C.K. ; Xu, T. ; Aspelund, T. ; Thorand, B. ; Montrone, C. ; Meisinger, C. ; Dunger-Kaltenbach, I. ; Zierer, A. ; Yu, Z. ; Helgadottir, I.R. ; Harris, T.B. ; ... ; Waldenberger, M. ; Prehn, C. ; Suhre, K. ; Adamski, J. ; Ruepp, A. ; Wang-Sattler, R. ; Peters, A.

Improvement of myocardial infarction risk prediction via inflammation-associated metabolite biomarkers.

2016 Scientific Article in Cell Chemical Biology Cell Chem. Bio. 23, 1302-1313 (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.

Systematic identification of pharmacological targets from small-molecule phenotypic screens.

2016 Scientific Article in PLoS ONE PLoS ONE 11:e0163362 (2016)

Kostareva, A. ; Kiselev, A. ; Gudkova, A. ; Frishman, G. ; Ruepp, A. ; Frishman, D. ; Smolina, N. ; ... ; Shlyakhto, E.

Genetic spectrum of idiopathic restrictive cardiomyopathy uncovered by next-generation sequencing.

2015 Scientific Article in Diabetes Care Diabetes Care 38, 1858-1867 (2015)

Xu, T. ; Brandmaier, S. ; Messias, A.C. ; Herder, C. ; Draisma, H.H. ; Demirkan, A. ; Yu, Z. ; Ried, J.S. ; ... ; Heier, M. ; Campillos, M. ; Fobo, G. ; Stark, R.G. ; Adam, J. ; Chi, S. ; Rotter, M. ; Panni, T. ; Quante, A.S. ; Prehn, C. ; Römisch-Margl, W. ; Kastenmüller, G. ; Meisinger, C. ; Thorand, B. ; Ruepp, A. ; Hrabě de Angelis, M. ; Wichmann, H.-E. ; Strauch, K. ; Gieger, C. ; Suhre, K. ; Adamski, J. ; Illig, T. ; Peters, A. ; Meitinger, T. ; Wang-Sattler, R.

Effects of metformin on metabolite profiles and LDL cholesterol in patients with type 2 diabetes.

2015 Scientific Article in Neuron Neuron 86, 1189-1202 (2015)

Knauer-Arloth, J. ; Bogdan, R. ; Weber, P. ; Frishman, G. ; Menke, A. ; ... ; Trümbach, D. ; Wurst, W. ; Ruepp, A. ; Binder, E.B.

Genetic differences in the immediate transcriptome response to stress predict risk-related brain function and psychiatric disorders.

2014 Scientific Article in European Journal of Epidemiology Eur. J. Epidemiol. 29, 325-336 (2014)

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.

2014 Scientific Article in Psychological Medicine Psychol. Med. 44, 2309-2322 (2014)

Mehta, D. ; Newport, D.J. ; Frishman, G. ; Kraus, L. ; Rex-Haffner, M. ; Ritchie, J.C. ; ... ; Ruepp, A. ; Binder, E.B.

Early predictive biomarkers for postpartum depression point to a role for estrogen receptor signaling.

2014 Scientific Article in Nucleic Acids Research Nucleic Acids Res. 42, D396-D400 (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.

2014 Scientific Article in Nucleic Acids Research Nucleic Acids Res. 42, D671-D676 (2014)

Bleves, S. ; Dunger, I. ; Walter, M.C. ; Frangoulidis, D. ; Kastenmüller, G. ; Voulhoux, R. ; Ruepp, A.

HoPaCI-DB: Host-Pseudomonas and Coxiella interaction database.

2013 Scientific Article in PLoS ONE PLoS ONE 8:e70348 (2013)

Montrone, C. ; Kokkaliaris, K.D. ; Loeffler, D. ; Lechner, M. ; Kastenmüller, G. ; Schroeder, T. ; Ruepp, A.

HSC-Explorer: A curated database for hematopoietic stem cells.

2012 Scientific Article in Methods in Molecular Biology Methods Mol. Biol. 822, 249-260 (2012)

Ruepp, A. ; Kowarsch, A. ; Theis, F.J.

PhenomiR: MicroRNAs in human diseases and biological processes.

2012 Scientific Article in Genome Biology Genome Biol. 13:R62 (2012)

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.

2011 Scientific Article in BMC Systems Biology BMC Syst. Biol. 5:136 (2011)

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.

2010 Scientific Article in Nucleic Acids Research Nucleic Acids Res. 38, 1, D497-D501 (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.

2010 Scientific Article in Nucleic Acids Research Nucleic Acids Res. 39, 1, D220-D224 (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.

2010 Scientific Article in PLoS ONE PLoS ONE 5:e11154 (2010)

Kowarsch, A. ; Marr, C. ; Schmidl, D. ; Ruepp, A. ; Theis, F.J.

Tissue-specific target analysis of disease-associated microRNAs in human signaling pathways.

2010 Scientific Article in Genome Biology Genome Biol. 11:R6 (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.

2010 Scientific Article in Nucleic Acids Research Nucleic Acids Res. 38, 1, D540-D544 (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.

2009 Scientific Article in Journal of Molecular Microbiology and Biotechnology J. Mol. Microbiol. Biotechnol. 16, 81-90 (2009)

Antranikian, G. ; Ruepp, A. ; Gordon, P.M. ; Ballschmiter, M. ; Zibat, A. ; ... ; Klenk, H.P.

Rapid access to genes of biotechnologically useful enzymes by partial genome sequencing: The thermoalkaliphile Anaerobranca gottschalkii.

2009 Scientific Article in Bioinformatics Bioinformatics 25, 141-143 (2009)

Wägele, B. ; Dunger-Kaltenbach, I. ; Fobo, G. ; Montrone, C. ; Mewes, H.-W. ; Ruepp, A.

CRONOS: The cross-reference navigation server.

2008 Scientific Article in BMC Genomics BMC Genomics 9:629 (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.

2008 Scientific Article in Journal of Food Protection J. Food Prot. 71, 13-18 (2008)

Grimm, M. ; Stephan, R. ; Iversen, C. ; Manzardo, G.G. ; ... ; Ruepp, A. ; Lehner, A.

Cellulose as an extracellular matrix component present in Enterobacter sakazakii biofilms.

2008 Scientific Article in Nucleic Acids Research Nucleic Acids Res. 36, W140-W144 (2008)

Wägele, B. ; Schmidt, T. ; Mewes, H.-W. ; Ruepp, A.

OREST: The online resource for EST analysis.

2008 Scientific Article in Genomics Genomics 91, 553-554 (2008)

Pfeiffer, F. ; Schuster, S.C. ; Broicher, A. ; Falb, M. ; ... ; Ruepp, A. ; Oesterhelt, D.

Genome sequences of Halobacterium salinarum: A reply.

2008 Scientific Article in Nucleic Acids Research Nucleic Acids Res. 36, D646-D650 (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.

2008 Scientific Article in Nucleic Acids Research Nucleic Acids Res. 36, D196-D201 (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.

2008 Scientific Article in Genomics Genomics 91, 335-346 (2008)

Pfeiffer, F. ; Schuster, S.C. ; Broicher, A. ; Falb, M. ; ... ; Ruepp, A. ; Oesterhelt, D.

Evolution in the laboratory: The genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1.

2007 Scientific Article in BMC Bioinformatics BMC Bioinformatics 8:261 (2007)

Artamonova, I.I. ; Frishman, G. ; Frishman, D.

Applying negative rule mining to improve genome annotation.

2007 Scientific Article in BMC Genomics BMC Genomics 8:190 (2007)

Datson, N.A. ; Morsink, M.C. ; Atanasova, S. ; Armstrong, V.W. ; ... ; Wägele, B. ; Ruepp, A. ; 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.

2007 Scientific Article in Archaea Archaea 2, 127-135 (2007)

Brügger, K. ; Chen, L. ; Stark, M. ; Zibat, A. ; ... ; Ruepp, A. ; Klenk, H.P.

The genome of Hyperthermus butylicus: A sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 °C.

2006 Scientific Article in Systematic and Applied Microbiology Syst. Appl. Microbiol. 29, 609-625 (2006)

Lehner, A. ; Riedel, K. ; Rattei, T. ; Ruepp, A. ; Frishman, D. ; ... ; Stephan, R.

Molecular characterization of the alpha-glucosidase activity in Enterobacter sakazakii reveals the presence of a putative gene cluster for palatinose metabolism.

2006 Scientific Article in Drug Discovery Today: Technologies Drug Discov. To. Techn. 3, 145-151 (2006)

Ruepp, A. ; Mewes, H.-W.

Prediction and classification of protein functions.

2006 Scientific Article in Nucleic Acids Research Nucleic Acids Res. 34, D568–D571 (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.