Rainer König

Prof. Dr. Rainer König

Netzwerkmodellierung · Abteilungsleiter

Telefon: +49 3641 532-1189 Telefax: +49 3641 532-2189 E-Mail: rainer.koenig@leibniz-hki.de

Forschungsschwerpunkte
  • Regulationsanalyse von Metabolismus und Signaltransduktion
  • Modellierung zellulärer Netzwerke
  • Lineare Programmierung
Curriculum vitae

Wissenschaftlicher Werdegang

2013 Rufannahme der W2 Professur Systembiologie der Sepsis an der Medizinischen Fakultät der Universität Jena
2010 Habilitation in der Bioinformatik, Universität Heidelberg
2007-2013 Forschungsgruppenleiter am Institut für Pharmazie und Molekulare Biotechnologie, Universität Heidelberg
2004-2007 Assistent (C1) am Institut für Pharmazie und Molekulare Biotechnologie, Universität Heidelberg
2000-2004 Wiss. Mitarbeiter am Deutschen Krebsforschungszentrum, Heidelberg
1999 Dr. sc. hum. in Biochemie, magna cum laude, Universität Heidelberg
1997 Staatsexamen in Physik und Mathematik, Universität Heidelberg
1996 Physik Diplom, Universität Heidelberg

Auszeichnungen · Ämter · wissenschaftliche Aktivitäten

Ab 2014 Projektleiter des eMed/BMBF Projekts Modellierung von Telomer- Erhaltungsmechanismusnetzwerken in Tumoren
seit 2013 Koordinator des eBio/BMBF Projekts Systembiologie der metabolischen Transformation in Brustkrebs (SYSMET-BC)
seit 2013 Projektleiter des BMBF/IFB Projektes Systembiologie der Sepsis
seit 2012 Projektleiter des BMBF/CancerSys Systembiologieprojekts Analyse Genregulatorischer Netzwerke in neuroektodermalen Tumoren (MYCNET)
seit 2011 Projektleiter des Helmholtz/DKFZ/MOST Israel Projekts Systembiologische Untersuchung der Telomerbiologie
Publikationen

Hassan MIA, Kruse J, Krüger T, Dahse HM, Cseresnyés Z, Blango MG, Slevogt H, Hörhold F, Ast V, König R, Figge MT, Kniemeyer O, Brakhage AA, Voigt K (2020) Functional surface proteomic profiling reveals the host heat-shock protein A8 as a mediator of Lichtheimia corymbifera recognition by murine alveolar macrophages. Environmental Microbiology [Epub ahead of print] Details PubMed Open Access

Sommerfeld O, Medyukhina A, Neugebauer S, Ghait M, Ulferts S, Lupp A, König R, Wetzker R, Schulz S, Figge MT, Bauer M, Press AT (2020) Targeting complement C5a receptor 1 for the treatment of immunosuppression in sepsis. Molecular Therapy [Accepted] Details

Eisel D, Das K, Dickes E, König R, Osen W, Eichmüller SB (2019) Cognate interaction with CD4+ T cells instructs tumor-associated macrophages to acquire M1-like phenotype. Front Immunol 10, 219. Details PubMed Open Access PDF

Kolte A, König R (2019) Temporal progression of gene regulation of peripheral white blood cells explains gender dimorphism of critically ill patients after trauma. Mol Med 25(1), 19. Details PubMed Open Access PDF

Kresinsky A, Schnöder TM, Jacobsen ID, Rauner M, Hofbauer LC, Ast V, König R, Hoffmann B, Svensson CM, Figge MT, Hilger I, Heidel FH, Böhmer FD, Müller JP (2019) Lack of CD45 in FLT3-ITD mice results in a myeloproliferative phenotype, cortical porosity, and ectopic bone formation. Oncogene 38(24), 4773-4787. Details PubMed

Mallm JP, Iskar M, Ishaque N, Klett LC, Kugler SJ, Muino JM, Teif VB, Poos AM, Großmann S, Erdel F, Tavernari D, Koser SD, Schumacher S, Brors B, König R, Remondini D, Vingron M, Stilgenbauer S, Lichter P, Zapatka M, Mertens D, Rippe K (2019) Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks. Mol Sys Biol 15(5), e8339. Details PubMed Open Access PDF

Ansari SS, Sharma AK, Soni H, Ali DM, Tews B, König R, Eibl H, Berger MR (2018) Induction of ER and mitochondrial stress by the alkylphosphocholine erufosine in oral squamous cell carcinoma cells. Cell Death and Disease 9, 296. Details Open Access

Aramillo Irizar P, Schäuble S, Esser D, Groth M, Frahm C, Priebe S, Baumgart M, Hartmann N, Marthandan S, Menzel U, Müller J, Schmidt S, Ast V, Caliebe A, König R, Krawczak M, Ristow M, Schuster S, Cellerino A, Diekmann S, Englert C, Hemmerich P, Sühnel J, Guthke R, Witte OW, Platzer M, Ruppin E, Kaleta C (2018) Transcriptomic alterations during ageing reflect the shift from cancer to degenerative diseases in the elderly. Nat Commun 9(1), 327. Details PubMed Open Access

Ast V, Kordaß T, Oswald M, Kolte A, Eisel D, Osen W, Eichmüller SB, Berndt A, König R (2018) MiR-192, miR-200c and miR-17 are fibroblast-mediated inhibitors of colorectal cancer invasion. Oncotarget 9(85), 35559-35580. Details PubMed Open Access

Kresinsky A, Bauer R, Schnöder TM, Berg T, Meyer D, Ast V, König R, Serve H, Heidel FH, Böhmer FD, Müller JP (2018) Loss of DEP-1 (Ptprj) promotes myeloproliferative disease in FLT3-ITD acute myeloid leukemia. Haematologica 103(11), e505-e509. Details PubMed Open Access

Meinel C, Spartà G, Dahse HM, Hörhold F, König R, Westermann M, Cseresnyés Z, Coldewey SM, Figge MT, Hammerschmidt S, Skerka C, Zipfel PF (2018) Streptococcus pneumoniae from patients with hemolytic uremic syndrome binds human plasminogen via the surface protein PspC and uses plasmin to damage human endothelial cells. Journal of Infectious Diseases 217(3), 358-370. Details PubMed Open Access

Minner S, Lutz J, Hube-Magg C, Kluth M, Simon R, Höflmayer D, Burandt E, Tsourlakis MC, Sauter G, Büscheck F, Wilczak W, Steurer S, Schlomm T, Huland H, Graefen M, Haese A, Heinzer H, Jacobsen F, Hinsch A, Poos A, Oswald M, Rippe K, König R, Schroeder C (2018) Loss of CCAAT/Enhancer binding protein alpha (CEBPA) is linked to poor prognosis in PTEN deleted and TMPRSS2:ERG fusion type prostate cancers. Prostate [Accepted] Details PubMed

Ansari SS, Sharma AK, Zepp M, Ivanova E, Bergmann F, König R, Berger MR (2017) Upregulation of cell cycle genes in head and neck cancer patients may be antagonized by erufosine's down regulation of cell cycle processes in OSCC cell. Oncotarget 9, 5797-5810. Details

Markowsky P, Reith S, Zuber TE, König R, Rohr K, Schnörr C (2017) Segmentation of cell structures using Model-Based Set Covering with iterative reweighting In: IEEE International Symposium on Biomedical Imaging, Melbourne, Australia, 04/18/2017-04/21/2017, pp. 392-396.IEEE. ISBN: 1945-8452. Details

Saraiva JP, Oswald M, Biering A, Röll D, Assmann C, Klassert T, Blaess M, Czakai K, Claus R, Löffler J, Slevogt H, König R. (2017) Fungal biomarker discovery by integration of classifiers. BMC Genomics 18, 601. Details

Saraiva JP, Zubiria-Barrera C, Klassert T, Lautenbach MJ, Blaess M, Claus RA, Slevogt H, König R (2017) Combination of classifiers identifies fungal-specific activation of lysosome genes in human monocytes Front Microbiol 8, 2366. Details

Dieckmann A, Babin V, Harari Y, Eils R, König R, Kupiec M, Luke B (2016) Role of the ESCRT Complexes in Telomere Biology mBio 7(6), e01793-16. Details

Gietzelt M, Ganzinger M, Höfer T, Knaup-Gregori P, König R, Löpprich M, Poos A (2016) The Use of Tools, Modelling Methods, Data Types, and Endpoints in Systems Medicine: A Survey on Projects of the e:Med-Programme Stud Health Technol Inform 228, 670-674. Details

Kordaß T, Weber CEM, Oswald M, Ast V, Bernhardt M, Novak D, Utikal J, Eichmüller SB, König R. (2016) SOX5 is involved in balanced MITF regulation in human melanoma cells BMC Medical Genomics, 9(1):10. , Details

Petersen I, Salah F, Ebbinghaus M, Muley V, Zhou Z, Al-Saadi K, Pacyna-Gengelbach M, O'Sullivan GA, Betz H, König R, Wang ZQ, Bräuer R. (2016) Tumor suppression in mice lacking GABARAP, an Atg8/LC3 family member implicated in autophagy, is associated with alterations in cytokine secretion and cell death Cell Death and Disease 7, e2205. Details

Plaimas K, König R (2016) Identifying antimalarial drug targets by cellular network analysis In: Rodriguez-Morales A (ed.) Current Topics in Malaria pp. 267-283. InTech, Rieka. ISBN: 978-953-51-2789. (Review) Details Open Access

Poos AM, Maicher A, Dieckmann AK, Oswald M, Eils R, Kupiec M, Luke B, König R (2016) Mixed Integer Linear Programming based machine learning approach identifies regulators of telomerase in yeast Nucleic Acids Res 44(10), e93. Details

Saraiva J, Oswald M, Biering A, Assmann C, Klassert T, Blaess M, Czakai K, Claus R, Löffler J, Slevogt H, König R (2016) Integrating classifiers across datasets improves consistency of biomarker predictions in sepsis. In: Proceedings of the 6th IFAC Conference on Foundations of Systems Biology in Engineering IFAC-PapersOnLine, Magdeburg, 10/09/2016-10/12/2016, 49, pp. 95-102.Elsevier ScienceDirect. Details Open Access

Sharma AK, Eils R, König R (2016) Copy number alterations in enzyme-coding and cancer-causing genes reprogram tumor metabolism Cancer Research 76(14), 4058-4067. Details

Harder N, Batra R, Diessl N, Gogolin S, Eils R, Westermann F, König R, Rohr K (2015) Large-scale tracking and classification for automatic analysis of cell migration and proliferation, and experimental optimization of high-throughput screens of neuroblastoma cells. Cytometry A, 87(6):524-40 , Details PubMed

Khandelwal N, Breinig M, Speck T, Michels T, Kreutzer C, Sorrentino A, Sharma AK, Umansky L, Conrad H, Poschke I, Offringa R, König R, Bernhard H, Machlenkin A, Boutros M, Beckhove P (2015) A high-throughput RNAi screen for detection of immune-checkpoint molecules that mediate tumor resistance to cytotoxic T lymphocytes. EMBO Mol Med, 7(4):450-63 , Details PubMed

Shukla K, Sharma AK, Ward A, Will R, Hielscher T, Balwierz A, Breunig C, Münstermann E, König R, Keklikoglou I, Wiemann S (2015) MicroRNA-30c-2-3p negatively regulates NF-κB signaling and cell cycle progression through downregulation of TRADD and CCNE1 in breast cancer. Mol Oncol 9(6), 1106-1119. Details PubMed

Stark H, Fichtner M, König R, Lorkowski S, Schuster S (2015) Causes of upregulation of glycolysis in lymphocytes upon stimulation. A comparison with other cell types. Biochimie 118, 185-194. Details PubMed

Kool M, Jones DT, Jäger N, Northcott PA, Pugh TJ, Hovestadt V, Piro RM, Esparza LA, Markant SL, Remke M, Milde T, Bourdeaut F, Ryzhova M, Sturm D, Pfaff E, Stark S, Hutter S, Seker-Cin H, Johann P, Bender S, Schmidt C, Rausch T, Shih D, Reimand J, Sieber L, Wittmann A, Linke L, Witt H, Weber UD, Zapatka M, König R, Beroukhim R, Bergthold G, van Sluis P, Volckmann R, Koster J, Versteeg R, Schmidt S, Wolf S, Lawerenz C, Bartholomae CC, von Kalle C, Unterberg A, Herold-Mende C, Hofer S, Kulozik AE, von Deimling A, Scheurlen W, Felsberg J, Reifenberger G, Hasselblatt M, Crawford JR, Grant GA, Jabado N, Perry A, Cowdrey C, Croul S, Zadeh G, Korbel JO, Doz F, Delattre O, Bader GD, McCabe MG, Collins VP, Kieran MW, Cho YJ, Pomeroy SL, Witt O, Brors B, Taylor MD, Schüller U, Korshunov A, Eils R, Wechsler-Reya RJ, Lichter P, Pfister SM (2014) Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition. Cancer Cell 25(3), 393-405. Details PubMed

Piro RM, Wiesberg S, Schramm G, Rebel N, Oswald M, Eils R, Reinelt G, König R (2014) Network topology-based detection of differential gene regulation and regulatory switches in cell metabolism and signaling. BMC Syst Biol 8, 56. Details PubMed

Schacht T, Oswald M, Eils R, Eichmüller SB, König R (2014) Estimating the activity of transcription factors by the effect on their target genes. Bioinformatics 30(17), i401-i407. Details PubMed

Sonntag J, Bender C, Soons Z, Aulmann S, von der Heyde S, Nietert M, Lier A, König R, Wiemann S, Beißbarth T, Sinn HP, Schneeweiss A, Korf U (2014) Reverse phase protein array based tumor profiling identifies a biomarker signature for risk classification of hormone receptor-positive breast cancer Trans Proteomics 2, 52-59. Details

Suratanee A, Schaefer MH, Betts MJ, Soons Z, Mannsperger H, Harder N, Oswald M, Gipp M, Ramminger E, Marcus G, Männer R, Rohr K, Wanker E, Russell RB, Andrade-Navarro MA, Eils R, König R (2014) Characterizing Protein Interactions Employing a Genome-Wide siRNA Cellular Phenotyping Screen. PLOS Comput Biol 10(9), e1003814. Details PubMed

Ummanni R, Mannsperger HA, Sonntag J, Oswald M, Sharma AK, König R, Korf U (2014) Evaluation of reverse phase protein array (RPPA)-based pathway-activation profiling in 84 non-small cell lung cancer (NSCLC) cell lines as platform for cancer proteomics and biomarker discovery. Biochim Biophys Acta 1844(5), 950-959. Details PubMed

Ward A, Shukla K, Balwierz A, Soons Z, König R, Sahin O, Wiemann S (2014) MicroRNA-519a is a novel oncomir conferring tamoxifen resistance by targeting a network of tumour-suppressor genes in ER+ breast cancer. J Pathol 233(4), 368-379. Details PubMed

Aschoff M, Hotz-Wagenblatt A, Glatting KH, Fischer M, Eils R, König R (2013) SplicingCompass: differential splicing detection using RNA-seq data. Bioinformatics 29(9), 1141-1148. Details PubMed

Gogolin S, Batra R, Harder N, Ehemann V, Paffhausen T, Diessl N, Sagulenko V, Benner A, Gade S, Nolte I, Rohr K, König R, Westermann F (2013) MYCN-mediated overexpression of mitotic spindle regulatory genes and loss of p53-p21 function jointly support the survival of tetraploid neuroblastoma cells. Cancer Lett 331(1), 35-45. Details PubMed

Piro RM, Molineris I, Di Cunto F, Eils R, König R (2013) Disease-gene discovery by integration of 3D gene expression and transcription factor binding affinities. Bioinformatics 29(4), 468-475. Details PubMed

Plaimas K, Wang Y, Rotimi SO, Olasehinde G, Fatumo S, Lanzer M, Adebiyi E, König R (2013) Computational and experimental analysis identified 6-diazo-5-oxonorleucine as a potential agent for treating infection by Plasmodium falciparum. Infect Genet Evol 20, 389-395. Details PubMed

Reuss DE, Piro RM, Jones DT, Simon M, Ketter R, Kool M, Becker A, Sahm F, Pusch S, Meyer J, Hagenlocher C, Schweizer L, Capper D, Kickingereder P, Mucha J, Koelsche C, Jäger N, Santarius T, Tarpey PS, Stephens PJ, Andrew Futreal P, Wellenreuther R, Kraus J, Lenartz D, Herold-Mende C, Hartmann C, Mawrin C, Giese N, Eils R, Collins VP, König R, Wiestler OD, Pfister SM, von Deimling A (2013) Secretory meningiomas are defined by combined KLF4 K409Q and TRAF7 mutations. Acta Neuropathol 125(3), 351-358. Details PubMed

Schweizer L, Koelsche C, Sahm F, Piro RM, Capper D, Reuss DE, Pusch S, Habel A, Meyer J, Göck T, Jones DT, Mawrin C, Schittenhelm J, Becker A, Heim S, Simon M, Herold-Mende C, Mechtersheimer G, Paulus W, König R, Wiestler OD, Pfister SM, von Deimling A (2013) Meningeal hemangiopericytoma and solitary fibrous tumors carry the NAB2-STAT6 fusion and can be diagnosed by nuclear expression of STAT6 protein. Acta Neuropathol 125(5), 651-658. Details PubMed

Sharma AK, König R (2013) Metabolic network modeling approaches for investigating the "hungry cancer". Semin Cancer Biol 23(4), 227-234. (Review) Details PubMed

Tönjes M, Barbus S, Park YJ, Wang W, Schlotter M, Lindroth AM, Pleier SV, Bai AH, Karra D, Piro RM, Felsberg J, Addington A, Lemke D, Weibrecht I, Hovestadt V, Rolli CG, Campos B, Turcan S, Sturm D, Witt H, Chan TA, Herold-Mende C, Kemkemer R, König R, Schmidt K, Hull WE, Pfister SM, Jugold M, Hutson SM, Plass C, Okun JG, Reifenberger G, Lichter P, Radlwimmer B (2013) BCAT1 promotes cell proliferation through amino acid catabolism in gliomas carrying wild-type IDH1. Nat Med 19(7), 901-908. Details PubMed

Batra R, Harder N, Gogolin S, Diessl N, Soons Z, Jäger-Schmidt C, Lawerenz C, Eils R, Rohr K, Westermann F, König R (2012) Time-lapse imaging of neuroblastoma cells to determine cell fate upon gene knockdown. PLOS One 7(12), e50988. Details PubMed

Costa B, Kean MJ, Ast V, Knight JD, Mett A, Levy Z, Ceccarelli DF, Badillo BG, Eils R, König R, Gingras AC, Fainzilber M (2012) STK25 protein mediates TrkA and CCM2 protein-dependent death in pediatric tumor cells of neural origin. J Biol Chem 287(35), 29285-29289. Details PubMed

Bauer T, Eils R, König R (2011) RIP: the regulatory interaction predictor - a machine learning-based approach for predicting target genes of transcription factors. Bioinformatics 27(16), 2239-2247. Details PubMed

Bauer T, König R (2011) Automatisierte regulatorische Interaktionsvorhersage. Laborwelt (6), 32-34. Details

Fatumo S, Plaimas K, Adebiyi E, König R (2011) Comparing metabolic network models based on genomic and automatically inferred enzyme information from Plasmodium and its human host to define drug targets in silico. Infect Genet Evol 11(4), 708-715. Details PubMed

Henrich KO, Bauer T, Schulte J, Ehemann V, Deubzer H, Gogolin S, Muth D, Fischer M, Benner A, König R, Schwab M, Westermann F (2011) CAMTA1, a 1p36 tumor suppressor candidate, inhibits growth and activates differentiation programs in neuroblastoma cells. Cancer Res 71(8), 3142-3151. Details PubMed

Kranz AL, Eils R, König R (2011) Enhancers regulate progression of development in mammalian cells. Nucleic Acids Res 39(20), 8689-8702. Details PubMed

Krupp M, Maass T, Marquardt JU, Staib F, Bauer T, König R, Biesterfeld S, Galle PR, Tresch A, Teufel A (2011) The functional cancer map: a systems-level synopsis of genetic deregulation in cancer. BMC Med Genomics 4, 53-53. Details PubMed

Fischer M, Bauer T, Oberthür A, Hero B, Theissen J, Ehrich M, Spitz R, Eils R, Westermann F, Brors B, König R, Berthold F (2010) Integrated genomic profiling identifies two distinct molecular subtypes with divergent outcome in neuroblastoma with loss of chromosome 11q. Oncogene 29(6), 865-875. Details PubMed

Lewis NE, Hixson KK, Conrad TM, Lerman JA, Charusanti P, Polpitiya AD, Adkins JN, Schramm G, Purvine SO, Lopez-Ferrer D, Weitz KK, Eils R, König R, Smith RD, Palsson BØ (2010) Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models. Mol Syst Biol 6, 390. Details PubMed

Lewis NE, Schramm G, Bordbar A, Schellenberger J, Andersen MP, Cheng JK, Patel N, Yee A, Lewis RA, Eils R, König R, Palsson BØ (2010) Large-scale in silico modeling of metabolic interactions between cell types in the human brain. Nat Biotechnol 28(12), 1279-1285. Details PubMed

Plaimas K, Eils R, König R (2010) Identifying essential genes in bacterial metabolic networks with machine learning methods. BMC Syst Biol 4, 56. Details PubMed

Riehl A, Bauer T, Brors B, Busch H, Mark R, Németh J, Gebhardt C, Bierhaus A, Nawroth P, Eils R, König R, Angel P, Hess J (2010) Identification of the Rage-dependent gene regulatory network in a mouse model of skin inflammation. BMC Genomics 11, 537. Details PubMed

Schramm G, Kannabiran N, König R (2010) Regulation patterns in signaling networks of cancer. BMC Syst Biol 4, 162. Details PubMed

Schramm G, Surmann EM, Wiesberg S, Oswald M, Reinelt G, Eils R, König R (2010) Analyzing the regulation of metabolic pathways in human breast cancer. BMC Med Genomics 3, 39. Details PubMed

Schramm G, Wiesberg S, Diessl N, Kranz AL, Sagulenko V, Oswald M, Reinelt G, Westermann F, Eils R, König R (2010) PathWave: discovering patterns of differentially regulated enzymes in metabolic pathways. Bioinformatics 26(9), 1225-1231. Details PubMed

Suratanee A, Rebhan I, Matula P, Kumar A, Kaderali L, Rohr K, Bartenschlager R, Eils R, König R (2010) Detecting host factors involved in virus infection by observing the clustering of infected cells in siRNA screening images. Bioinformatics 26(18), i653-i658. Details PubMed

Dittami SM, Scornet D, Petit JL, Ségurens B, Da Silva C, Corre E, Dondrup M, Glatting KH, König R, Sterck L, Rouzé P, Van de Peer Y, Cock JM, Boyen C, Tonon T (2009) Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress. Genome Biol 10(6), R66. Details PubMed

Fatumo S, Plaimas K, Mallm JP, Schramm G, Adebiyi E, Oswald M, Eils R, König R (2009) Estimating novel potential drug targets of Plasmodium falciparum by analysing the metabolic network of knock-out strains in silico. Infect Genet Evol 9(3), 351-358. Details PubMed

Plaimas K, Mallm JP, Oswald M, Svara F, Sourjik V, Eils R, König R (2008) Machine learning based analyses on metabolic networks supports high-throughput knockout screens. BMC Syst Biol 2, 67. Details PubMed

Westermann F, Muth D, Benner A, Bauer T, Henrich KO, Oberthuer A, Brors B, Beissbarth T, Vandesompele J, Pattyn F, Hero B, König R, Fischer M, Schwab M (2008) Distinct transcriptional MYCN/c-MYC activities are associated with spontaneous regression or malignant progression in neuroblastomas. Genome Biol 9(10), R150. Details PubMed

Schramm G, Zapatka M, Eils R, König R (2007) Using gene expression data and network topology to detect substantial pathways, clusters and switches during oxygen deprivation of Escherichia coli. BMC Bioinformatics 8, 149. Details PubMed

Westermann F, Henrich KO, Wei JS, Lutz W, Fischer M, König R, Wiedemeyer R, Ehemann V, Brors B, Ernestus K, Leuschner I, Benner A, Khan J, Schwab M (2007) High Skp2 expression characterizes high-risk neuroblastomas independent of MYCN status. Clin Cancer Res 13(16), 4695-4703. Details PubMed

König R, Schramm G, Oswald M, Seitz H, Sager S, Zapatka M, Reinelt G, Eils R (2006) Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms. BMC Bioinformatics 7, 119. Details PubMed

Oberthuer A, Berthold F, Warnat P, Hero B, Kahlert Y, Spitz R, Ernestus K, König R, Haas S, Eils R, Schwab M, Brors B, Westermann F, Fischer M (2006) Customized oligonucleotide microarray gene expression-based classification of neuroblastoma patients outperforms current clinical risk stratification. J Clin Oncol 24(31), 5070-5078. Details PubMed

Vinayagam A, del Val C, Schubert F, Eils R, Glatting KH, Suhai S, König R (2006) GOPET: a tool for automated predictions of Gene Ontology terms. BMC Bioinformatics 7, 161. Details PubMed

Baldessari D, Shin Y, Krebs O, König R, Koide T, Vinayagam A, Fenger U, Mochii M, Terasaka C, Kitayama A, Peiffer D, Ueno N, Eils R, Cho KW, Niehrs C (2005) Global gene expression profiling and cluster analysis in Xenopus laevis. Mech Dev 122(3), 441-475. Details PubMed

König R, Baldessari D, Pollet N, Niehrs C, Eils R (2004) Reliability of gene expression ratios for cDNA microarrays in multiconditional experiments with a reference design. Nucleic Acids Res 32(3), e29. Details PubMed

König R, Eils R (2004) Gene expression analysis on biochemical networks using the Potts spin model. Bioinformatics 20(10), 1500-1505. Details PubMed

Vinayagam A, König R, Moormann J, Schubert F, Eils R, Glatting KH, Suhai S (2004) Applying Support Vector Machines for Gene Ontology based gene function prediction. BMC Bioinformatics 5, 116. Details PubMed

König R, Dandekar T (2001) Solvent entropy-driven searching for protein modeling examined and tested in simplified models. Protein Eng 14(5), 329-335. Details PubMed

König R, Dandekar T (1999) Improving genetic algorithms for protein folding simulations by systematic crossover. Biosystems 50(1), 17-25. Details PubMed

Dandekar T, König R (1997) Computational methods for the prediction of protein folds. Biochim Biophys Acta 1343(1), 1-15. (Review) Details PubMed