Prof. Dr. Rainer König
- Gene regulation analysis of metabolism and signal transduction
- Modelling of cellular networks
- Linear programming
|2013||Acceptance of a W2 professorship in systems biology of sepsis at the medical faculty of the University Jena|
|2010||Habilitation in bioinformatics, University Heidelberg|
|2007-2013||Head of a research group at the Institute of Pharmacy and Molecular Biotechnology University Heidelberg|
|2004-2007||Research assistant (C1) at the Institute of Pharmacy and Molecular Biotechnology University Heidelberg|
|2000-2004||Research assistant at the Deutsches Krebsforschungszentrum, Heidelberg|
|1999||Dr. sc. hum. in biochemistry, magna cum laude, University Heidelberg|
|1997||„Staatsexamen“ (state examination) in physics and mathematics, University Heidelberg|
|1996||Diploma in physics, University Heidelberg|
Awards · Appointments · Scientific Activities
|From 2014||Project leader of the eMed/BMBF project „modelling of telomere maintenance mechanism networks in tumours“|
|Since 2013||Coordinator of the eBio/BMBF project „systems biology of the metabolic transformation in breast cancer“(SYSMET-BC)|
|Since 2013||Project leader of the des BMBF/IFB project „systems biology of sepsis”|
|Since 2012||Project leader of the BMBF/CancerSys systems biology project „analysis of gene regulatory networks in neuroectodermal tumours” (MYCNET)|
|Since 2011||Project leader of the Helmholtz/DKFZ/MOST Israel project „systems biological investigation of telomere biology”|
(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]
(2020) Targeting complement C5a receptor 1 for the treatment of immunosuppression in sepsis. Molecular Therapy [In press]
(2019) Cognate interaction with CD4+ T cells instructs tumor-associated macrophages to acquire M1-like phenotype. Front Immunol 10, 219.
(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.
(2019) Lack of CD45 in FLT3-ITD mice results in a myeloproliferative phenotype, cortical porosity, and ectopic bone formation. Oncogene 38(24), 4773-4787.
(2019) Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks. Mol Sys Biol 15(5), e8339.
(2018) Induction of ER and mitochondrial stress by the alkylphosphocholine erufosine in oral squamous cell carcinoma cells. Cell Death and Disease 9, 296.
(2018) Transcriptomic alterations during ageing reflect the shift from cancer to degenerative diseases in the elderly. Nat Commun 9(1), 327.
(2018) MiR-192, miR-200c and miR-17 are fibroblast-mediated inhibitors of colorectal cancer invasion. Oncotarget 9(85), 35559-35580.
(2018) Loss of DEP-1 (Ptprj) promotes myeloproliferative disease in FLT3-ITD acute myeloid leukemia. Haematologica 103(11), e505-e509.
(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. J Infect Dis 217(3), 358-370.
(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]
(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.
(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.
(2017) Fungal biomarker discovery by integration of classifiers. BMC Genomics 18, 601.
(2017) Combination of classifiers identifies fungal-specific activation of lysosome genes in human monocytes Front Microbiol 8, 2366.
(2016) Role of the ESCRT Complexes in Telomere Biology mBio 7(6), e01793-16.
(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.
(2016) SOX5 is involved in balanced MITF regulation in human melanoma cells BMC Medical Genomics, 9(1):10. ,
(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.
(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)
(2016) Mixed Integer Linear Programming based machine learning approach identifies regulators of telomerase in yeast Nucleic Acids Res 44(10), e93.
(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.
(2016) Copy number alterations in enzyme-coding and cancer-causing genes reprogram tumor metabolism Cancer Research 76(14), 4058-4067.
(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 ,
(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 ,
(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.
(2015) Causes of upregulation of glycolysis in lymphocytes upon stimulation. A comparison with other cell types. Biochimie 118, 185-194.
(2014) Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition. Cancer Cell 25(3), 393-405.
(2014) Network topology-based detection of differential gene regulation and regulatory switches in cell metabolism and signaling. BMC Syst Biol 8, 56.
(2014) Estimating the activity of transcription factors by the effect on their target genes. Bioinformatics 30(17), i401-i407.
(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.
(2014) Characterizing Protein Interactions Employing a Genome-Wide siRNA Cellular Phenotyping Screen. PLOS Comput Biol 10(9), e1003814.
(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.
(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.
(2013) SplicingCompass: differential splicing detection using RNA-seq data. Bioinformatics 29(9), 1141-1148.
(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.
(2013) Disease-gene discovery by integration of 3D gene expression and transcription factor binding affinities. Bioinformatics 29(4), 468-475.
(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.
(2013) Secretory meningiomas are defined by combined KLF4 K409Q and TRAF7 mutations. Acta Neuropathol 125(3), 351-358.
(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.
(2013) Metabolic network modeling approaches for investigating the "hungry cancer". Semin Cancer Biol 23(4), 227-234. (Review)
(2013) BCAT1 promotes cell proliferation through amino acid catabolism in gliomas carrying wild-type IDH1. Nat Med 19(7), 901-908.
(2012) Time-lapse imaging of neuroblastoma cells to determine cell fate upon gene knockdown. PLOS One 7(12), e50988.
(2012) STK25 protein mediates TrkA and CCM2 protein-dependent death in pediatric tumor cells of neural origin. J Biol Chem 287(35), 29285-29289.
(2011) RIP: the regulatory interaction predictor - a machine learning-based approach for predicting target genes of transcription factors. Bioinformatics 27(16), 2239-2247.
(2011) Automatisierte regulatorische Interaktionsvorhersage. Laborwelt (6), 32-34.
(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.
(2011) CAMTA1, a 1p36 tumor suppressor candidate, inhibits growth and activates differentiation programs in neuroblastoma cells. Cancer Res 71(8), 3142-3151.
(2011) Enhancers regulate progression of development in mammalian cells. Nucleic Acids Res 39(20), 8689-8702.
(2011) The functional cancer map: a systems-level synopsis of genetic deregulation in cancer. BMC Med Genomics 4, 53-53.
(2010) Integrated genomic profiling identifies two distinct molecular subtypes with divergent outcome in neuroblastoma with loss of chromosome 11q. Oncogene 29(6), 865-875.
(2010) Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models. Mol Syst Biol 6, 390.
(2010) Large-scale in silico modeling of metabolic interactions between cell types in the human brain. Nat Biotechnol 28(12), 1279-1285.
(2010) Identifying essential genes in bacterial metabolic networks with machine learning methods. BMC Syst Biol 4, 56.
(2010) Identification of the Rage-dependent gene regulatory network in a mouse model of skin inflammation. BMC Genomics 11, 537.
(2010) Regulation patterns in signaling networks of cancer. BMC Syst Biol 4, 162.
(2010) Analyzing the regulation of metabolic pathways in human breast cancer. BMC Med Genomics 3, 39.
(2010) PathWave: discovering patterns of differentially regulated enzymes in metabolic pathways. Bioinformatics 26(9), 1225-1231.
(2010) Detecting host factors involved in virus infection by observing the clustering of infected cells in siRNA screening images. Bioinformatics 26(18), i653-i658.
(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.
(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.
(2008) Machine learning based analyses on metabolic networks supports high-throughput knockout screens. BMC Syst Biol 2, 67.
(2008) Distinct transcriptional MYCN/c-MYC activities are associated with spontaneous regression or malignant progression in neuroblastomas. Genome Biol 9(10), R150.
(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.
(2007) High Skp2 expression characterizes high-risk neuroblastomas independent of MYCN status. Clin Cancer Res 13(16), 4695-4703.
(2006) Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms. BMC Bioinformatics 7, 119.
(2006) Customized oligonucleotide microarray gene expression-based classification of neuroblastoma patients outperforms current clinical risk stratification. J Clin Oncol 24(31), 5070-5078.
(2006) GOPET: a tool for automated predictions of Gene Ontology terms. BMC Bioinformatics 7, 161.
(2005) Global gene expression profiling and cluster analysis in Xenopus laevis. Mech Dev 122(3), 441-475.
(2004) Reliability of gene expression ratios for cDNA microarrays in multiconditional experiments with a reference design. Nucleic Acids Res 32(3), e29.
(2004) Gene expression analysis on biochemical networks using the Potts spin model. Bioinformatics 20(10), 1500-1505.
(2004) Applying Support Vector Machines for Gene Ontology based gene function prediction. BMC Bioinformatics 5, 116.
(2001) Solvent entropy-driven searching for protein modeling examined and tested in simplified models. Protein Eng 14(5), 329-335.
(1999) Improving genetic algorithms for protein folding simulations by systematic crossover. Biosystems 50(1), 17-25.
(1997) Computational methods for the prediction of protein folds. Biochim Biophys Acta 1343(1), 1-15. (Review)