Publications

Grünewald B, Wickel J, Hahn N, Rahmati V, Rupp H, Chung HY, Haselmann H,
Strauss  AS, Schmidl L, Hempel N, Grünewald L, Urbach A, Bauer M, Toyka
KV, Blaess M, Claus RA, König R, Geis C. (2024). Targeted rescue of
synaptic plasticity improves cognitive decline in sepsis-associated
encephalopathy, Mol Ther. 2024 May 23, S1525.-0016(24)00301-0.

Adedeji EO, Beder T, Damiani C, Cappelli A, Accoti A, Tapanelli S,
Ogunlana OO, Fatumo S, Favia G, Koenig R, Adebiyi E (2024). Combination of
computational techniques and RNAi reveal targets in Anopheles gambiae
for malaria vector control, PloS ONE, 19, e0305207.

Gheitasi R, Röll D, Müller MM, Naseri M, König R, Slevogt HG, Pletz MW,
Makarewicz O (2024). Exploring Secretory Proteome and Cytokine kinetic of Human
Peripheral Blood Mononuclear Cells Exposed to Staphylococcus aureus
Biofilms and Planktonic Bacteria, Frontiers Immunology, 15, 1334616.

Kelch MA, Vera-Guapi A, Beder T, Oswald M, Hiemisch A, Beil N, Wajda P,
Ciesek S, Erfle H, Toptan T, Koenig R (2023). Machine learning on large
scale perturbation screens for SARS-CoV-2 host factors identifies
β-catenin/CBP inhibitor PRI-724 as a potent antiviral, Front Microbiol,
14:1193320.

Mahajan UM, Erber J, Shamsrizi P, Voit F, Vielhauer J, Johlke AL,
Benesch C, Khaled NB, Reinecke F, Rudi WS, Klein M, Jakob C, König R,
Oswald M, Schulz C, Mayerle J, Stubbe HC (2023). Validation of the
SACOV-19 score for identifying patients at risk of complicated or more
severe COVID-19: a prospective study, Infection, May 11:1-10.

Aromolaran OT, Isewon I, Adedeji E, Oswald M, Adebiyi E, Koenig R,
Oyelade J (2023). Heuristic-enabled active machine learning: A case
study of predicting essential developmental stage and immune response
genes in Drosophila melanogaster, PloS one, August 9.

Chung HY, Wickel J, Oswald M, Dargvainiene J, Rupp J, Rohde G,
Witzenrath M, Leypoldt F, König R, Pletz MW, Geis C; CAPNETZ Study Group
(2023). Neurofilament light chain levels predict encephalopathy and
outcome in community-acquired pneumonia, Ann Clin Transl Neurol, 10,
204-212.

Adedeji EO, Oduselu GO, Ogunlana OO, Fatumo S, Koenig R, Adebiyi E
(2022). Anopheles gambiae trehalase inhibitors for malaria vector
control: A molecular docking and molecular dynamics study, Insects, 13,
1070.

Thanamit K, Hoerhold F, Oswald M, Koenig R (2022). Linear Programming based Gene Expression Model (LPM-GEM) predicts the carbon source for Bacillus subtilis, BMC Bioinformatics, 23, 226.

Poos AM, Schröder C, Jaishankar N, Röll D, Oswald M, Meiners J, Braun DM, Bauer C, Frank L, Gunkel M, Spilger R, Wollmann T, Polonski A, Makrypidi-Fraune G, Fraune C, Graefen M, Chung I, Stenzel A, Erfle H, Rohr K, Baniahmad A, Sauter G, Rippe K, Simon R & König R (2022). PITX1 is a regulator of TERT expression in prostate cancer with prognostic power, Cancers, 14, 1267.

Afolabi R, Chinedu S, Ajamma Y, Adam Y, Koenig R, Adebiyi E (2022). Computational identification of Plasmodium falciparum RNA pseudouridylate synthase as a viable drug target, its physicochemical properties, 3D structure prediction and prediction of potential inhibitors, Infect Genet Evol, 97, 105194.

Muley VY,  König R (2022). Human transcriptional gene regulatory network compiled from 14 data resources, Biochimie, 193, 115.

Beder T, Aromolaran O, Dönitz J, Tapanelli S, Adedeji EO, Adebiyi E, Bucher G & Koenig R (2021). Identifying essential genes across eukaryotes by machine learning, NAR Genomics and Bioinformatics, 3, lqab110.

Aromolaran O, Beder T, Adedeji E, Ajamma Y, Oyelade J, Adebiyi E, Koenig R. Predicting host dependency factors of pathogens in Drosophila melanogaster using machine learning,  Comput Struct Biotechnol J, 19:4581-4592.

Jakob, CEM, Mahajan UM, Oswald M, Stecher M, Schons M, Mayerle J,  Rieg S,  Pletz M, Merle U, Wille K, Borgmann S, Spinner CD, Dolff S, SchererC, Pilgram L, Rüthrich M, Hanses F, Hower M, Strauß R, Massberg S, Görkem Er A, Jung N, Vehreschild JJ, Stubbe H, Tometten L & König R, on behalf of the LEOSS Study group (2021). Prediction 1 of COVID-19
deterioration in high-risk patients at diagnosis - an Early Warning Score for Advanced Covid-19 developed by machine learning, Infection, 19 July,  doi.org/10.1007/s15010-021-01656-z.

König R, Kolte A, Ahlers O, Oswald M, Krauss V, Roell D, Sommerfeld O, Dimopoulos G, Tsangaris I, Antoniadou E, Jaishankar N, Bogatsch H, Löffler M, Rödel M, Garcia-Moreno M, Tuchscherr L, Sprung CL, Singer M, Brunkhorst F, Oppert M, Gerlach H, Claus RA, Coldewey SM, Briegel J, Giamarellos-Bourboulis EJ, Keh D, Bauer M (2021) Use of IFNγ/IL10 ratio for stratification of hydrocortisone therapy in patients with septic shock, Frontiers Immunol, doi: 10.3389/fimmu.2021.607217.

Adedeji EO, Ogunlana OO, Fatumo S, Beder T, Ajamma Y, Koenig R, Adebiyi E (2020) Anopheles metabolic proteins in malaria transmission, prevention and control: a review. Parasites & Vectors 13: 465 (review article).

Bär I, Ast V, Meyer D, König R, Rauner M, Hofbauer LC, Müller JP (2020) Aberrant Bone Homeostasis in AML Is Associated with Activated Oncogenic FLT3-Dependent Cytokine Networks. Cells 9: 2443

Börries M, Busch H & König R (2020). Cellular systems biology, In: An Introduction to Molecular Biotechnology: Fundamentals, Methods and Applications, Third Edition. Edited by Michael Wink, Wiley-VCH Verlag GmbH & Co KGaA, Weinheim, Germany

Hassan M, Kruse J, Krueger T, Dahse HM, Cseresnyes Z, Blango M, Slevogt H, Hoerhold F, Ast V, Koenig R, Figge MT, Kniemeyer O, Brakhage A 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 and Environmental Microbiology Reports, doi: 10.1111/1462‐2920.15140.

Hörhold F, Eisel D, Oswald M, Kolte A, Röll D, Osen W, Eichmüller SB, König R (2020) Reprogramming of macrophages employing gene regulatory and metabolic network models. PLoS Comput Biol 16: e1007657

Aromolaran O, Beder T, Oswald M, Oyelade J, Adebiyi E, Koenig R (2020) Essential gene prediction in Drosophila melanogaster using machine learning approaches based on sequence and functional features. Computational and Structural Biotechnology Journal 18: 612-621

Höflmayer D, Soltow A, Hube-Magg C, Kluth M, Simon R, Burandt E, Tsourlakis MC, Minner S, Sauter G, Büscheck F, Wilczak W, Steurer S, Schlomm T, Huland H, Graefen M, Haese A, Heinzer H, Jacobsen F, Hinsch A, Poos AM, Oswald M, Rippe K, König R, Schroeder C (2020). Expression of CCCTC-binding factor (CTCF) is linked to poor prognosis in prostate cancer. Molecular Oncology, 14, 129.

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.

Kolte Amol, König Rainer (2019) Temporal progression of gene regulation of peripheral white blood cells explains gender dimorphism of critically ill patients after trauma Molecular medicine 25, 19.

König R, Cao X, Oswald M, Forstner C, Rohde G, Rupp J, Witzenrath M, Welte T, Kolditz M, Pletz M (2019) Macrolide combination therapy for hospitalized CAP patients? An individualized approach supported by machine learning, European Respiratory Journal 54: 11.  (doi: 10.1183/13993003.00824-2019)

Kresinsky A, Schnöder TM, Jacobsen ID, Rauner M, Hofbauer LC, Ast V, König R, Hoffmann B, Svensson C-M, 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, 4773-4787.

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, e8339.

Alexandra M. Poos, Theresa Kordaß, Amol Kolte, Volker Ast, Marcus Oswald, Karsten Rippe, Rainer König (2019) Modelling TERT regulation across 19 different cancer types based on the MIPRIP 2.0 gene regulatory network approach. BMC Bioinformatics, 20:737.

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.

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, 327.

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, 35559-35580.

Beder T and Saluz HP (2018) Virulence-related comparative transcriptomics of infectious and non-infectious chlamydial particles. BMC Genomics 19, 575.

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, e505.

Meinel C, Spartà G, Dahse H-M, 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. The Journal of Infectious Diseases 217(3), 358-370.

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. The Prostate, 79, 302-311.

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.

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.

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.

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.

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

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. 2016;228:670-4.

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.

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, Apr 28; 7:e2205

Plaimas K, König R (2016) Identifying antimalarial drug targets by cellular network analysis. In: Rodriguez-Morales A (ed.) Current Topics in Malaria, InTech, Rijeka, Croatia, ISBN: 978-953-51-2789.

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 Research, 44, e93

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 6th IFAC Conference on Foundations of Systems Biology in Engineering, Magdeburg, 10/09/2016-10/12/2016, pp. 95-102. Elsevier ScienceDirect.

Sharma AK, Eils R, König R (2016) Copy number alterations in enzyme-coding and cancer-causing genes reprogram tumor metabolism Cancer Research, 76(14):4058-67.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Aschoff M, Hotz-Wagenblatt A, Glatting KH, Fischer M, Eils R, König R: SplicingCompass: differential splicing detection using RNA-Seq sequencing data, Bioinformatics, 29, 1141

Goglin S, Batra R, Harder N, Ehemann V, Paffhausen T , Diessl N, 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 Letters, 331, 35-45.

Plaimas K, Wang Y, Rotimi, SO, Olasehinde, G, Fatumo S, Lanzer M, Adebiyi E, König R: Computational and experimental analysis identified 6-diazo-5-oxonorleucine as a potential agent for treating infection by Plasmodium falciparum, Infection, Genetics and Evolution, 20, 389-395

Reuss DE, Piro R, 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, Kölsche C, Jäger N, Wellenreuther R, Kraus J, Lenartz D, Herold-Mende C, Hartmann C, Mawrin C, Giese N, Eils R, Collins P, König R, Wiestler OD, Pfister S, von Deimling D: Secretory meningiomas are defined by combined KLF4 K409Q and TRAF7 mutations, Acta Neuropathol, 125, 351

Tönjes M, Barbus S, Park YJ, Wang W, Schlotter M, Lindroth AM, Pleier SV, Bai AH, Karra D, Felsberg J, Addington A, Lemke D, Hovestadt V, Piro R, König R, Rolli CG, Sturm D, Witt H, Kemkemer R, Schmidt K, Hull WE, Pfister SM, Hutson SM, Plass C, Okun JG, Reifenberger G, Lichter P, Radlwimmer B: BCAT1 promotes cell proliferation via amino acid catabolism in IDH1 wildtype gliomas, Nat Medicine, 19, 901-8

Schweizer L, Koelsche C, Sahm F,  Piro RM, Capper D, Reuss DE, Pusch S, Habel A, Meyer J, Göck T, Jones DTW, 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: Meningeal hemangiopericytoma and solitary fibrous tumors carry the NAB2-STAT6 fusion and can be diagnosed by nuclear expression of STAT6 protein, Acta Neuropathol, 125, 651

Reviews (Übersichtsartikel)

Sharma AK, König R: Metabolic network modeling approaches for investigating the "hungry cancer". Seminars in Cancer Biology, 23, 227-34

Batra R, Harder N, Gogolin S, Diessl N, Soons Z, Jäger-Schmidt C, Lawerenz C, Eils R, Rohr K, Westermann F, König R: Time-lapse imaging of neuroblastoma cells to determine cell fate upon gene knockdown, PLoS ONE, 7:e50988

Piro MR, Molineris I, Di Cunto F, Eils R, König R: Disease-gene discovery by integration of 3D gene expression and transcription factor binding affinities, Bioinformatics, 29, 468-475

Costa B, Kean MJ, Ast V, Knight JDR, Mett A, Levy Z, Ceccarelli DF,Badillo BD, Eils R, König R, Gingras AC, Fainzilber M: Stk25 mediates TrkA and CCM2 dependent death in pediatric tumor cells of neural origin, J Biol Chem., 287, 29285-29289

Ausführlich publizierte Kongressbeiträge

Harder N, Batra R, Gogolin S, Diessl N, Eils R, Westermann F, König R, Rohr K: Cell Tracking for Automatic Migration and Proliferation Analysis in High-Throughput Screens, Bildverarbeitung für die Medizin 2012: 243-248

Harder N, Batra R, Gogolin S, Diessl N, Eils R, Westermann F, König R, Rohr K: Cell Tracking for Automatic Migration and Proliferation Analysis in High-Throughput Screens, in: Proc. Workshop Bildverarbeitung für die Medizin 2012 (BVM 2012), Informatik aktuell, Editor(s): Handels H, Ehrhardt J, Deserno TM, Meinzer HP, Tolxdorff T, Springer-Verlag, 2012

Kranz AL, Eils R, König R: Enhancers regulate progression of development in mammalian cells. Nucleic Acids Res., 39, 8689-702

Bauer T, Eils R, König R: RIP: the regulatory interaction predictor--a machine learning-based approach for predicting target genes of transcription factors, Bioinformatics, 27, 2239-47

Henrich KO, Bauer T, Schulte J, Ehemann V, Deubzer H, Gogolin S, Muth D, Fischer M, Benner A, König R, Schwab M, Westermann F: CAMTA1, a 1p36 tumor suppressor candidate, inhibits growth and activates differentiation programs in neuroblastoma cells, Cancer Res., 71, 3142-51

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

Fatumo S, Plaimas K, Adebiyi E, König R: 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, 708-15

Ausführlich publizierte Kongressbeiträge

Harder N, Batra R, Gogolin S, Diessl N, Eils R, Westermann F, König R, Rohr K: Large-Scale Tracking for Cell Migration and Proliferation Analysis and Experimental Optimization of High-Throughput Screens. In Proceedings of ICSB 2011 Workshop, Microscopic Image Analysis with Applications in Biology, Heidelberg, Germany, September 2, 2011

Übersichtsartikel

Bauer T, König R: Automatisierte regulatorische Interaktionsvorhersage, Laborwelt, 6, S32-34 [in German]

Buchbeiträge

König R, Brors B, Legewie S, Schmidt-Glenewinkel H, Cellular Systems Biology, in: Molecular Biotechnology, edited by Wink M, Wiley VCH, Weinheim, Germany

König R, Brors B, Legewie S, Schmidt-Glenewinkel H: Zelluläre Systembiologie, in: Molekulare Biotechnologie, edited by Wink M, Wiley VCH, Weinheim, Germany [in German]

König R, Plaimas K: Machine learning methods for identifying essential genes and proteins in networks in: Applied Statistics for Network Biology, edited by Dehmer, M., VCH Wiley, Weinheim

Lewis N, Schramm G, Bordbar A,Schellenberger J, Andersen M, Cheng J, Patel M, Yee A, Lewis R, Eils R, König R, Palsson B: Formulating multi-cellular models of metabolism in tissues: application to energy metabolism in the human brain, Nat. Biotechnology, 28, 1279

Schramm G, Kannabiran N, König R: Regulation patterns in signaling networks of cancer, BMC Systems Biology, 4, 162

Schramm G, Surmann EM, Wiesberg S, Oswald M, Reinelt G, Eils R, König R: Analyzing the regulation of metabolic pathways in human breast cancer, BMC Medical Genomics, 3:39

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

Suratanee A, Rebhan I, Matula P, Kaderali L, Rohr K, Bartenschlager R, Eils R, König R: Detecting host factors involved in virus infection by observing the clustering of infected cells in siRNA screening images, Bioinformatics, 26 ECCB 2010, i1-i6

Schramm G, Wiesberg S, Diessl N, Kranz AL, Sagulenko V, Oswald M, Reinelt G, Westermann F, Eils R, König R: PathWave: Discovering patterns of differentially regulated enzymes in metabolic pathways, Bioinformatics, 26, 1225-31

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

Plaimas K, Eils R, König R: Identifying Essential Genes in Bacterial Metabolic Networks with Machine Learning Methods, BMC Syst Biol, 4:56

Fischer M, Bauer T, Oberthür A, Hero B, Theissen J, Ehrich M, Spitz R, Eils R, Westermann F, Brors B, König R, Berthold F: Integrated genomic profiling identifies two distinct molecular subtypes with divergent outcome in neuroblastoma with loss of chromosome 11q, Oncogene, 29, 866-875

Gipp M, Marcus G, Harder N, Suratanee A, Rohr K, König R, Männer R: Haralick's Texture Features Computed by GPUs for Biological Applications, IAENG International Journal of Computer Science, 36:1, IJCS_36_1_09

Dittami SM, Scornet D, Corre E, Dondrup M, Glatting KH, König R, Cock JM, Boyen C, Tonon T: Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large scale reprogramming of the transcriptome in response to abiotic stress, Genome Biology, 10:R66

Fatumo S, Plaimas K, Mallm JP, Schramm G, Adebiyi E, Oswald M, Eils R, König R: Estimating novel potential drug targets of Plasmodium falciparum by analysing the metabolic network of knock-out strains in silico, Infection, Genetics and Evolution, 9, 351-358

Ausführlich publizierte Kongressbeiträge

Surmann EM, Schramm G, Wiesberg S, Oswald M, Reinelt G, Eils R, König R: Analyzing the regulation of metabolic pathways in human breast cancer, Proceedings of the KDML 2009: Knowledge Discovery, Data Mining, and Machine Learning, Darmstadt, September 21-23

Gipp M, Marcus G, Harder N, Suratanee A, Rohr K, König R, Männer R: Haralicks Texture Features Computation Accelerated by GPUs for Biological Applications, 4th International Conference on High Performance Scientific Computing, Modeling, Simulation and Optimization of Complex Processes March 2-6, 2009, Hanoi, Vietnam

Fatumo S, Adebiyi E, Schramm G, Eils R, König R: An in silico approach to design an efficient malaria drug to combat the malaria resistance problem, Proceedings of the International Conference on Bioinformatics and Biomedical Technology (ICBBT 2009), April 17 - 20, 2009, Singapore

Plaimas K, Mallm JP, Oswald M, Svara F, Sourjik V, Eils R, König R: Machine learning based analyses on metabolic networks identifies essential genes, BMC Systems Biology, 2:67

Westermann F, Muth D, Benner A, Bauer T, Henrich KO, Oberthür A, Brors B, Beissbarth T, Pattyn F, Vandesompele J, Speleman F, König R, Fischer M, Schwab M: Distinct transcriptional MYCN/c-MYC activities are associated with spontaneous regression or malignant progression in neuroblastomas, Genome Biology, 9, R150

Ausführlich publizierte Kongressbeiträge

Gipp M, Marcus G, Harder N, Suratanee A, Rohr K, König R, Männer R: Accelerating the computation of Haralick’s Texture Features using Graphics Processing Units (GPUs), Proceedings of the World Congress on Engineering, London, U.K., 2-4 July, 2008 (best paper award of the conference)

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: High Skp2 expression characterizes high-risk neuroblastomas independent of MYCN status. Clin Cancer Res, 13, 4695-703

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

Ausführlich publizierte Kongressbeiträge

Plaimas K, Oswald M, Eils R, König R: Integrating Genomic and Transcriptomic Data into Graph Based Approaches for Defining Essential Reactions in the Metabolic Network of Escherichia Coli, Proceedings of the KDML 2007: Knowledge Discovery, Data Mining, and Machine Learning, 24-26 October, 2007, Halle, Germany, 55-60

Oberthür 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: Customized oligonucleotide microarray gene expression-based classification of neuroblastoma patients outperforms current clinical risk stratification, J Clin Oncol, 24, 5070-78

Oberthuer A, Berthold F, Warnat P, Hero B, Spitz R, Ernestus K, König R, Eils R, Schwab M, Brors B, Westermann F, Fischer M: Gene-expression based classification of neuroblastoma patients using a customized oligonucleotide-microarray outperforms current clinical risk stratification, Klinische Pädiatrie, 218, 192

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

Vinayagam A, del Val C, Schubert F, Eils R, Glatting KH, Suhai S, König R: GOPET: a tool for automated Gene Ontology term prediction, BMC Bioinformatics, 7:161

Ausführlich publizierte Kongressbeiträge

Schramm A, Oswald M, Seitz H, Sager S, Zapatka M, Reinelt G, Eils R, König R: Pattern recognition of gene expression data on biochemical networks with simple wavelets transforms, Proceedings of the KDML 2006: Knowledge Discovery, Data Mining, and Machine Learning, 9-13 October, 2006, Hildesheim, Germany, 350-355

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: Global gene expression profiling and cluster analysis in Xenopus laevis, Mech Dev, 122, 441-75

Ausführlich publizierte Kongressbeiträge

Vinayagam A, del Val C, Schubert F, Eils R, Glatting KH, Suhai S, König R: GOPET: a tool for automatic Gene Ontology term prediction, Proceedings of the Automatic Function Prediction SIG-meeting at the 13th International Conference on Intelligent Systems for Molecular Biology, 24 July, 2005, Detroit, MI, USA, 37-38

Vinayagam A, König R, Moormann J, Schubert F, Eils R, Glatting KH, Suhai S: Applying Support Vector Machines for Gene ontology based gene function prediction, BMC Bioinformatics, 5:116

König R, Eils R: Gene expression analysis on biochemical networks using the Potts spin model, Bioinformatics, 20, 1500-1505

König R, Baldessari D, Pollet N, Niehrs C, Eils R: Reliability of gene expression ratios for cDNA microarrays in multi-conditional experiments with a reference design, Nucleic Acids Res, 32, e29

Ausführlich publizierte Kongressbeiträge

König R, Eils R: Gene expression analysis on biochemical networks with the Potts spin model, Proceedings of the German Conference on Bioinformatics, 12-14 October, 2003, Neuherberg, Germany, 69-72

Ausführlich publizierte Kongressbeiträge

Weismüller M, König R, Eils R: Modelling of information flow in cells, Proceedings of the 16th European Simulation Multiconference, Darmstadt, 3-5 June, 2002, 413-417

König R, Dandekar T: Solvent entropy-driven searching for protein modelling examined and tested in simplified models, Protein Eng, 14, 329-335

König R, Dandekar T: Improving genetic algorithms for protein folding simulations by systematic crossover, Biosystems, 50, 17-25

König R, Dandekar T: Refined genetic algorithms simulations to model proteins, J Mol Mod, 5, 317-324

Übersichtsartikel

König R, Dandekar T: condensation and commentary of "DeRisi, V.R. & Brown, P.O. (1997). Exploring the metabolic and genetic control of gene expression on a genomic scale, Science, 278, 680-686", Chemtracts, 12, 148-152

Übersichtsartikel

Dandekar T, König R: Computational methods for the prediction of protein folds, Biochim Biophys Acta, 1343, 1-15