Reinhard Guthke

Prof. Dr. Reinhard Guthke

Systembiologie und Bioinformatik

Forschungsschwerpunkte
  • Bioprozess-Datenanalyse (Data Mining) und mathematische Modellierung
  • Analyse von Transkriptom- und Proteomdaten
  • Inferenz genregulatorischer Netzwerke (Reverse Engineering)
  • Systembiologie der Infektion und von Autoimmunerkrankungen
  • Entscheidungsunterstützende Systeme für die Individualisierte Therapie
Curriculum vitae

Wissenschaftlicher Werdegang

Seit 2008 Leiter der Forschungsgruppe Systembiologie und Bioinformatik, HKI
2004-2008 Stellv. Leiter der Abt. Molekulare und Angewandte Mikrobiologie, HKI
2000-2004 Kommissarischer Leiter der Abt. Angewandte Mikrobiologie, HKI
1992-2000 Stellv. Leiter der Abt. Bioregulation bzw. Angewandte Mikrobiologie, HKI
1980-1982 Stellv. Leiter der Abt. Biophysik, ZIMET
seit 2004 Privatdozent für Biotechnologie, Friedrich-Schiller-Universität Jena
1994 Habilitation in Biotechnologie, Friedrich-Schiller-Universität Jena
1988 Dr. sc. nat. in Biotechnologie, Friedrich-Schiller-Universität Jena
seit 1992 Wiss. Mitarbeiter, Hans-Knöll-Institut für Naturstoff-Forschung bzw. Leibniz Institut für Naturstoff-Forschung und Infektionsbiologie-Hans-Knöll-Institut (HKI) Jena
1973-1992 Wiss. Mitarbeiter, Zentralinstitut für Mikrobiologie und Experimentelle Therapie (ZIMET), Jena
1978 Dr. rer. nat. in Biophysik, „magna cum laude“ Friedrich-Schiller-Universität Jena
1973 Diplom in Physik an der Friedrich-Schiller-Universität Jena

Auszeichnungen · Ämter · wissenschaftliche Aktivitäten

seit 2010 Deputy Section Editor/Associate Editor BMC Systems Biology
seit 2008 Koordinator eines FORSYS-Partner-Projektes (BMBF)
2005-2008 Mitglied des Lenkungskomitees des EU-Projektes NiSiS (Nature inspired Smart Information Systems) 
2001-2004 Koordinator der Task Force „Intelligent Technologies for Gene Expression Based Individualized Medicine“ innerhalb des European Network of Intelligent Technologies
seit 2001 Mitglied des Steering Committees Jena Centre for Bioinformatics
seit 1990 Principal investigator in DFG-, BMBF-, EU-, Industrie-Projekten
Publikationen

Barber AE, Weber M, Kaerger K, Linde J, Gölz H, Duerschmied D, Markert A, Guthke R, Walther G, Kurzai O (2019) Comparative genomics of serial Candida glabrata isolates and the rapid acquisition of echinocandin resistance during therapy. Antimicrob Agents Chemother Volume 62(Issue 2), e01628-18. Details PubMed

Kaur S, Rawal P, Siddiqui H, Rohilla S, Sharma S, Tripathi DM, Baweja S, Hassan M, Vlaic S, Guthke R, Thomas M, Dayoub R, Bihari C, Sarin SK, Weiss TS (2019) Increased Expression of RUNX1 in Liver Correlates with NASH Activity Score in Patients with Non-Alcoholic Steatohepatitis (NASH). Cells 8(10), Details PubMed

Marbach-Breitrück E, Matz-Soja M, Abraham U, Schmidt-Heck W, Sales S, Rennert C, Kern M, Aleithe S, Spormann L, Thiel C, Gerlini R, Arnold K, Klöting N, Guthke R, Rozman D, Teperino R, Shevchenko A, Kramer A, Gebhardt R (2019) Tick-Tock Hedgehog-Mutual crosstalk with liver circadian clock promotes liver steatosis. J Hepatol [Epub ahead of print] Details PubMed

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

Baumeister T*, Ueberschaar N*, Schmidt-Heck W*, Mohr JF, Deicke M, Wichard T, Guthke R, Pohnert G (2018) DeltaMS: A tool to track isotopologues in GC- and LC-MS data. Metabolomics 14(4), 41. Details PubMed

Conrad T, Kniemeyer O, Henkel SG, Krüger T, Mattern DJ, Valiante V, Guthke R, Jacobsen ID, Brakhage AA, Vlaic S, Linde J (2018) Module-detection approaches for the integration of multilevel omics data highlight the comprehensive response of Aspergillus fumigatus to caspofungin. BMC System Biol 12(1), 88. Details PubMed Open Access

Lehmann R, Müller MM, Klassert TE, Driesch D, Stock M, Conrad T, Moore C, Schier U, Guthke R, Slevogt H (2018) Differential regulation of the transcriptomic and secretomic landscape of sensor and effector functions of human airway epithelial cells. Mucosal Immunol 11(3), 627-642. Details PubMed

Ravichandran M, Priebe S, Grigolon G, Rozarov L, Groth M, Laube B, Guthke R, Platzer M, Zarse K, Ristow M (2018) Impairing L-Threonine Catabolism Promotes Helthspan Through Proteotoxic Methylglyoxal. Cell Metabolism 27(4), 914-925. Details PubMed

Schmidt H, Vlaic S, Krüger T, Schmidt F, Balkenhohl J, Dandekar T, Guthke R, Kniemeyer O, Heinekamp T, Brakhage AA (2018) Proteomics of Aspergillus fumigatus conidia-containing phagolysosomes identifies processes governing immune evasion. Mol Cell Proteomics 17(6), 1084-1096. Details PubMed

Scholz SS, Schmidt-Heck W, Guthke R, Furch ACU, Reichelt M, Gershenzon J, Oelmüller R (2018) Verticillium dahliae-Arabidopsis interaction causes changes in gene expression profiles and jasmonate levels on different time scales. Front Microbiol 9, 217. Details PubMed Open Access

Vlaic S, Conrad T, Tokarski-Schnelle C, Gustafsson M, Dahmen U, Guthke R, Schuster S (2018) ModuleDiscoverer: Identification of regulatory modules in protein-protein interaction networks. Sci Rep 8(1), 433. Details PubMed

Dix A, Czakai K, Leonhardt I, Schäferhoff K, Bonin M, Einsele H, Guthke R, Kurzai O, Löffler J, Linde J (2017) Specific and novel microRNAs are regulated as response to fungal infection in human dendritic cells. Front Microbiol 8, 270. Details PubMed Open Access

Müller MM, Lehmann R, Klassert TE, Reifenstein S, Conrad T, Moore C, Kuhn A, Behnert A, Guthke R, Driesch D, Slevogt H (2017) Global analysis of glycoproteins identifies markers of endotoxin tolerant monocytes and GPR84 as a modulator of TNFα expression. Sci Rep 7(1), 838. Details PubMed Open Access

Rennert C, Eplinius F, Hofmann U, Johänning J, Rolfs F, Schmidt-Heck W, Guthke R, Gebhardt R, Ricken AM, Matz-Soja M (2017) Conditional loss of hepatocellular Hedgehog signaling in female mice leads to the persistence of hepatic steroidogenesis, androgenization and infertility. Arch Toxicol 91(11), 3677-3687. Details PubMed

Schleicher J, Dahmen U, Guthke R, Schuster S (2017) Zonation of hepatic fat accumulation: insights from mathematical modelling of nutrient gradients and fatty acid uptake. J R Soc Interface 14(133), pii: 20170443. Details PubMed

Schmidt-Heck W, Wönne EC, Hiller T, Menzel U, Koczan D, Damm G, Seehofer D, Knöspel F, Freyer N, Guthke R, Dooley S, Zeilinger K (2017) Global transcriptional response of human liver cells to ethanol stress of different strength reveals hormetic behavior. Alcohol Clin Exp Res 41(5), 883-894. Details PubMed

Valiante V, Mattern DJ, Schüffler A, Horn F, Walther G, Scherlach K, Petzke L, Dickhaut J, Guthke R, Hertweck C, Nett M, Thines E, Brakhage AA (2017) Discovery of an Extended Austinoid Biosynthetic Pathway in Aspergillus calidoustus. ACS Chem Biol 12(5), 1227-1234. Details PubMed Supplement

Baumgart M, Priebe S, Groth M, Hartmann N, Menzel U, Pandolfini L, Ristow M, Englert C, Guthke R, Platzer M, Cellerino A (2016) Longitudinal transcriptional analysis of vertebrate aging identifies mitochondrial complex I as a small molecule-sensitive modifier of lifespan. Cell Systems 2(2), 122-132. Details PubMed

Böhringer M, Pohlers S, Schulze S, Albrecht-Eckardt D, Piegsa J, Weber M, Martin R, Hünniger K, Linde J, Guthke R, Kurzai O (2016) Candida albicans infection leads to barrier breakdown and a MAPK/NF-κB mediated stress response in the intestinal epithelial cell line C2BBe1. Cellular Microbiology 18(7), 889-904. Details PubMed

Dix A, Czakai K, Springer J, Fliesser M, Bonin M, Guthke R, Schmitt AL, Einsele H, Linde J, Löffler J (2016) Genome-wide Expression Profiling Reveals S100B as Biomarker for Invasive Aspergillosis. Front Microbiol 7, 320. Details PubMed PDF

Dix A, Vlaic S, Guthke R, Linde J (2016) Use of systems biology to decipher host-pathogen interaction networks and predict biomarkers. Clin Microbiol Infect 22(7), 600-606. Details PubMed Open Access

Durmus S, Cakir T, Guthke R (2016) Computational systems biology of pathogen-host interactions Front. Microbiol. 7, 21. (Review) Details PubMed Open Access

Godoy P, Widera A, Schmidt-Heck W, Campos G, Meyer C, Cadenas C, Reif R, Stöber R, Hammad S, Pütter L, Gianmoena K, Marchan R, Ghallab A, Edlund K, Nüssler A, Thasler WE, Damm G, Seehofer D, Weiss TS, Dirsch O, Dahmen U, Gebhardt R, Chaudhari U, Meganathan K, Sachinidis A, Kelm J, Hofmann U, Zahedi RP, Guthke R, Blüthgen N, Dooley S, Hengstler JG (2016) Gene network activity in cultivated primary hepatocytes is highly similar to diseased mammalian liver tissue. Arch Toxicol 90(10), 2513-2529. Details PubMed

Guthke R, Gerber S, Conrad T, Vlaic S, Durmus S, Cakir T, Sevilgen E, Shelest E, Linde J (2016) Data-based reconstruction of gene regulatory networks of fungal pathogens. Front Microbiol 7, 570. Details PubMed Open Access

Horn F, Linde J, Mattern DJ, Walther G, Guthke R, Scherlach K, Martin K, Brakhage AA, Petzke L, Valiante V (2016) Draft genome sequences of fungus Aspergillus calidoustus. Genome Announc 4(2), e00102-16. Details PubMed

Manchanda H, Seidel N, Blaess MF, Claus RA, Linde J, Slevogt H, Sauerbrei A, Guthke R, Schmidtke M (2016) Differential Biphasic Transcriptional Host Response Associated with Coevolution of Hemagglutinin Quasispecies of Influenza A Virus Front Microbiol 7, 1167. Details PubMed

Marthandan S, Baumgart M, Priebe S, Groth M, Schaer J, Kaether C, Guthke R, Cellerino A, Platzer M, Diekmann S, Hemmerich P (2016) Conserved Senescence Associated Genes and Pathways in Primary Human Fibroblasts Detected by RNA-Seq. PLOS ONE 11(5), e0154531. Details PubMed

Matz-Soja M, Rennert C, Schönefeld K, Aleithe S, Boettger J, Schmidt-Heck W, Weiss TS, Hovhannisyan A, Zellmer S, Klöting N, Schulz A, Kratzsch J, Guthke R, Gebhardt R (2016) Hedgehog signaling is a potent regulator of liver lipid metabolism and reveals a GLI-code associated with steatosis eLife 5, e13308. Details Open Access

Schulze S, Schleicher J, Guthke R, Linde J (2016) How to Predict Molecular Interactions between Species? Front Microbiol 7, 442. Details PubMed

Teutschbein J, Simon S, Lother J, Springer J, Hortschansky P, Morton CO, Löffler J, Einsele H, Conneally E, Rogers TR, Guthke R, Brakhage AA, Kniemeyer O (2016) Proteomic profiling of serological responses to Aspergillus fumigatus antigens in patients with invasive aspergillosis. J Proteome Res 15(5), 1580-1591. Details PubMed

Altwasser R, Baldin C, Weber J, Guthke R, Kniemeyer O, Brakhage AA, Linde J, Valiante V (2015) Network Modeling Reveals Cross Talk of MAP Kinases during Adaptation to Caspofungin Stress in Aspergillus fumigatus. PLOS One 10(9), e0136932. Details PubMed Open Access

Dix A, Hünniger K, Weber M, Guthke R, Kurzai O, Linde J (2015) Biomarker-based classification of bacterial and fungal whole-blood infections in a genome-wide expression study. Front Microbiol 6, 171. Details PubMed Open Access

Durmus S, Cakir T, Ozgur A, Guthke R (2015) A review on Computational Systems Biology of Pathogen-Host Interactions Front Microbiol 6, 235. Details Open Access

Horn F, Habel A, Scharf DH, Dworschak J, Brakhage AA, Guthke R, Hertweck C, Linde J (2015) Draft Genome Sequence and Gene Annotation of the Entomopathogenic Fungus Verticillium hemipterigenum. Genome Announc 3(1), pii: e01439-14. Details PubMed Open Access

Horn F, Linde J, Mattern DJ, Walther G, Guthke R, Brakhage AA, Valiante V (2015) Draft Genome Sequence of the Fungus Penicillium brasilianum MG11. Genome Announc 3(5), e00724-15. Details PubMed

Horn F, Üzüm Z, Möbius N, Guthke R, Linde J, Hertweck C (2015) Draft Genome Sequences of Symbiotic and Nonsymbiotic Rhizopus microsporus Strains CBS 344.29 and ATCC 62417. Genome Announc 3(1), pii: e01370-14. Details PubMed Open Access

Linde J, Duggan S, Weber M, Horn F, Sieber P, Hellwig D, Riege K, Marz M, Martin R, Guthke R, Kurzai O (2015) Defining the transcriptomic landscape of Candida glabrata by RNA-Seq. Nucleic Acids Res 43(3), 1392-1406. Details PubMed Open Access

Linde J, Schulze S, Henkel SG, Guthke R (2015) Data- and knowledge-based modeling of gene regulatory networks: An update EXCLI Journal - Experimental and Clinical Sciences 14, 346-378. Details PDF

Mansfeld J, Urban N, Priebe S, Groth M, Frahm C, Hartmann N, Gebauer J, Ravichandran M, Dommaschk A, Schmeisser S, Kuhlow D, Monajembashi S, Bremer-Streck S, Hemmerich P, Kiehntopf M, Zamboni N, Englert C, Guthke R, Kaleta C, Platzer M, Sühnel J, Witte O, Zarse K, Ristow M (2015) Branched-Chain Amino Acid Catabolism is a Conserved Genetic Regulator of Physiological Aging Nature Communications 6, 10043. Details PubMed Open Access

Marthandan S*, Priebe S*, Baumgart M, Groth M, Cellerino A, Guthke R, Platzer P, Hemmerich P and Diekmann S (2015) Similarities in gene expression profiles during in vitro aging of primary human embryonic lung and foreskin fibroblasts BioMed Research International 2015, ID 731938. Details Open Access

Marthandan S, Priebe S, Groth M, Guthke R, Platzer M, Hemmerich P, Diekmann S (2015) Hormetic effect of rotenone in primary human fibroblasts. Immunity & Ageing 12, 11. Details PubMed Open Access

Prauße MTE, Schäuble S, Guthke R, Schuster S (2015) Computing the various pathways of penicillin synthesis and their molar yields. Biotechnology and Bioengineering 113(1), 173-181. Details PubMed

Priebe S, Kreisel C, Horn F, Guthke R, Linde J (2015) FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species. Bioinformatics 31(3), 445-446. Details PubMed

Schleicher J(+), Conrad T(+), Gustafsson M, Cedersund G, Guthke R, Linde J (2015) Facing the challenges of multiscale modelling of bacterial and fungal pathogen-host interactions Briefings in Functional Genomics 2016, pii: elv064. (Review) Details PubMed Open Access

Schmidt-Heck W+, Matz-Soja M+, Aleithe S, Guthke R, Gebhardt R (2015) Fuzzy modeling reveals a dynamic self-sustaining network of the GLI transcription factors controlling important metabolic regulators in adult mouse hepatocytes Molecular BioSystems 11(8), 2190-2197. Details PubMed

Schulze S, Henkel SG, Driesch D, Guthke R, Linde J (2015) Computational prediction of molecular pathogen-host interactions based on dual transcriptome data Front Microbiol 6, 65. Details PubMed Open Access

Vlaic S, Altwasser R, Kupfer P, Nilsson CL, Emmett M, Meyer-Baese A, Guthke R (2015) Inference of Predictive Phospho-Regulatory Networks from LC-MS/MS Phosphoproteomics Data In: INSTICC, Portugal (eds.) Communications in Computer and Information Science BIOINFOMATICS 2016 - 7th Int. Conf. Bioinformatics Models, Methods and Algorithms, Rome, Italy, 02/21/2016-02/23/2016, Springer. Details

Baumgart M, Groth M, Priebe S, Savino A, Testa G, Dix A, Ripa R, Spallotta F, Gaetano C, Ori M, Terzibasi Tozzini E, Guthke R, Platzer M, Cellerino A (2014) RNA-seq of the aging brain in the short-lived fish N. furzeri - conserved pathways and novel genes associated with neurogenesis. Aging Cell 13(6), 965-974. Details PubMed

Hillmann F, Linde J, Beckmann N, Cyrulies M, Strassburger M, Heinekamp T, Haas H, Guthke R, Kniemeyer O, Brakhage AA (2014) The novel globin protein fungoglobin is involved in low oxygen adaptation of Aspergillus fumigatus. Mol Microbiol 93(3), 539-553. Details PubMed

Horn F, Rittweger M, Taubert J, Lysenko A, Rawlings C, Guthke R (2014) Interactive exploration of integrated biological datasets using context-sensitive workflows Front Genet 5, 21. Details PubMed

Horn F, Schroeckh V, Netzker T, Guthke R, Brakhage AA, Linde J (2014) Draft genome sequence of Streptomyces iranensis. Genome Announc 2(4), e00616-14. Details PubMed

Horn F, Valiante V, Guthke R, Brakhage AA (2014) Data-driven systems biology of fungal infections. In: Sullivan D, Moran GP (eds.) Human pathogenic Fungi: Molecular biology and pathogenic mechanisms Caister Academic Press, Norfolk, U.K.. ISBN: 978-1-908230-44. Details

Kupfer P, Huber R, Weber M, Vlaic S, Häupl T, Koczan D, Guthke R, Kinne RW (2014) Novel application of multi-stimuli network inference to synovial fibroblasts of rheumatoid arthritis patients. BMC Med Genomics 7(1), 40-40. Details PubMed

Manchanda H, Seidel N, Krumbholz A, Sauerbrei A, Schmidtke M, Guthke R (2014) Within-host influenza dynamics: a small-scale mathematical modeling approach. Biosystems 118, 51-59. Details PubMed

Ramachandra S, Linde J, Brock M, Guthke R, Hube B, Brunke S (2014) Regulatory networks controlling nitrogen sensing and uptake in Candida albicans. PLOS One 9(3), e92734. Details PubMed Open Access

Schleicher J, Guthke R, Dahmen U, Dirsch O, Holzhuetter HG, Schuster S (2014) A theoretical study of lipid accumulation in the liver-implications for nonalcoholic fatty liver disease. Biochim Biophys Acta 1841(1), 62-69. Details PubMed

Schliess F, Hoehme S, Henkel S, Ghallab A, Driesch D, Böttger J, Guthke R, Pfaff M, Hengstler J, Gebhardt R, Häussinger D, Drasdo D, Zellmer S (2014) Integrated metabolic spatial-temporal model for prediction of ammonia detoxification during liver damage and regeneration Hepatology 60(6), 2040-2051. Details PubMed PDF

Wartenberg A, Linde J, Martin R, Schreiner M, Horn F, Jacobsen ID, Jenull S, Wolf T, Kuchler K, Guthke R, Kurzai O, Forche A, d'Enfert C, Brunke S, Hube B (2014) Microevolution of Candida albicans in macrophages restores filamentation in a nonfilamentous mutant. PLOS Genet 10(12), e1004824. Details PubMed Open Access

Altwasser R, Guthke R, Vlaic S, Emmett MR, Conrad CA, Meyer-Baese A (2013) Model order reduction of deterministic and stochastic gene regulatory networks. In: Hamid R. Arabnia, Quoc-Nam Tran (eds.) Proceedings of the International Conference on Bioinformatics and Computational Biology BIOCOMP'13 13th Int. Conf. Bioinformatics and Computational Biology, Las Vegas/USA, 09/16/2012-09/19/2012, pp. 487-496.CSREA Press, USA. ISBN: 1-60132-234-8. Details

Altwasser R, Guthke R, Vlaic S, Emmett MR, Conrad CA, Meyer-Baese A (2013) Almost sure stability of stochastic gene regulatory networks with mode-dependent interval delays. In: Proc. BIOCOMP'13, BIOCOMP'12, Proc. 13th Int. Conf. Bioinformatics and Computational Biology, Las Vegas/USA, 09/16/2012-09/19/2012, pp. 468-477.CSREA Press, Las Vegas, USA. ISBN: 1-60132-234-8. Details

Kupfer P, Vlaic S, Huber R, Kinne RW, Guthke R (2013) Different stimuli for inference of gene regulatory network in rheumatoid arthritis In: Conference Proceedings International Conference on Bioinformatics Models, Methods and Algorithms, Barcelona/Spain, 02/11/2013-02/14/2013, pp. 282-287. Details

Kupfer P, Vlaic S, Huber R, Kinnne RW, Guthke R (2013) Different stimuli for inference of gene regulatory network in rheumatoid arthritis In: Pedro Fernandes, Jordi Solé-Casals, Ana Fred and Hugo Gamboa (eds.) Bioinformatics 2013 - 4th Int. Conf. on Bioinformatics Models, Methods and Algorithms International Conference on Bioinformatics Models, Methods and Algorithms, Barcelona /Spain, 02/11/2013-02/14/2013, pp. 282-287.SCITEPRESS – Science and Technology Publications, Lissabon /Portugal. ISBN: 978-989-8565358. Details Open Access

Schmeisser K, Mansfeld J, Kuhlow D, Weimer S, Priebe S, Heiland I, Birringer M, Groth M, Segref A, Kanfi Y, Price NL, Schmeisser S, Schuster S, Pfeiffer AF, Guthke R, Platzer M, Hoppe T, Cohen HY, Zarse K, Sinclair DA, Ristow M (2013) Role of sirtuins in lifespan regulation is linked to methylation of nicotinamide. Nat Chem Biol 9(11), 693-700. Details PubMed

Schmeisser S, Priebe S, Groth M, Monajembashi S, Hemmerich P, Guthke R, Platzer M, Ristow M (2013) Neuronal ROS signaling rather than AMPK/sirtuin-mediated energy sensing links dietary restriction to lifespan extension. Mol Metab 2(2), 92-9102. Details PubMed

Schmeisser S, Schmeisser K, Weimer S, Groth M, Priebe S, Fazius E, Kuhlow D, Pick D, Einax JW, Guthke R, Platzer M, Zarse K, Ristow M (2013) Mitochondrial hormesis links low-dose arsenite exposure to lifespan extension. Aging Cell 12(3), 508-517. Details PubMed

Weber M, Henkel SG, Vlaic S, Guthke R, van Zoelen EJ, Driesch D (2013) Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0. BMC Syst Biol 7, 1. Details PubMed

Altwasser R, Linde J, Buyko E, Hahn U, Guthke R (2012) Genome-wide scale-free network inference for Candida albicans. Front Microbiol 3, 51. Details PubMed

Baumgart M, Groth M, Priebe S, Appelt J, Guthke R, Platzer M, Cellerino A (2012) Age-dependent regulation of tumor-related microRNAs in the brain of the annual fish Nothobranchius furzeri. Mech Ageing Dev 133(5), 226-233. Details PubMed

Guthke R, Linde J, Mech F, Figge MT (2012) Systems biology of microbial infection. Front Microbiol 3, 328. Details PubMed Open Access

Hecker M, Goertsches RH, Fatum C, Koczan D, Thiesen HJ, Guthke R, Zettl UK (2012) Network analysis of transcriptional regulation in response to intramuscular interferon-β-1a multiple sclerosis treatment. Pharmacogenomics J 12(4), 360. Details PubMed

Kastner S, Müller S, Natesan L, König GM, Guthke R, Nett M (2012) 4-Hydroxyphenylglycine biosynthesis in Herpetosiphon aurantiacus: a case of gene duplication and catalytic divergence. Arch Microbiol 194(6), 557-566. Details PubMed

Kupfer P, Guthke R, Pohlers D, Huber R, Koczan D, Kinne RW (2012) Batch correction of microarray data substantially improves the identification of genes differentially expressed in rheumatoid arthritis and osteoarthritis. BMC Med Genomics 5, 23. Details PubMed

Linde J, Hortschansky P, Fazius E, Brakhage AA, Guthke R, Haas H (2012) Regulatory interactions for iron homeostasis in Aspergillus fumigatus inferred by a Systems Biology approach. BMC Syst Biol 6, 6. Details PubMed

Müller S, Baldin C, Groth M, Guthke R, Kniemeyer O, Brakhage AA, Valiante V (2012) Comparison of transcriptome technologies in the pathogenic fungus Aspergillus fumigatus reveals novel insights into the genome and MpkA dependent gene expression. BMC Genomics 13, 519. Details PubMed

Rauchfuss F, Lambeck S, Claus RA, Ullmann J, Schulz T, Weber M, Katenkamp K, Guthke R, Bauer M, Settmacher U (2012) Sustained liver regeneration after portal vein embolization - a human molecular pilot study. Dig Liver Dis 44(8), 681-688. Details PubMed

Simon S, Guthke R, Kamradt T, Frey O (2012) Multivariate analysis of flow cytometric data using decision trees. Front Microbiol 3, 114. Details PubMed

Tierney L, Linde J, Müller S, Brunke S, Molina JC, Hube B, Schöck U, Guthke R, Kuchler K (2012) An interspecies regulatory network inferred from simultaneous RNA-seq of Candida albicans invading innate immune cells. Front Microbiol 3, 85. Details PubMed

Vlaic S, Schmidt-Heck W, Matz-Soja M, Marbach E, Linde J, Meyer-Baese A, Zellmer S, Guthke R, Gebhardt R (2012) The extended TILAR approach: a novel tool for dynamic modeling of the transcription factor network regulating the adaption to in vitro cultivation of murine hepatocytes. BMC Syst Biol 6, 147. Details PubMed

Zarse K, Schmeisser S, Groth M, Priebe S, Beuster G, Kuhlow D, Guthke R, Platzer M, Kahn CR, Ristow M (2012) Impaired insulin/IGF1 signaling extends life span by promoting mitochondrial L-proline catabolism to induce a transient ROS signal. Cell Metab 15(4), 451-465. Details PubMed

Albrecht D, Kniemeyer O, Mech F, Gunzer M, Brakhage A, Guthke R (2011) On the way toward systems biology of Aspergillus fumigatus infection. Int J Med Microbiol 301(5), 453-459. Details PubMed

Burmester A, Shelest E, Glöckner G, Heddergott C, Schindler S, Staib P, Heidel A, Felder M, Petzold A, Szafranski K, Feuermann M, Pedruzzi I, Priebe S, Groth M, Winkler R, Li W, Kniemeyer O, Schroeckh V, Hertweck C, Hube B, White TC, Platzer M, Guthke R, Heitman J, Wöstemeyer J, Zipfel PF, Monod M, Brakhage AA (2011) Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi. Genome Biol 12(1), R7. Details PubMed

Göhler AK, Kökpinar Ö, Schmidt-Heck W, Geffers R, Guthke R, Rinas U, Schuster S, Jahreis K, Kaleta C (2011) More than just a metabolic regulator - elucidation and validation of new targets of PdhR in Escherichia coli. BMC Syst Biol 5, 197. Details PubMed

Kaleta C, de Figueiredo LF, Werner S, Guthke R, Ristow M, Schuster S (2011) In silico evidence for gluconeogenesis from fatty acids in humans. PLOS Comput Biol 7(7), e1002116. Details PubMed

Keller J, Ringseis R, Priebe S, Guthke R, Kluge H, Eder K (2011) Effect of L-carnitine on the hepatic transcript profile in piglets as animal model. Nutr Metab (Lond) 8, 76. Details PubMed

Keller J, Ringseis R, Priebe S, Guthke R, Kluge H, Eder K (2011) Dietary L-carnitine alters gene expression in skeletal muscle of piglets. Mol Nutr Food Res 55(3), 419-429. Details PubMed

Mech F*, Thywissen A*, Guthke R, Brakhage AA, Figge MT (2011) Automated image analysis of the host-pathogen interaction between phagocytes and Aspergillus fumigatus. PLOS ONE 6(5), e19591, *authors contributed equally. Details PubMed Open Access

Priebe S, Linde J, Albrecht D, Guthke R, Brakhage AA (2011) FungiFun: A web-based application for functional categorization of fungal genes and proteins. Fungal Genet Biol 48(4), 353-358. Details PubMed

Wessely F, Bartl M, Guthke R, Li P, Schuster S, Kaleta C (2011) Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs. Mol Syst Biol 7, 515. Details PubMed

Albrecht D, Guthke R, Brakhage AA, Kniemeyer O (2010) Integrative analysis of the heat shock response in Aspergillus fumigatus. BMC Genomics 11, 32. Details PubMed

Albrecht D, Kniemeyer O, Brakhage AA, Guthke R (2010) Missing values in gel-based proteomics. Proteomics 10(6), 1202-1211. Details PubMed

El-Kased RF, Koy C, Lorenz P, Drynda S, Guthke R, Qian Z, Koczan D, Li Y, Kekow J, Thiesen HJ, Glocker MO (2010) Mass spectrometric and peptide chip epitope analysis on the RA33 autoantigen with sera from rheumatoid arthritis patients. Eur J Mass Spectrom (Chichester, Eng) 16(3), 443-451. Details PubMed

Kaleta C, Göhler A, Schuster S, Jahreis K, Guthke R, Nikolajewa S (2010) Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis. BMC Syst Biol 4, 116. Details PubMed

Linde J, Wilson D, Hube B, Guthke R (2010) Regulatory network modelling of iron acquisition by a fungal pathogen in contact with epithelial cells. BMC Syst Biol 4, 148. Details PubMed

Zellmer S, Schmidt-Heck W, Godoy P, Weng H, Meyer C, Lehmann T, Sparna T, Schormann W, Hammad S, Kreutz C, Timmer J, von Weizsäcker F, Thürmann PA, Merfort I, Guthke R, Dooley S, Hengstler JG, Gebhardt R (2010) Transcription factors ETF, E2F, and SP-1 are involved in cytokine-independent proliferation of murine hepatocytes. Hepatology 52(6), 2127-2136. Details PubMed

Hecker M, Goertsches RH, Engelmann R, Thiesen HJ, Guthke R (2009) Integrative modeling of transcriptional regulation in response to antirheumatic therapy. BMC Bioinformatics 10, 262. Details PubMed

Hecker M, Lambeck S, Toepfer S, van Someren E, Guthke R (2009) Gene regulatory network inference: data integration in dynamic models-a review. Biosystems 96(1), 86-8103. (Review) Details PubMed

Kienbaum M, Koy C, Montgomery HV, Drynda S, Lorenz P, Illges H, Tanaka K, Kekow J, Guthke R, Thiesen HJ, Glocker MO (2009) MS characterization of apheresis samples from rheumatoid arthritis patients for the improvement of immunoadsorption therapy - a pilot study. Proteomics Clin Appl 3(7), 797-809. Details PubMed

Vödisch M, Albrecht D, Lessing F, Schmidt AD, Winkler R, Guthke R, Brakhage AA, Kniemeyer O (2009) Two-dimensional proteome reference maps for the human pathogenic filamentous fungus Aspergillus fumigatus. Proteomics 9(5), 1407-1415. Details PubMed

Wollbold J, Huber R, Pohlers D, Koczan D, Guthke R, Kinne RW, Gausmann U (2009) Adapted Boolean network models for extracellular matrix formation. BMC Syst Biol 3, 77. Details PubMed

Zellmer S, Sickinger S, Schmidt-Heck W, Guthke R, Gebhardt R (2009) Heterogeneous expression of suppressor of cytokine signalling 2 (SOCS-2) in liver tissue. J Anat 215(2), 176-183. Details PubMed

Dürrschmid K, Reischer H, Schmidt-Heck W, Hrebicek T, Guthke R, Rizzi A, Bayer K (2008) Monitoring of transcriptome and proteome profiles to investigate the cellular response of E. coli towards recombinant protein expression under defined chemostat conditions. J Biotechnol 135(1), 34-44. Details PubMed

Glahn F, Schmidt-Heck W, Zellmer S, Guthke R, Wiese J, Golka K, Hergenröder R, Degen GH, Lehmann T, Hermes M, Schormann W, Brulport M, Bauer A, Bedawy E, Gebhardt R, Hengstler JG, Foth H (2008) Cadmium, cobalt and lead cause stress response, cell cycle deregulation and increased steroid as well as xenobiotic metabolism in primary normal human bronchial epithelial cells which is coordinated by at least nine transcription factors. Arch Toxicol 82(8), 513-524. Details PubMed

Huber R, Hummert C, Gausmann U, Pohlers D, Koczan D, Guthke R, Kinne RW (2008) Identification of intra-group, inter-individual, and gene-specific variances in mRNA expression profiles in the rheumatoid arthritis synovial membrane. Arthritis Res Ther 10(4), R98. Details PubMed

Koczan D, Drynda S, Hecker M, Drynda A, Guthke R, Kekow J, Thiesen HJ (2008) Molecular discrimination of responders and nonresponders to anti-TNF alpha therapy in rheumatoid arthritis by etanercept. Arthritis Res Ther 10(3), R50. Details PubMed

Guthke R, Kniemeyer O, Albrecht D, Brakhage AA, Moeller U (2007) Discovery of gene regulatory networks in Aspergillus fumigatus Lect Notes Bioinf 4366, Details

Glocker MO, Guthke R, Kekow J, Thiesen HJ (2006) Rheumatoid arthritis, a complex multifactorial disease: on the way toward individualized medicine. Med Res Rev 26(1), 63-87. Details PubMed

Guthke R, Zeilinger K, Sickinger S, Schmidt-Heck W, Buentemeyer H, Iding K, Lehmann J, Pfaff M, Pless G, Gerlach JC (2006) Dynamics of amino acid metabolism of primary human liver cells in 3D bioreactors. Bioprocess Biosyst Eng 28(5), 331-340. Details PubMed

Müller U, Ernst G, Melle C, Guthke R, von Eggeling F (2006) Convergence of the proteomic pattern in cancer. Bioinformatics 22(11), 1293-1296. Details PubMed

Guthke R, Möller U, Hoffmann M, Thies F, Töpfer S (2005) Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection. Bioinformatics 21(8), 1626-1634. Details PubMed

Klenk M, Koczan D, Guthke R, Nakata M, Thiesen HJ, Podbielski A, Kreikemeyer B (2005) Global epithelial cell transcriptional responses reveal Streptococcus pyogenes Fas regulator activity association with bacterial aggressiveness. Cell Microbiol 7(9), 1237-1250. Details PubMed

Koczan D, Guthke R, Thiesen HJ, Ibrahim SM, Kundt G, Krentz H, Gross G, Kunz M (2005) Gene expression profiling of peripheral blood mononuclear leukocytes from psoriasis patients identifies new immune regulatory molecules. Eur J Dermatol 15(4), 251-257. Details PubMed