
Prof. Dr. Reinhard Guthke
Systembiologie und Bioinformatik
- 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
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 |
(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
(2019) Increased Expression of RUNX1 in Liver Correlates with NASH Activity Score in Patients with Non-Alcoholic Steatohepatitis (NASH). Cells 8(10), Details PubMed
(2019) Tick-Tock Hedgehog-Mutual crosstalk with liver circadian clock promotes liver steatosis. J Hepatol [Epub ahead of print] Details PubMed
(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
(2018) DeltaMS: A tool to track isotopologues in GC- and LC-MS data. Metabolomics 14(4), 41. Details PubMed
(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
(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
(2018) Impairing L-Threonine Catabolism Promotes Helthspan Through Proteotoxic Methylglyoxal. Cell Metabolism 27(4), 914-925. Details PubMed
(2018) Proteomics of Aspergillus fumigatus conidia-containing phagolysosomes identifies processes governing immune evasion. Mol Cell Proteomics 17(6), 1084-1096. Details PubMed
(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
(2018) ModuleDiscoverer: Identification of regulatory modules in protein-protein interaction networks. Sci Rep 8(1), 433. Details PubMed
(2017) Specific and novel microRNAs are regulated as response to fungal infection in human dendritic cells. Front Microbiol 8, 270. Details PubMed Open Access
(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
(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
(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
(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
(2017) Discovery of an Extended Austinoid Biosynthetic Pathway in Aspergillus calidoustus. ACS Chem Biol 12(5), 1227-1234. Details PubMed Supplement
(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
(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
(2016) Genome-wide Expression Profiling Reveals S100B as Biomarker for Invasive Aspergillosis. Front Microbiol 7, 320. Details PubMed PDF
(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
(2016) Computational systems biology of pathogen-host interactions Front. Microbiol. 7, 21. (Review) Details PubMed Open Access
(2016) Gene network activity in cultivated primary hepatocytes is highly similar to diseased mammalian liver tissue. Arch Toxicol 90(10), 2513-2529. Details PubMed
(2016) Data-based reconstruction of gene regulatory networks of fungal pathogens. Front Microbiol 7, 570. Details PubMed Open Access
(2016) Draft genome sequences of fungus Aspergillus calidoustus. Genome Announc 4(2), e00102-16. Details PubMed
(2016) Differential Biphasic Transcriptional Host Response Associated with Coevolution of Hemagglutinin Quasispecies of Influenza A Virus Front Microbiol 7, 1167. Details PubMed
(2016) Conserved Senescence Associated Genes and Pathways in Primary Human Fibroblasts Detected by RNA-Seq. PLOS ONE 11(5), e0154531. Details PubMed
(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
(2016) How to Predict Molecular Interactions between Species? Front Microbiol 7, 442. Details PubMed
(2016) Proteomic profiling of serological responses to Aspergillus fumigatus antigens in patients with invasive aspergillosis. J Proteome Res 15(5), 1580-1591. Details PubMed
(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
(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
(2015) A review on Computational Systems Biology of Pathogen-Host Interactions Front Microbiol 6, 235. Details Open Access
(2015) Draft Genome Sequence and Gene Annotation of the Entomopathogenic Fungus Verticillium hemipterigenum. Genome Announc 3(1), pii: e01439-14. Details PubMed Open Access
(2015) Draft Genome Sequence of the Fungus Penicillium brasilianum MG11. Genome Announc 3(5), e00724-15. Details PubMed
(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
(2015) Defining the transcriptomic landscape of Candida glabrata by RNA-Seq. Nucleic Acids Res 43(3), 1392-1406. Details PubMed Open Access
(2015) Data- and knowledge-based modeling of gene regulatory networks: An update EXCLI Journal - Experimental and Clinical Sciences 14, 346-378. Details PDF
(2015) Branched-Chain Amino Acid Catabolism is a Conserved Genetic Regulator of Physiological Aging Nature Communications 6, 10043. Details PubMed Open Access
(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
(2015) Hormetic effect of rotenone in primary human fibroblasts. Immunity & Ageing 12, 11. Details PubMed Open Access
(2015) Computing the various pathways of penicillin synthesis and their molar yields. Biotechnology and Bioengineering 113(1), 173-181. Details PubMed
(2015) FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species. Bioinformatics 31(3), 445-446. Details PubMed
(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
(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
(2015) Computational prediction of molecular pathogen-host interactions based on dual transcriptome data Front Microbiol 6, 65. Details PubMed Open Access
(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
(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
(2014) The novel globin protein fungoglobin is involved in low oxygen adaptation of Aspergillus fumigatus. Mol Microbiol 93(3), 539-553. Details PubMed
(2014) Interactive exploration of integrated biological datasets using context-sensitive workflows Front Genet 5, 21. Details PubMed
(2014) Draft genome sequence of Streptomyces iranensis. Genome Announc 2(4), e00616-14. Details PubMed
(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
(2014) Novel application of multi-stimuli network inference to synovial fibroblasts of rheumatoid arthritis patients. BMC Med Genomics 7(1), 40-40. Details PubMed
(2014) Within-host influenza dynamics: a small-scale mathematical modeling approach. Biosystems 118, 51-59. Details PubMed
(2014) Regulatory networks controlling nitrogen sensing and uptake in Candida albicans. PLOS One 9(3), e92734. Details PubMed Open Access
(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
(2014) Integrated metabolic spatial-temporal model for prediction of ammonia detoxification during liver damage and regeneration Hepatology 60(6), 2040-2051. Details PubMed PDF
(2014) Microevolution of Candida albicans in macrophages restores filamentation in a nonfilamentous mutant. PLOS Genet 10(12), e1004824. Details PubMed Open Access
(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
(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
(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
(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
(2013) Role of sirtuins in lifespan regulation is linked to methylation of nicotinamide. Nat Chem Biol 9(11), 693-700. Details PubMed
(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
(2013) Mitochondrial hormesis links low-dose arsenite exposure to lifespan extension. Aging Cell 12(3), 508-517. Details PubMed
(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
(2012) Genome-wide scale-free network inference for Candida albicans. Front Microbiol 3, 51. Details PubMed
(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
(2012) Systems biology of microbial infection. Front Microbiol 3, 328. Details PubMed Open Access
(2012) Network analysis of transcriptional regulation in response to intramuscular interferon-β-1a multiple sclerosis treatment. Pharmacogenomics J 12(4), 360. Details PubMed
(2012) 4-Hydroxyphenylglycine biosynthesis in Herpetosiphon aurantiacus: a case of gene duplication and catalytic divergence. Arch Microbiol 194(6), 557-566. Details PubMed
(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
(2012) Regulatory interactions for iron homeostasis in Aspergillus fumigatus inferred by a Systems Biology approach. BMC Syst Biol 6, 6. Details PubMed
(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
(2012) Sustained liver regeneration after portal vein embolization - a human molecular pilot study. Dig Liver Dis 44(8), 681-688. Details PubMed
(2012) Multivariate analysis of flow cytometric data using decision trees. Front Microbiol 3, 114. Details PubMed
(2012) An interspecies regulatory network inferred from simultaneous RNA-seq of Candida albicans invading innate immune cells. Front Microbiol 3, 85. Details PubMed
(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
(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
(2011) On the way toward systems biology of Aspergillus fumigatus infection. Int J Med Microbiol 301(5), 453-459. Details PubMed
(2011) Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi. Genome Biol 12(1), R7. Details PubMed
(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
(2011) In silico evidence for gluconeogenesis from fatty acids in humans. PLOS Comput Biol 7(7), e1002116. Details PubMed
(2011) Effect of L-carnitine on the hepatic transcript profile in piglets as animal model. Nutr Metab (Lond) 8, 76. Details PubMed
(2011) Dietary L-carnitine alters gene expression in skeletal muscle of piglets. Mol Nutr Food Res 55(3), 419-429. Details PubMed
(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
(2011) FungiFun: A web-based application for functional categorization of fungal genes and proteins. Fungal Genet Biol 48(4), 353-358. Details PubMed
(2011) Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs. Mol Syst Biol 7, 515. Details PubMed
(2010) Integrative analysis of the heat shock response in Aspergillus fumigatus. BMC Genomics 11, 32. Details PubMed
(2010) Missing values in gel-based proteomics. Proteomics 10(6), 1202-1211. Details PubMed
(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
(2010) Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis. BMC Syst Biol 4, 116. Details PubMed
(2010) Regulatory network modelling of iron acquisition by a fungal pathogen in contact with epithelial cells. BMC Syst Biol 4, 148. Details PubMed
(2010) Transcription factors ETF, E2F, and SP-1 are involved in cytokine-independent proliferation of murine hepatocytes. Hepatology 52(6), 2127-2136. Details PubMed
(2009) Integrative modeling of transcriptional regulation in response to antirheumatic therapy. BMC Bioinformatics 10, 262. Details PubMed
(2009) Gene regulatory network inference: data integration in dynamic models-a review. Biosystems 96(1), 86-8103. (Review) Details PubMed
(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
(2009) Two-dimensional proteome reference maps for the human pathogenic filamentous fungus Aspergillus fumigatus. Proteomics 9(5), 1407-1415. Details PubMed
(2009) Adapted Boolean network models for extracellular matrix formation. BMC Syst Biol 3, 77. Details PubMed
(2009) Heterogeneous expression of suppressor of cytokine signalling 2 (SOCS-2) in liver tissue. J Anat 215(2), 176-183. Details PubMed
(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
(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
(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
(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
(2007) Discovery of gene regulatory networks in Aspergillus fumigatus Lect Notes Bioinf 4366, Details
(2006) Rheumatoid arthritis, a complex multifactorial disease: on the way toward individualized medicine. Med Res Rev 26(1), 63-87. Details PubMed
(2006) Dynamics of amino acid metabolism of primary human liver cells in 3D bioreactors. Bioprocess Biosyst Eng 28(5), 331-340. Details PubMed
(2006) Convergence of the proteomic pattern in cancer. Bioinformatics 22(11), 1293-1296. Details PubMed
(2005) Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection. Bioinformatics 21(8), 1626-1634. Details PubMed
(2005) Global epithelial cell transcriptional responses reveal Streptococcus pyogenes Fas regulator activity association with bacterial aggressiveness. Cell Microbiol 7(9), 1237-1250. Details PubMed
(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