Prof. Dr. Reinhard Guthke
(2020) Inflammation-associated suppression of metabolic gene networks in acute and chronic liver disease. Arch Toxicol 94(1), 205-217.
(2019) Comparative genomics of serial Candida glabrata isolates and the rapid acquisition of echinocandin resistance during therapy. Antimicrob Agents Chemother 63(2), e01628-18.
(2019) Increased expression of RUNX1 in liver correlates with NASH activity score in patients with non-alcoholic Steatohepatitis (NASH). Cells 8(10), 1277.
(2019) Tick-Tock Hedgehog-Mutual crosstalk with liver circadian clock promotes liver steatosis. J Hepatol 70(6), 1192-1202.
(2018) Transcriptomic alterations during ageing reflect the shift from cancer to degenerative diseases in the elderly. Nat Commun 9(1), 327.
(2018) DeltaMS: A tool to track isotopologues in GC- and LC-MS data. Metabolomics 14(4), 41.
(2018) Module-detection approaches for the integration of multilevel omics data highlight the comprehensive response of Aspergillus fumigatus to caspofungin. BMC Syst Biol 12(1), 88.
(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.
(2018) Impairing L-threonine catabolism promotes helthspan through proteotoxic methylglyoxal. Cell Metabolism 27(4), 914-925.e5..
(2018) Proteomics of Aspergillus fumigatus conidia-containing phagolysosomes identifies processes governing immune evasion. Mol Cell Proteomics 17(6), 1084-1096.
(2018) Verticillium dahliae-Arabidopsis interaction causes changes in gene expression profiles and jasmonate levels on different time scales. Front Microbiol 9, 217.
(2018) ModuleDiscoverer: Identification of regulatory modules in protein-protein interaction networks. Sci Rep 8(1), 433.
(2017) Specific and novel microRNAs are regulated as response to fungal infection in human dendritic cells. Front Microbiol 8, 270.
(2017) Global analysis of glycoproteins identifies markers of endotoxin tolerant monocytes and GPR84 as a modulator of TNFα expression. Sci Rep 7(1), 838.
(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.
(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.
(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.
(2017) Discovery of an Extended Austinoid Biosynthetic Pathway in Aspergillus calidoustus. ACS Chem Biol 12(5), 1227-1234.
(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.
(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.
(2016) Genome-wide Expression Profiling Reveals S100B as Biomarker for Invasive Aspergillosis. Front Microbiol 7, 320.
(2016) Use of systems biology to decipher host-pathogen interaction networks and predict biomarkers. Clin Microbiol Infect 22(7), 600-606.
(2016) Computational systems biology of pathogen-host interactions Front. Microbiol. 7, 21. (Review)
(2016) Gene network activity in cultivated primary hepatocytes is highly similar to diseased mammalian liver tissue. Arch Toxicol 90(10), 2513-2529.
(2016) Data-based reconstruction of gene regulatory networks of fungal pathogens. Front Microbiol 7, 570.
(2016) Draft genome sequences of fungus Aspergillus calidoustus. Genome Announc 4(2), e00102-16.
(2016) Differential Biphasic Transcriptional Host Response Associated with Coevolution of Hemagglutinin Quasispecies of Influenza A Virus Front Microbiol 7, 1167.
(2016) Conserved Senescence Associated Genes and Pathways in Primary Human Fibroblasts Detected by RNA-Seq. PLOS ONE 11(5), e0154531.
(2016) Hedgehog signaling is a potent regulator of liver lipid metabolism and reveals a GLI-code associated with steatosis eLife 5, e13308.
(2016) How to Predict Molecular Interactions between Species? Front Microbiol 7, 442.
(2016) Proteomic profiling of serological responses to Aspergillus fumigatus antigens in patients with invasive aspergillosis. J Proteome Res 15(5), 1580-1591.
(2015) Network Modeling Reveals Cross Talk of MAP Kinases during Adaptation to Caspofungin Stress in Aspergillus fumigatus. PLOS One 10(9), e0136932.
(2015) Biomarker-based classification of bacterial and fungal whole-blood infections in a genome-wide expression study. Front Microbiol 6, 171.
(2015) A review on Computational Systems Biology of Pathogen-Host Interactions Front Microbiol 6, 235.
(2015) Draft Genome Sequence and Gene Annotation of the Entomopathogenic Fungus Verticillium hemipterigenum. Genome Announc 3(1), pii: e01439-14.
(2015) Draft Genome Sequence of the Fungus Penicillium brasilianum MG11. Genome Announc 3(5), e00724-15.
(2015) Draft Genome Sequences of Symbiotic and Nonsymbiotic Rhizopus microsporus Strains CBS 344.29 and ATCC 62417. Genome Announc 3(1), pii: e01370-14.
(2015) Defining the transcriptomic landscape of Candida glabrata by RNA-Seq. Nucleic Acids Res 43(3), 1392-1406.
(2015) Data- and knowledge-based modeling of gene regulatory networks: An update EXCLI Journal - Experimental and Clinical Sciences 14, 346-378.
(2015) Branched-Chain Amino Acid Catabolism is a Conserved Genetic Regulator of Physiological Aging Nature Communications 6, 10043.
(2015) Similarities in gene expression profiles during in vitro aging of primary human embryonic lung and foreskin fibroblasts BioMed Research International 2015, ID 731938.
(2015) Hormetic effect of rotenone in primary human fibroblasts. Immunity & Ageing 12, 11.
(2015) Computing the various pathways of penicillin synthesis and their molar yields. Biotechnology and Bioengineering 113(1), 173-181.
(2015) FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species. Bioinformatics 31(3), 445-446.
(2015) Facing the challenges of multiscale modelling of bacterial and fungal pathogen-host interactions Briefings in Functional Genomics 2016, pii: elv064. (Review)
(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.
(2015) Computational prediction of molecular pathogen-host interactions based on dual transcriptome data Front Microbiol 6, 65.
(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.
(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.
(2014) The novel globin protein fungoglobin is involved in low oxygen adaptation of Aspergillus fumigatus. Mol Microbiol 93(3), 539-553.
(2014) Interactive exploration of integrated biological datasets using context-sensitive workflows Front Genet 5, 21.
(2014) Draft genome sequence of Streptomyces iranensis. Genome Announc 2(4), e00616-14.
(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.
(2014) Novel application of multi-stimuli network inference to synovial fibroblasts of rheumatoid arthritis patients. BMC Med Genomics 7(1), 40-40.
(2014) Within-host influenza dynamics: a small-scale mathematical modeling approach. Biosystems 118, 51-59.
(2014) Regulatory networks controlling nitrogen sensing and uptake in Candida albicans. PLOS One 9(3), e92734.
(2014) A theoretical study of lipid accumulation in the liver-implications for nonalcoholic fatty liver disease. Biochim Biophys Acta 1841(1), 62-69.
(2014) Integrated metabolic spatial-temporal model for prediction of ammonia detoxification during liver damage and regeneration Hepatology 60(6), 2040-2051.
(2014) Microevolution of Candida albicans in macrophages restores filamentation in a nonfilamentous mutant. PLOS Genet 10(12), e1004824.
(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.
(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.
(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.
(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.
(2013) Role of sirtuins in lifespan regulation is linked to methylation of nicotinamide. Nat Chem Biol 9(11), 693-700.
(2013) Neuronal ROS signaling rather than AMPK/sirtuin-mediated energy sensing links dietary restriction to lifespan extension. Mol Metab 2(2), 92-9102.
(2013) Mitochondrial hormesis links low-dose arsenite exposure to lifespan extension. Aging Cell 12(3), 508-517.
(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.
(2012) Genome-wide scale-free network inference for Candida albicans. Front Microbiol 3, 51.
(2012) Age-dependent regulation of tumor-related microRNAs in the brain of the annual fish Nothobranchius furzeri. Mech Ageing Dev 133(5), 226-233.
(2012) Systems biology of microbial infection. Front Microbiol 3, 328.
(2012) Network analysis of transcriptional regulation in response to intramuscular interferon-β-1a multiple sclerosis treatment. Pharmacogenomics J 12(4), 360.
(2012) 4-Hydroxyphenylglycine biosynthesis in Herpetosiphon aurantiacus: a case of gene duplication and catalytic divergence. Arch Microbiol 194(6), 557-566.
(2012) Batch correction of microarray data substantially improves the identification of genes differentially expressed in rheumatoid arthritis and osteoarthritis. BMC Med Genomics 5, 23.
(2012) Regulatory interactions for iron homeostasis in Aspergillus fumigatus inferred by a Systems Biology approach. BMC Syst Biol 6, 6.
(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.
(2012) Sustained liver regeneration after portal vein embolization - a human molecular pilot study. Dig Liver Dis 44(8), 681-688.
(2012) Multivariate analysis of flow cytometric data using decision trees. Front Microbiol 3, 114.
(2012) An interspecies regulatory network inferred from simultaneous RNA-seq of Candida albicans invading innate immune cells. Front Microbiol 3, 85.
(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.
(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.
(2011) On the way toward systems biology of Aspergillus fumigatus infection. Int J Med Microbiol 301(5), 453-459.
(2011) Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi. Genome Biol 12(1), R7.
(2011) More than just a metabolic regulator - elucidation and validation of new targets of PdhR in Escherichia coli. BMC Syst Biol 5, 197.
(2011) In silico evidence for gluconeogenesis from fatty acids in humans. PLOS Comput Biol 7(7), e1002116.
(2011) Effect of L-carnitine on the hepatic transcript profile in piglets as animal model. Nutr Metab (Lond) 8, 76.
(2011) Dietary L-carnitine alters gene expression in skeletal muscle of piglets. Mol Nutr Food Res 55(3), 419-429.
(2011) Automated image analysis of the host-pathogen interaction between phagocytes and Aspergillus fumigatus. PLOS ONE 6(5), e19591, *authors contributed equally.
(2011) FungiFun: A web-based application for functional categorization of fungal genes and proteins. Fungal Genet Biol 48(4), 353-358.
(2011) Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs. Mol Syst Biol 7, 515.
(2010) Integrative analysis of the heat shock response in Aspergillus fumigatus. BMC Genomics 11, 32.
(2010) Missing values in gel-based proteomics. Proteomics 10(6), 1202-1211.
(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.
(2010) Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis. BMC Syst Biol 4, 116.
(2010) Regulatory network modelling of iron acquisition by a fungal pathogen in contact with epithelial cells. BMC Syst Biol 4, 148.
(2010) Transcription factors ETF, E2F, and SP-1 are involved in cytokine-independent proliferation of murine hepatocytes. Hepatology 52(6), 2127-2136.
(2009) Integrative modeling of transcriptional regulation in response to antirheumatic therapy. BMC Bioinformatics 10, 262.
(2009) Gene regulatory network inference: data integration in dynamic models-a review. Biosystems 96(1), 86-8103. (Review)
(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.
(2009) Two-dimensional proteome reference maps for the human pathogenic filamentous fungus Aspergillus fumigatus. Proteomics 9(5), 1407-1415.
(2009) Adapted Boolean network models for extracellular matrix formation. BMC Syst Biol 3, 77.
(2009) Heterogeneous expression of suppressor of cytokine signalling 2 (SOCS-2) in liver tissue. J Anat 215(2), 176-183.
(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.
(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.
(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.
(2008) Molecular discrimination of responders and nonresponders to anti-TNF alpha therapy in rheumatoid arthritis by etanercept. Arthritis Res Ther 10(3), R50.
(2007) Discovery of gene regulatory networks in Aspergillus fumigatus Lect Notes Bioinf 4366,
(2006) Rheumatoid arthritis, a complex multifactorial disease: on the way toward individualized medicine. Med Res Rev 26(1), 63-87.
(2006) Dynamics of amino acid metabolism of primary human liver cells in 3D bioreactors. Bioprocess Biosyst Eng 28(5), 331-340.
(2006) Convergence of the proteomic pattern in cancer. Bioinformatics 22(11), 1293-1296.
(2005) Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection. Bioinformatics 21(8), 1626-1634.
(2005) Global epithelial cell transcriptional responses reveal Streptococcus pyogenes Fas regulator activity association with bacterial aggressiveness. Cell Microbiol 7(9), 1237-1250.
(2005) Gene expression profiling of peripheral blood mononuclear leukocytes from psoriasis patients identifies new immune regulatory molecules. Eur J Dermatol 15(4), 251-257.