- Medizinische & Umweltmetagenomik: Mensch, Maus, Pflanzen, marine Lebewesen
- Systembiologie: Integration von –omics-Daten; Molekül/ Protein & Protein/ Protein Netzwerke
- Metabolische Modellierung auf Genomausmaß
- “Metabolic Engineering”: maßgeschneiderte Hefezellfabrik
(2021) The peroxiredoxin asp f3 acts as redox sensor in Aspergillus fumigatus. Genes 12(5), 668.
(2021) Expansion and persistence of antibiotic-specific resistance genes following antibiotic treatment. Gut Microbes 13(1), 1-19.
(2021) DAnIEL: a user-friendly web server for fungal ITS amplicon sequencing data. Front Microbiol [Accepted]
(2021) An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness. Gut Microbes [Accepted]
(2021) Metabolic modeling predicts specific gut bacteria as key determinants for Candida albicans colonization levels. ISME J 15, 1257-1270.
(2021) Distinct composition and metabolic functions of human gut microbiota are associated with cachexia in lung cancer patients. ISMEJ [Epub ahead of print]
(2021) Horseshoe crab genomes reveal the evolution of genes and microRNAs after three rounds of whole genome duplication. Commun Biol 4(1), 83.
(2021) MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome. PLoS Comput Biol 17(1), e1008487.
(2021) Decreased abundance of Akkermansia muciniphila leads to the impairment of insulin secretion and glucose homeostasis in lean type 2 diabetes. Adv Sci [Epub ahead of print]
(2020) Effects of agricultural fungicide use on Aspergillus fumigatus abundance, antifungal susceptibility, and population structure. mBio 11(6), e02213-20.
(2020) Dynamic surface proteomes of allergenic fungal conidia. J Proteome Res 19(5), 2092-2104.
(2020) Novel approaches for systems biology of metabolism-oriented pathogen-human interactions: A mini-review Front Cell Infect Microbiol 10, 52. (Review)
(2020) Comparative transcriptomic analysis of rhinovirus and influenza virus infection. Front Microbiol 11(1580), 1-13.
(2020) Myeloproliferative neoplasms treated with hydroxyurea, pegylated interferon alpha-2A orruxolitinib: Clinicohematologic responses, quality-of-life changes and safety in the real-world setting. Hematology 25(1), 247-257.
(2020) Clofarabine, cytarabine, and mitoxantrone in refractory/relapsed acute myeloid leukemia: High response rates and effective bridge to allogeneic hematopoietic stem cell transplantation. Cancer Med 9(10), 3371-3382.
(2020) Gastric bypass surgery in a rat model alters the community structure and functional composition of the intestinal microbiota independently of weight loss. Microbiome 8(1), 13.
(2020) Predictable modulation of cancer treatment outcomes by the gut microbiota. Microbiome 8(1), 28.
(2020) Lipid metabolic signatures deviate in sepsis survivors compared to non-survivors. Comput Struct Biotechnol J 18, 3678-3691.
(2020) Gut microbiome fermentation determines the efficacy of exercise for diabetes prevention. Cell Metab 31(1), 77-91.
(2020) Proteome analysis of bronchoalveolar lavage fluids reveals host and fungal proteins highly expressed during invasive pulmonary aspergillosis in mice and humans. Virulence 11(1), 1337-1351.
(2020) A metagenome-wide association study of gut microbiome and visceral fat accumulation. Comput Struct Biotechnol J 18, 2596-2609.
(2020) Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria. Microbiome 8(1), 133.
(2020) Triple RNA-seq reveals synergy in a human virus-fungus co-infection model. Cell Reports 33(7), 108389.
(2019) A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments. Microbiome 7(1), 104.
(2019) Linking genetic, metabolic and phenotypic diversity among S. cerevisiae strains using multi-omics associations Gigascience 8(4), giz015.
(2019) Antibiotic treatment drives the diversification of the human gut resistome. Genom Proteom Bioinf 17(1), 39-51.
(2019) Phagocytic predation by the fungivorous amoeba Protostelium aurantium targets metal ion and redox homeostasis. bioRxiv 690503, preprint.
(2019) Metabolic phenotypes and the gut microbiota in response to dietary resistant starch type 2 in normal-weight subjects: a randomized crossover trial. Sci Rep 9(1), 4736.
(2019) Mining, analyzing, and integrating viral signals from metagenomic data. Microbiome 7(1), 42.
(2018) Next-generation sequencing with a 54-gene panel identified unique mutational profile and prognostic markers in Chinese patients with myelofibrosis. Ann Hematol 98(4), 869-879.
(2018) Complete genome sequence of Escherichia coli strain WG5. Genome Announc 6(2), e01403-17.
(2018) The environmental exposures and inner- and intercity traffic flows of the metro system may contribute to the human skin microbiome and resistome. Cell Reports 24(5), 1190-1202.
(2018) Differential microbial communities of omnivorous and herbivorous cattle in Southern China. Comput Struct Biotechnol J 16, 54-60.
(2017) Toward a Metagenomic Understanding on the Bacterial Composition and Resistome in Hong Kong Banknotes. Front Microbiol 8, 632.
(2017) NutriChem 2.0: exploring the effect of plant-based foods on human health and drug efficacy. Database (2017),
(2017) A metagenomic study of the preventive effect of Lactobacillus rhamnosus GG on intestinal polyp formation in ApcMin/+ mice. J Appl Microbiol 122(3), 770-784.
(2017) Designing Dietary Recommendations Using System Level Interactomics Analysis and Network-Based Inference. Front Physiol 8, 753.
(2016) Probiotics modulated gut microbiota suppresses hepatocellular carcinoma growth in mice. Proc Natl Acad Sci U S A 113(9), E1306-E1315.
(2016) Transcriptomic, proteomic and metabolic changes in Arabidopsis thaliana leaves after the onset of illumination. BMC Plant Biol 16, 43.
(2016) COMAN: a web server for comprehensive metatranscriptomics analysis. BMC Genomics 17(1), 622.
(2015) Developing a molecular roadmap of drug-food interactions. PLOS Comput Biol 11(2), e1004048.
(2015) NutriChem: a systems chemical biology resource to explore the medicinal value of plant-based foods. Nucleic Acids Res 43(Database issue), D940-D945.
(2015) MESSI: metabolic engineering target selection and best strain identification tool. Database (Oxford) 2015,
(2015) A Molecular-Level Landscape of Diet-Gut Microbiome Interactions: Toward Dietary Interventions Targeting Bacterial Genes. MBio 6(6), e01263.
(2015) Multiple nucleophilic elbows leading to multiple active sites in a single module esterase from Sorangium cellulosum. J Struct Biol 190(3), 314-327.
(2015) Deciphering the signaling mechanisms of the plant cell wall degradation machinery in Aspergillus oryzae. BMC Syst Biol 9, 77.
(2014) Integrated text mining and chemoinformatics analysis associates diet to health benefit at molecular level. PLOS Comput Biol 10(1), e1003432.
(2014) Exploring mechanisms of diet-colon cancer associations through candidate molecular interaction networks. BMC Genomics 15, 380.
(2013) The chemical interactome space between the human host and the genetically defined gut metabotypes. ISME J 7(4), 730-742.
(2013) Characteristics, sources, production and applications. Xylanases. In: Yang S-T, El Ensashy H, Thongchul N (eds.) Bioprocessing Technologies in Biorefinery for Sustainable Production of Fuels, Chemicals, and Polymers pp. 147-169. Wiley. ISBN: 978-0-470-54195.
(2013) Targeted metabolic engineering guided by computational analysis of single-nucleotide polymorphisms (SNPs). Methods Mol Biol 985, 409-428.
(2012) Analyzing the genomic variation of microbial cell factories in the era of "New Biotechnology" Comput Struct Biotechnol J 3, e201210012.
(2012) Mapping the genome of Plasmodium falciparum on the drug-like chemical space reveals novel anti-malarial targets and potential drug leads. Mol Biosyst 8(6), 1678-1685.
(2012) The impact of network biology in pharmacology and toxicology. SAR QSAR Environ Res 23(3-4), 221-235. (Review)
(2012) Common and distant structural characteristics of feruloyl esterase families from Aspergillus oryzae. PLOS One 7(6), e39473.
(2012) How well do the substrates KISS the enzyme? Molecular docking program selection for feruloyl esterases. Sci Rep 2, 323.
(2011) Navigating the human metabolome for biomarker identification and design of pharmaceutical molecules. J Biomed Biotechnol 2011,
(2011) Linking genotype and phenotype of Saccharomyces cerevisiae strains reveals metabolic engineering targets and leads to triterpene hyper-producers. PLOS One 6(3), e14763.
(2011) Studying the ability of Fusarium oxysporum and recombinant Saccharomyces cerevisae to efficiently cooperate in decomposition and ethanolic fermentation of wheat straw. Biomass and Bioenergy 35(8), 3727-3732.
(2011) The interplay of descriptor-based computational analysis with pharmacophore modeling builds the basis for a novel classification scheme for feruloyl esterases. Biotechnol Adv 29(1), 94-9110.
(2010) Combining substrate specificity analysis with support vector classifiers reveals feruloyl esterase as a phylogenetically informative protein group. PLOS One 5(9), e12781.
(2010) Yeast biological networks unfold the interplay of antioxidants, genome and phenotype, and reveal a novel regulator of the oxidative stress response. PLOS One 5(10), e13606.
(2010) Feruloyl esterases as biosynthetic tools for the organic synthesis of nutraceutical compounds In: Heldman DR, Hoover DG, Wheeler MB (eds.) Encyclopedia of Biotechnology in Agriculture and Food CRC Press, Boca Raton, FL, USA. ISBN: 978-0849350276.
(2009) Studies of the production of fungal polyketides in Aspergillus nidulans by using systems biology tools. Appl Environ Microbiol 75(7), 2212-2220.
(2009) Overexpression of a novel endogenous NADH kinase in Aspergillus nidulans enhances growth. Metab Eng 11(1), 31-39.
(2009) Nutritional systems biology: definitions and approaches. Annu Rev Nutr 29, 329-339.
(2009) Uncovering transcriptional regulation of glycerol metabolism in Aspergilli through genome-wide gene expression data analysis. Mol Genet Genomics 282(6), 571-586.
(2008) A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species. Proc Natl Acad Sci U S A 105(11), 4387-4392.
(2008) Identification of biomarkers for genotyping Aspergilli using non-linear methods for clustering and classification. BMC Bioinformatics 9, 59.
(2008) Systems analysis unfolds the relationship between the phosphoketolase pathway and growth in Aspergillus nidulans. PLOS One 3(12), e3847.
(2008) Fermentation characteristics of Fusarium oxysporum grown on acetate. Bioresour Technol 99(15), 7397-7401.
(2008) Identification of NADH kinase activity in filamentous fungi and structural modelling of the novel enzyme from Fusarium oxysporum Process Biochemistry 43(10), 1114-1120.
(2007) Physiological characterization of xylose metabolism in Aspergillus niger under oxygen-limited conditions. Biotechnol Bioeng 98(2), 462-475.
(2007) Fueling industrial biotechnology growth with bioethanol. Adv Biochem Eng Biotechnol 108, 1-40.
(2007) Monitoring novel metabolic pathways using metabolomics and machine learning: induction of the phosphoketolase pathway in Aspergillus nidulans cultivations Metabolomics 3(4), 503-516.
(2007) Penicillium brasilianum as an enzyme factory; the essential role of feruloyl esterases for the hydrolysis of the plant cell wall. J Biotechnol 130(3), 219-228.
(2007) Effect of compounds released during pretreatment of wheat straw on microbial growth and enzymatic hydrolysis rates. Biotechnol Bioeng 96(2), 250-258.
(2006) Engineering of the redox imbalance of Fusarium oxysporum enables anaerobic growth on xylose. Metab Eng 8(5), 474-482.
(2006) Production and partial characterization of arabinoxylan-degrading enzymes by Penicillium brasilianum under solid-state fermentation. Appl Microbiol Biotechnol 72(6), 1117-1124.
(2005) The influence of different cultivation conditions on the metabolome of Fusarium oxysporum. J Biotechnol 118(3), 304-315.
(2005) Simultaneous saccharification and fermentation of cellulose by Fusarium oxysporum F3—growth characteristics and metabolite profiling Enzyme and Microbial Technology 36(5-6), 693-699.
(2005) Fermentation performance and intracellular metabolite profiling of Fusarium oxysporum cultivated on a glucose-xylose mixture. Enzyme and Microbial Technology 36, 100-106.
(2005) Intracellular metabolite profiling of Fusarium oxysporum converting glucose to ethanol. J Biotechnol 115(4), 425-434.
(2004) NADPH-dependent D-aldose reductases and xylose fermentation in Fusarium oxysporum. J Biosci Bioeng 97(5), 299-304.
(2003) Production of cellulolytic and xylanolytic enzymes by Fusarium oxysporum grown on corn stover in solid state fermentation. Industrial Crops and Products 18(1), 37-45.
(2003) Induction, purification, and characterization of two extracellular alpha-L-arabinofuranosidases from Fusarium oxysporum. Can J Microbiol 49(10), 639-644.
(2002) Purification and characterisation of NAD+-dependent xylitol dehydrogenase from Fusarium oxysporum Biotechnology Letters 24(24), 2089-2092.