Gianni Panagiotou

Dr. Gianni Panagiotou

Systems Biology and Bioinformatics · Head

Phone: +49 3641 532-1759 Fax: +49 3641 532-2759 Email: gianni.panagiotou@leibniz-hki.de

Main Research Areas
  • Integration and interrogation of large datasets for studying the interplay between genomes, metagenomes and the exposome, e.g. drugs, nutraceuticals, bioactive compounds, to discover new molecular mechanisms related to healthy and disease states.
  • Understand the metabolism of eukaryotic organisms for the design of production platforms for added- and high-added value molecules.


Selected Publications

  • J. Li, C. Ying Ju Sung, N. Lee, Y. Ni, J. Pihlajamäki, G. Panagiotou*, H. El-Nezami. Probiotics modulated gut microbiota suppresses hepatocellular carcinoma growth in mice. Proceedings of the National Academy of Sciences (PNAS),. 2016. doi: 10.1073/pnas.1518189113
  • Y. Ni, J. Li, G. Panagiotou*. A Molecular-Level Landscape of Diet-Gut Microbiome Interactions: Towards Dietary Interventions Targeting Bacterial Genes. mBIO. 2015. 6(6):e01263-15. doi:10.1128/mBio.01263-15
  • K. Jensen, Y. Ni, G. Panagiotou*, I. Kouskoumvekaki. Developing a Molecular Roadmap of Drug-Food Interactions. PLoS Comput Biol. 2015. 11(2): e1004048. doi:10.1371/journal.pcbi.1004048
  • K. Jensen, G. Panagiotou, I. Kouskoumvekaki. NutriChem: a systems chemical biology resource to explore the medicinal value of plant-based foods. Nucleic Acids Research. 2015. doi: 10.1093/nar/gku724
  • D. Westergaard, J. Li, K. Jensen, I. Kouskoumvekaki, G. Panagiotou*. Exploring mechanisms of diet-colon cancer associations through candidate molecular interaction networks. BMC Genomics. 2014, 15:380 . doi:10.1186/1471-2164-15-380
  • K. Jensen, G. Panagiotou*, I. Kouskoumvekaki. Integrated Text Mining and Chemoinformatics Analysis Associates Diet to Health Benefit at Molecular Level. PLOS Comput Biol. 2014, 10(1): e1003432. doi:10.1371/journal.pcbi.1003432
  • U.P. Jacobsen, H.B. Nielsen, T. Sicheritz-Ponten, I. Kouskoumvekaki, G. Panagiotou*. The chemical interactome space between the human host and the genetically defined metabotybes of our gut. ISME J. 2013. doi: 10.1038/ismej.2012.141.
  • K. Jensen, D. Plitchta, S. Brunak, G. Panagiotou*, I. Kouskoumvekaki. Mapping the genome of Plasmodium falciparum on the druglike chemical space reveals novel antimalarial targets and potential drug leads. Molecular Biosystems. 2012. 8(6): 1678-85
  • Panagiotou G, Grotkjaer T, Hofmann G, Bapat PM, Olsson L (2009) Overexpression of a novel endogenous NADH kinase in Aspergillus nidulans enhances growth. Metab Eng 11(1), 31-39.
  • M.R Andersen, W. Vongsangnak, G. Panagiotou, M.P. Salazar, L. Lehmann, J. Nielsen. A tri-species Aspergillus microarray – advancing comparative transcriptomics. Proceedings of the National Academy of Sciences (PNAS), 2008. 105, 4387-4392.
Curriculum vitae

Professional Career

Education

2000-2004 PhD in chemical engineering, National Technical University of Athens, Greece
1993-1999 MSc in chemical engineering, National Technical University of Athens, Greece

Employment

2017- Head of Systems Biology & Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Jena, Germany
2013-2020 Associate Professor (2017-2020 Honorary Associate Professor) (http://sbb.hku.hk), School of Biological Sciences, The University of Hong Kong
2009-2013 Associate Professor, CMB, CBS, CfB, Technical University of Denmark (DTU-Systems Biology)
2007-2009 Assistant Professor, CMB, Technical University of Denmark (DTU-Systems Biology)
2004-2007 Post doctoral researcher at CMB, Technical University of Denmark (DTU-Systems Biology)

Visiting Professor

2010 Industrial Biotechnology lab, Department of Chemical and Biological Engineering, Chalmers University, Sweden (6 months)
2008 Natural Products Chemistry lab, Department of Pharmaceutical Sciences, The University of Tokyo, Japan (12 months)

Management Experience

2015- Organizer of an annual international Next Generation Sequencing Data Analysis workshop at HKU
2014- Advisor, Open Communications Press (OCP) (http://www.open-communications.org/)
2012- Editor-in-Chief, Computational & Structural Biotechnology Journal (Elsevier)

Supervision Experience

2006- Ten PhD students, sixteen BSc and MSc students and fifteen internships
Publications

Heshiki Y, Dissanayake T, Zheng T, Kang K, Yueqiong N, Xu Z, Sarkar C, Woo PCY, Chow BKC, Baker D, Yan A, Webster CJ, Panagiotou G, Li J (2017) Toward a Metagenomic Understanding on the Bacterial Composition and Resistome in Hong Kong Banknotes Front Microbiol 8(632), Details Open Access

Ni Y, Jensen K, Kouskoumvekaki I, Panagiotou G (2017) NutriChem 2.0: exploring the effect of plant-based foods on human health and drug efficacy Database (2017), Details Open Access

Ni Y, Wong VHY, Tai WCS, Li J, Wong WY, Lee MML, Fong FLY, El-Nezami H, Panagiotou G (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. Details PubMed

Zheng T*, Ni Y*, Li J, Chow BKC, Panagiotou G (2017) Designing Dietary Recommendations Using System Level Interactomics Analysis and Network-Based Inference Front. Physiol. 8(753), Details Open Access

Li J, Sung CY, Lee N, Ni Y, Pihlajamäki J, Panagiotou G, El-Nezami H (2016) Probiotics modulated gut microbiota suppresses hepatocellular carcinoma growth in mice. Proc Natl Acad Sci U S A 113(9), E1306-E1315. Details PubMed

Liang C, Cheng S, Zhang Y, Sun Y, Fernie AR, Kang K, Panagiotou G, Lo C, Lim BL (2016) Transcriptomic, proteomic and metabolic changes in Arabidopsis thaliana leaves after the onset of illumination. BMC Plant Biol 16, 43. Details PubMed

Ni Y, Li J, Panagiotou G (2016) COMAN: a web server for comprehensive metatranscriptomics analysis. BMC Genomics 17(1), 622. Details PubMed

Jensen K, Ni Y, Panagiotou G, Kouskoumvekaki I (2015) Developing a molecular roadmap of drug-food interactions. PLoS Comput Biol 11(2), e1004048. Details PubMed

Jensen K, Panagiotou G, Kouskoumvekaki I (2015) NutriChem: a systems chemical biology resource to explore the medicinal value of plant-based foods. Nucleic Acids Res 43(Database issue), D940-D945. Details PubMed

Kang K, Li J, Lim BL, Panagiotou G (2015) MESSI: metabolic engineering target selection and best strain identification tool. Database (Oxford) 2015, Details PubMed

Ni Y, Li J, Panagiotou G (2015) A Molecular-Level Landscape of Diet-Gut Microbiome Interactions: Toward Dietary Interventions Targeting Bacterial Genes. MBio 6(6), e01263. Details PubMed

Udatha DB, Madsen KM, Panagiotou G, Olsson L (2015) Multiple nucleophilic elbows leading to multiple active sites in a single module esterase from Sorangium cellulosum. J Struct Biol 190(3), 314-327. Details PubMed

Udatha DB, Topakas E, Salazar M, Olsson L, Andersen MR, Panagiotou G (2015) Deciphering the signaling mechanisms of the plant cell wall degradation machinery in Aspergillus oryzae. BMC Syst Biol 9, 77. Details PubMed

Jensen K, Panagiotou G, Kouskoumvekaki I (2014) Integrated text mining and chemoinformatics analysis associates diet to health benefit at molecular level. PLoS Comput Biol 10(1), e1003432. Details PubMed

Westergaard D, Li J, Jensen K, Kouskoumvekaki I, Panagiotou G (2014) Exploring mechanisms of diet-colon cancer associations through candidate molecular interaction networks. BMC Genomics 15, 380. Details PubMed

Jacobsen UP, Nielsen HB, Hildebrand F, Raes J, Sicheritz-Ponten T, Kouskoumvekaki I, Panagiotou G (2013) The chemical interactome space between the human host and the genetically defined gut metabotypes. ISME J 7(4), 730-742. Details PubMed

Topakas E, Panagiotou G, Christakopoulos P (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. Details

Udatha DB, Rasmussen S, Sicheritz-Pontén T, Panagiotou G (2013) Targeted metabolic engineering guided by computational analysis of single-nucleotide polymorphisms (SNPs). Methods Mol Biol 985, 409-428. Details PubMed

Herrgård M, Panagiotou G (2012) Analyzing the genomic variation of microbial cell factories in the era of "New Biotechnology" Comput Struct Biotechnol J 3, e201210012. Details PubMed

Jensen K, Plichta D, Panagiotou G, Kouskoumvekaki I (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. Details PubMed

Panagiotou G, Taboureau O (2012) The impact of network biology in pharmacology and toxicology. SAR QSAR Environ Res 23(3-4), 221-235. (Review) Details PubMed

Udatha DB, Mapelli V, Panagiotou G, Olsson L (2012) Common and distant structural characteristics of feruloyl esterase families from Aspergillus oryzae. PLoS One 7(6), e39473. Details PubMed

Udatha DB, Sugaya N, Olsson L, Panagiotou G (2012) How well do the substrates KISS the enzyme? Molecular docking program selection for feruloyl esterases. Sci Rep 2, 323. Details PubMed

Kouskoumvekaki I, Panagiotou G (2011) Navigating the human metabolome for biomarker identification and design of pharmaceutical molecules. J Biomed Biotechnol 2011, Details PubMed

Madsen KM, Udatha GD, Semba S, Otero JM, Koetter P, Nielsen J, Ebizuka Y, Kushiro T, Panagiotou G (2011) Linking genotype and phenotype of Saccharomyces cerevisiae strains reveals metabolic engineering targets and leads to triterpene hyper-producers. PLoS One 6(3), e14763. Details PubMed

Panagiotou G, Topakas E, Moukouli M, Christakopoulos P, Olsson L (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. Details

Udatha DB, Kouskoumvekaki I, Olsson L, Panagiotou G (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. Details PubMed

Olivares-Hernández R, Sunner H, Frisvad JC, Olsson L, Nielsen J, Panagiotou G (2010) Combining substrate specificity analysis with support vector classifiers reveals feruloyl esterase as a phylogenetically informative protein group. PLoS One 5(9), e12781. Details PubMed

Otero JM, Papadakis MA, Udatha DB, Nielsen J, Panagiotou G (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. Details PubMed

Panagiotou G, Topakas E, Olivares R, Christakopoulos P, Olsson L (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. Details

Panagiotou G, Andersen MR, Grotkjaer T, Regueira TB, Nielsen J, Olsson L (2009) Studies of the production of fungal polyketides in Aspergillus nidulans by using systems biology tools. Appl Environ Microbiol 75(7), 2212-2220. Details PubMed

Panagiotou G, Grotkjaer T, Hofmann G, Bapat PM, Olsson L (2009) Overexpression of a novel endogenous NADH kinase in Aspergillus nidulans enhances growth. Metab Eng 11(1), 31-39. Details PubMed

Panagiotou G, Nielsen J (2009) Nutritional systems biology: definitions and approaches. Annu Rev Nutr 29, 329-339. Details PubMed

Salazar M, Vongsangnak W, Panagiotou G, Andersen MR, Nielsen J (2009) Uncovering transcriptional regulation of glycerol metabolism in Aspergilli through genome-wide gene expression data analysis. Mol Genet Genomics 282(6), 571-586. Details PubMed

Andersen MR, Vongsangnak W, Panagiotou G, Salazar MP, Lehmann L, Nielsen J (2008) A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species. Proc Natl Acad Sci U S A 105(11), 4387-4392. Details PubMed

Kouskoumvekaki I, Yang Z, Jónsdóttir SO, Olsson L, Panagiotou G (2008) Identification of biomarkers for genotyping Aspergilli using non-linear methods for clustering and classification. BMC Bioinformatics 9, 59. Details PubMed

Panagiotou G, Andersen MR, Grotkjaer T, Regueira TB, Hofmann G, Nielsen J, Olsson L (2008) Systems analysis unfolds the relationship between the phosphoketolase pathway and growth in Aspergillus nidulans. PLoS One 3(12), e3847. Details PubMed

Panagiotou G, Pachidou F, Petroutsos D, Olsson L, Christakopoulos P (2008) Fermentation characteristics of Fusarium oxysporum grown on acetate. Bioresour Technol 99(15), 7397-7401. Details PubMed

Panagiotou G, Papadakis MA, Topakas E, Olsson L, Christakopoulos P (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. Details

Meijer S, Panagiotou G, Olsson L, Nielsen J (2007) Physiological characterization of xylose metabolism in Aspergillus niger under oxygen-limited conditions. Biotechnol Bioeng 98(2), 462-475. Details PubMed

Otero JM, Panagiotou G, Olsson L (2007) Fueling industrial biotechnology growth with bioethanol. Adv Biochem Eng Biotechnol 108, 1-40. Details PubMed

Panagiotou G, Kouskoumvekaki I, Jónsdóttir SO, Olsson L (2007) Monitoring novel metabolic pathways using metabolomics and machine learning: induction of the phosphoketolase pathway in Aspergillus nidulans cultivations Metabolomics 3(4), 503-516. Details

Panagiotou G, Olavarria R, Olsson L (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. Details PubMed

Panagiotou G, Olsson L (2007) Effect of compounds released during pretreatment of wheat straw on microbial growth and enzymatic hydrolysis rates. Biotechnol Bioeng 96(2), 250-258. Details PubMed

Panagiotou G, Christakopoulos P, Grotkjaer T, Olsson L (2006) Engineering of the redox imbalance of Fusarium oxysporum enables anaerobic growth on xylose. Metab Eng 8(5), 474-482. Details PubMed

Panagiotou G, Granouillet P, Olsson L (2006) Production and partial characterization of arabinoxylan-degrading enzymes by Penicillium brasilianum under solid-state fermentation. Appl Microbiol Biotechnol 72(6), 1117-1124. Details PubMed

Panagiotou G, Christakopoulos P, Olsson L (2005) The influence of different cultivation conditions on the metabolome of Fusarium oxysporum. J Biotechnol 118(3), 304-315. Details PubMed

Panagiotou G, Christakopoulos P, Olsson L (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. Details

Panagiotou G, Christakopoulos P, Villas-Boas SG, Olsson L (2005) Fermentation performance and intracellular metabolite profiling of Fusarium oxysporum cultivated on a glucose-xylose mixture. Enzyme and Microbial Technology 36, 100-106. Details

Panagiotou G, Villas-Bôas SG, Christakopoulos P, Nielsen J, Olsson L (2005) Intracellular metabolite profiling of Fusarium oxysporum converting glucose to ethanol. J Biotechnol 115(4), 425-434. Details PubMed

Panagiotou G, Christakopoulos P (2004) NADPH-dependent D-aldose reductases and xylose fermentation in Fusarium oxysporum. J Biosci Bioeng 97(5), 299-304. Details PubMed

Panagiotou G, Kekos D, Macris BJ, Christakopoulos P (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. Details

Panagiotou G, Topakas E, Economou L, Kekos D, Macris BJ, Christakopoulos P (2003) Induction, purification, and characterization of two extracellular alpha-L-arabinofuranosidases from Fusarium oxysporum. Can J Microbiol 49(10), 639-644. Details PubMed

Panagiotou G, Kekos D, Macris BJ, Christakopoulos P (2002) Purification and characterisation of NAD+-dependent xylitol dehydrogenase from Fusarium oxysporum Biotechnology Letters 24(24), 2089-2092. Details