- Medical & Environmental Metagenomics: human, mice, marine, plants;
- Systems Biology: -omics integration, chemical-protein & protein-protein interaction networks, genome-scale metabolic modelling;
- Metabolic Engineering: yeast cell factory
|2000-2004||PhD in metabolic engineering obtained from the National Technical University of Athens (16 months as guest PhD at the Technical University of Denmark).|
|1993-1999||Diploma (BSc & MSc) in chemical engineering obtained from the National Technical University of Athens, Greece|
EMPLOYMENT AND ACADEMIC AFFILIATIONS
|2017-||Head of Systems Biology & Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Jena, Germany.|
|2013-2017||Associate Professor at the Faculty of Science, School of Biological Sciences, The University of Hong Kong.
The University of Hong Kong places 25th in 2019 QS World University Rankings
|2009-2013||Associate Professor at the Department of Systems Biology, Technical University of Denmark.
The Technical University of Denmark places 112th in 2019 QS World University Rankings
|2007-2009||Assistant Professor at the Department of Systems Biology, Technical University of Denmark.|
|2004-2007||Post-doctoral researcher at the Department of Systems Biology, Technical University of Denmark.|
|2018-2020||(Honorary) Associate Professor at the Department of Microbiology at Li Ka Shing Faculty of Medicine, The University of Hong Kong.|
|2017-2020||(Honorary) Associate Professor at the Faculty of Science, School of Biological Sciences, The University of Hong Kong.|
|2010||Visiting Assoc. Professor at the Industrial Biotechnology lab, Department of Chemical and Biological Engineering, Chalmers University, Sweden (January – May)|
|2008||Visiting Assist. Professor at the Natural Products Chemistry Lab, Department of Pharmaceutical Sciences, The University of Tokyo, Japan (January – December)|
Awards · Appointments · Scientific Activities
|2019||Organizer of the Training School “Next Generation Data Analysis” offered to the 15 PhD students of the Innovative Training Network “BestTreat”, at Hans Knoell Institute, Jena, Germany, August 28-31 (15 participants).|
|2019||Organizer of the workshop “RNA Sequencing Processing and Data Analysis” at Hans Knoell Institute, Jena, Germany, April 10-11 (15 participants).|
|2019||Organizer of the 4th International Symposium on Systems Biology of Microbial Infection in Jena, Germany, September 26-27.|
|2018||Lecturer at NUGO: 5th Nutrition Winter School, “Breaking barriers: Gut, Brain Bugs – and Beyond”, Levi, Finland, January 21-26.|
|2017||Organizer of the 4th International Symposium on Systems Biology of Microbial Infection in Jena, Germany, September 21-22.|
|2016||Organizer of the International “Next Generation Sequencing Data Analysis” workshop at The University of Hong Kong, Hong Kong, 15th-21st of May (50 participants).|
|2016||Member of the Scientific Committee of the BBW2016: Frontiers in Human Microbiota Symbiotic Interactions, Organized by Fondation IPSEN and AAAS/Science and Science Translational Medicine, Hong Kong May 23-25, 2016.|
|2015||Organizer of the International “Next Generation Sequencing Data Analysis” workshop at The University of Hong Kong, Hong Kong, 27th-31st of May (30 participants) and 3rd-7th of June (30 participants).|
|2014-2016||Responsible for the development and teaching of the course #BIOL2102 “Biostatistics” (on average 250-300 students), The University of Hong Kong (details in the Teaching Portfolio).|
|2014-2016||Responsible for the development and teaching (50%) of the course #BIOL3307/3409 “Business Aspects of Biotechnology” (on average 30-40 students), The University of Hong Kong (details in the Teaching Portfolio).|
|2014||Organizer of the workshop “Analysis of transcriptome data-turbo version” for the students enrolled in the course #BIOL2102, The University of Hong Kong (June-August, 15 participants).|
|2013-2016||Course Coordinator of the course #BIOL6001 “Presentation Skills and Research Seminars in Biological Sciences”, The University of Hong Kong.|
|2013-2016||Course Selection Adviser (CSA) for the Biotechnology Major (3-year curriculum), The University of Hong Kong.|
|2005-2007||Group coordinator at the research cluster “Engineering of the Central Carbon Metabolism”, in the Centre for Microbial Biotechnology, Technical University of Denmark.|
STUDENT SUPERVISION EXPERIENCE AS MAIN SUPERVISOR
|Sara Leal, PhD||2019-2022||Humans as holobionts: systems level approaches for disease prevention and therapy | Hans Knoell Institute, Germany|
|Manos Nychas, PhD||2019-2022||Bioinformatics analysis of meta-omics datasets from human subjects and mice models | Hans Knoell Institute, Germany|
|Howell Leung, PhD||2019-2022||Metagenome mining for effective design of ecology-based treatments | Hans Knoell Institute, Germany|
|Albert Garcia, PhD||2019-2022||Systems Biology and Machine learning in Host-Pathogen Interactions | Hans Knoell Institute, Germany|
|Mohammadhassan Mirhakkak Esfahani, PhD||2017-2020||Integration of host, pathogen and microbiome -omics data in healthy and disease states | Hans Knoell Institute, Germany|
|Daniel Loos, PhD||2018-2021||Linking diseases with the human gut microbiome – biomarker discovery in multi meta-omics data | Hans Knoell Institute, Germany|
|Bastian Seelbinder, PhD||2018-2021||High-throughput sequencing data analysis for understanding host-pathogen interactions | Hans Knoell Institute, Germany|
|Tongta Sae-Ong, PhD||2018-2021||Systems level analysis to elucidate the interplay of host-microbiome in critical illness | Hans Knoell Institute, Germany|
|Jiarui Chen, PhD||2016-2020||Elucidating the complex interactions of microbial communities using high-throughput data integration | The University of Hong Kong, Hong Kong|
|Yoshitaro Heshiki, PhD||2015-2019||Studying microbial communities through next generation sequencing | The University of Hong Kong, Hong Kong|
|Tingting Zheng, PhD||2015-2019||A systems biology approach for studying human diseases | The University of Hong Kong, Hong Kong|
|Samuel Kang, PhD||2014-2018||Bioinformatic Approaches for Exploring the Genetic and Compositional Diversities of Human-Associated Microbial Worlds | The University of Hong Kong, Hong Kong|
|Yueqiong Ni, PhD||2013-2017||Integrative analysis of the human genome, metagenome and exposome | The University of Hong Kong, Hong Kong|
|Kasper Jensen, PhD||2011-2014||Nutritional Systems Biology | Technical University of Denmark, Denmark (joint supervision with Prof. Kouskoumvekaki)|
|Gupta Udatha, PhD||2009-2013||Towards Classification and Functional Description of Enzymes: A case study of Feruloyl Esterases | Chalmers University of Technology, Sweden (joint supervision with Prof. Olsson)|
||Supervisor of seventeen BSc and MSc students, fourteen internships and one research assistant at National Technical University of Athens, Greece, Technical University of Denmark, Denmark, The University of Hong Kong, Hong Kong, and Hans Knoell Institute, Germany|
|Jun Li||2013-2018||Post-Doctoral Researcher, The University of Hong, Hong Kong & Hans Knoell Institute | Currently Assistant Professor at the City University of Hong|
|Yueqiong Ni||2018-2020||Post-Doctoral Researcher, Hans Knoell Institute, Germany|
|Kang Kang||2018-2019||Post-Doctoral Researcher, Hans Knoell Institute, Germany|
|Thomas Wolf||2018-2019||Post-Doctoral Researcher, Hans Knoell Institute, Germany|
|Rakesh Santhanam||2018-2020||Post-Doctoral Researcher, Hans Knoell Institute, Germany|
|Sascha Schäuble||2018-2020||Post-Doctoral Researcher, Hans Knoell Institute, Germany|
|Wolfgang Schmidt-Heck||2018-2020||Scientific Co-worker, Hans Knoell Institute, Germany|
|Peter Großman||2018-2020||Scientific Co-worker, Hans Knoell Institute, Germany|
|2018||co-I||Area of Excellence of the Hong Kong Research Grants Council, “Institute of Metabolic Medicine”, Hong Kong||77,000,000 HKD|
|2018||co-I||Excellence Strategy of the Federal Government “Balance of the Microverse”, Deutsche Forschungsgemeinschaft (DFG), Germany||38,000,000 EURO|
|2018||PI||BestTreat “Building a Gut Microbiome Engineering Toolbox for In-Situ Therapeutic Treatments for Non-Alcoholic Fatty Liver Disease”, Horizon 2020-MSCA-ITN-ETN||4,100,000 EURO|
|2017||co-I||CRC/Transregio 124 “Pathogenic fungi and their human host: Networks of interaction”, Deutsche Forschungsgemeinschaft (DFG), Germany||8,200,000 EURO|
|2016||co-I||“Detection of HIV-1 minority drug-resistant and X4-tropic variants by Next-Generation Sequencing to improve the prediction of clinical antiretroviral treatment outcome”, AIDS Trust Fund, MSS 248 R, Hong Kong||2,597,960 HKD|
|2016||co-I||Environment and Conservation Fund (Hong Kong), MarineGEO - Hong Kong, “Towards an understanding of marine biodiversity and ecosystem function”, 67/2016, Hong Kong||3,200,000 HKD|
|2014||PI||co-funding from the Faculties of Science and Architecture for the project “How bacteria travel around Hong Kong: A metagenome-based mapping of the transportation system”, Hong Kong||400,000 HKD|
|2014-2015||PI||funding from the HKU Strategic Research Theme for Clean Energy for the project “Integration of Yeast Systems Biology into Biorefineries”, Hong Kong||354,000 HKD|
|2014-2015||PI||funding from the HKU Strategic Research Theme of Genomics for the project “Uncovering the complex interactions between anticancer drugs and gut-associated syntrophic consortia using integrated metagenomic sequence analysis”, Hong Kong||225,000 HKD|
|2014||PI||funding from the HKU Seed Funding for Applied Research Scheme, for the project “Designing a 3-hydroxy-propionic acid yeast cell factory using systems & synthetic biology approaches”, Hong Kong||96,000 HKD|
|2014||PI||funding from the HKU Seed Funding for Basic Research Scheme, for the project “Correlation of gut microbiota composition with diet and atherosclerosis development”, Hong Kong||46,000 HKD|
|2013||PI||funding from the HKU University Research Committee in the 30th Round: Post-doctoral Fellow/Research Assistant Professor Scheme, Hong Kong||336,000 HKD|
|2013||PI||funding from the HKU Seed Funding for Basic Research Scheme, for the project “Studying the antibiotic gut resistome and the collateral effects of antibiotics on gut microbes using massive sequencing”, Hong Kong||120,000 HKD|
|2010||PI||funding from the Wallenberg Foundation, Sweden, for designing a microarray chip for the enzyme producer A. oryzae, Sweden||116,000 DKK|
|2007||PI||funding from the Danish Research Council for Technology and Production Sciences, for the project ´´Biotransformation of agro-industrial residues to antibiotics by combinatorial protein chemistry and metabolic engineering´´, Denmark||2,077,500 DKK|
|2007||PI||funding from the Lundbeck Foundation, for the project ´´Use of cDNA microarrays of the filamentous fungus Aspergillus nidulans´´, Denmark||89,371 DKK|
|2006||funding from the Villum Kann Rasmussen Foundation for the project ´´Aspergillus as an efficient cell factory for production of polyketides – metabolic engineering strategies for efficient production of the Acetyl-CoA precursor molecule´´, Denmark||832,818 DKK|
EVIDENCE OF ESTEEM; EXTERNAL VISIBILITY AND PROFESSIONAL ACTIVITIES
|MEMBER||URC Working Group on Entrepreneurship Development under the University Research Committee, The University of Hong Kong (nominated by the Dean for representing the Faculty of Science), 2014 – 2017.|
|Science Faculty Information Technology Committee, The University of Hong Kong (HKU), 2014 - 2017.|
|Career Advisory Board, The University of Hong Kong (HKU), 2015 - 2017.|
|Strategic Research Theme of Genomics (HKU), 2013 - 2017; Strategic Research Theme for Clean Energy (HKU), 2013 - 2017; Strategic Research Theme of Integrative Biology (HKU), 2014.|
|EDITORIAL WORK||Editor-in-Chief: Computational and Structural Biotechnology Journal (2018 Impact Factor of 4.2, Elsevier), 2002-2019.|
|Guest Editor for the research topic “Systems Biology of Metabolism in Infection” for Frontiers in Cellular and Infection Microbiology, 2019|
|Ad hoc reviewer: Briefings in Bioinformatics; Bioinformatics; Cell Reports; Microbial Cell Factories, Scientific Reports etc|
|PEER EVALUATION||Electoral Committee: Member of the Electoral Committee, Researcher C, “Bioinformatics or Computational Biology’’, Institute of Computer Sciences of the Foundation for Research and Technology-Hellas 2013.|
|Electoral Committee: Member of the Electoral committee for the W3 Professorship for Genomics and Bioinformatics in Horticultural Sciences, at the Faculty of Science of the University of Potsdam, 2019.|
|Examiner: 5 PhD and 1 MSc thesis submitted at the School of Biological Sciences, Faculty of Science, The University of Hong Kong and 1 PhD thesis submitted at the Friedrich Schiller University, Jena, Germany.|
|AWARDS||Research Output Prize 2017 in the Faculty of Science, The University of Hong Kong, for the article “Probiotics Modulated Gut Microbiota Suppresses Hepatocellular Carcinoma Growth in Mice”.|
|MEDIA||My research has been featured in articles of South China Morning Post (Asia), Spiegel, Bild, Daily Mail (Europe), LA Times (US), among many others.|
|PATENTS||WO2009144245-A1 Gianni Panagiotou, Jens Nielsen, Lisbeth Olsson. 2008. “New recombinant filamentous fungal host cell having NADH kinase activity compared to identical wild type host cell, useful for production of a polypeptide of interest useful for increasing growth rate” (Novozymes has acquired the Patent Rights)|
|EP2062967-A1 Gianni Panagiotou, Torsten B. Regueira, Jens Nielsen, Lisbeth Olsson. 2008. ´´New genetically engineered Aspergillus overexpressing phosphoketolase useful for production of recombinant polypeptide´´|
(2020) Novel Approaches for Systems Biology of Metabolism-Oriented Pathogen-Human Interactions: A Mini-Review Frontiers in Cellular and Infection Microbiology 10, 52. (Review)
(2020) Clofarabine in combination with cytarabine and mitoxantrone (CLAM) is highly effective in patients with relapsed or refractory acute myeloid leukemia failing first-line induction chemotherapy Cancer Medicine [Accepted]
(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 [Accepted]
(2020) Gut microbiome fermentation determines the efficacy of exercise for diabetes prevention. Cell Metab 31(1), 77-91.
(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 5(4), pii: giz015.
(2019) Antibiotic Treatment Drives the Diversification of the Human Gut Resistome. Genomics Proteomics Bioinformatics [Epub ahead of print]
(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 [Epub ahead of print]
(2018) Complete Genome Sequence of Escherichia coli Strain WG5. Genome Announc 6(2), pii: e01403-pii: e01417.
(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.