Selected Publications

Here we developed COMAN, an integrated web server dedicated to comprehensive functional analysis of metatranscriptomic data, translating massive amount of reads to data tables and high-standard figures. It is expected to facilitate the researchers with less expertise in bioinformatics in answering microbiota-related biological questions and to increase the accessibility and interpretation of microbiota RNA-Seq data.
We adopted a mouse model and metagenome sequencing to investigate the efficacy of probiotic feeding in controlling subcutaneous hepatocellular carcinoma (HCC).Our study offers novel insights into the mechanism by which probiotic treatment modulates the microbiota and influences the regulation of the T cell differentiation in the gut, which in turn alters the level of the pro-inflammatory cytokines in the extra-intestinal tumor microenvironment.
By coupling metatranscriptomics, chemoinformatics and network biology, we demonstrated that a detailed knowledge of the phytochemical composition of food can be a predictor of the expected changes in functionality and activity of the gut microbiota., as well as a promising methodological approach for targeting specific bacterial proteins that impact human health.
Here we developed a web server MESSI (Metabolic Engineering target Selection and best Strain Identification tool), for predicting efficient chassis and regulatory components for yeast bio-based production. The server provides an integrative platform for users to analyse ready-to-use public high-throughput metabolomic data, which are transformed to metabolic pathway activities for identifying the most efficient S. cerevisiae strain for the production of a compound of interest.
With the use of NutriChem database, this work sets the ground for the understanding of the key molecular mechanisms of drug-food interactions with the scope to optimize therapeutic strategies and improve patient care. This systems chemical biology approach provides the basis for the identification and study of the substances in plant-based foods that affect the human proteins that are relevant for the pharmacokinetics and pharmacodynamics of current medicine.
The need for a more accurate assessment of environmental factors in epidemiological studies has given birth to a new ”––ome”, the exposome. Here, we provide a framework for elucidating the link between diet, molecular biological activity and diseases by developing NutriChem, a database source that translates the effect of plant-based food on health from concept to utility.
In the present work we carried out text mining to collect in a systematic and high-throughput way all available information that links plant-based diet with phytochemical content, and human disease phenotypes. Integrating various datasets with food-disease associations allowed us to use a statistical framework for identifying specific phytochemicals as perturbators of drug targets and disease related pathways.
Here, we mapped the entire metabolic potential of the gut microbiome based solely on metagenomics sequencing data derived from fecal samples of 124 Europeans (healthy, obese and with inflammatory bowel disease).
Metabolite profiling and metabolic network analysis with [1-(13)C] glucose were used for characterization of Aspergillus nidulans strains, and the results demonstrated that NADH kinase activity has paramount influence on growth physiology.
As a tool to explore the full-genome sequencing of the filamentous fungi Aspergillus nidulans, Aspergillus niger, and Aspergillus oryzae we are making available an Affymetrix GeneChip developed for transcriptome analysis of any of the three above-mentioned aspergilli
In this study we address the problem of selecting an appropriate docking and scoring function combination for substrate specificity predictions for an industrially relevant enzyme family. We also propose a more biochemically meaningful measure for evaluation of docking programs based on pose prediction accuracy.

List of Publications

  • T Zheng#, Y. Ni#, J Li, B.K.C.Chow, G. Panagiotou*. Designing Dietary Recommendations Using System Level Interactomics Analysis and Network-Based Inference. Frontiers in physiology. 2017.

  • Y. Ni, K. Jensen, I. Kouskoumvekaki, G. Panagiotou*. NutriChem 2.0: exploring the effect of plant-based foods on human health and drug efficacy. Database (Oxford). 2017. 2017(1). doi: 10.1093/database/bax044

  • Y. Heshiki, T. Dissanayake, T. Zheng, K. Kang, Y. Ni, Z. Xu, C. Sarkar, P.C.Y. Woo, B.K.C. Chow, D. Baker, A. Yan, C.J. Webster, G. Panagiotou*, J. Li. Toward a Metagenomic Understanding on the Bacterial Composition and Resistome in Hong Kong Banknotes. Front Microbiol. 2017. 8:632. doi: 10.3389/fmicb.2017.00632

  • Y. Ni, V.H.Y. Wong, W.C.S. Tai, J. Li, W.Y. Wong, M.M.L. Lee, F.L.Y. Fong, H. El-Nezami G. Panagiotou*. A metagenomic study of the preventive effect of Lactobacillus rhamnosus GG on intestinal polyp formation in ApcMin/+ mice. J Appl Microbiol. 2017. 122:770–784. doi: 10.1111/jam.13386

  • Y. Ni, J. Li, G. Panagiotou*. COMAN: a web server for COmprehensive Metatranscriptomics Analysis. BMC Genomics. 2016. 17(1):622. doi: 10.1186/s12864-016-2964-z

  • C. Liang, S. Cheng, Y, Zhang, Y. Sun, A.R. Fernie, K. Kang, G. Panagiotou, C. Lo, B.L. Lim. Transcriptomic, proteomic and metabolic changes in Arabidopsis thaliana leaves after the onset of illumination. BMC Plant Biology. 2016. 16:43. doi: 10.1186/s12870-016-0726-3

  • 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. 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

  • D.B.R.K.G. Udatha, E. Topakas, M. Salazar, L. Olsson, M.R. Andersen, G. Panagiotou*. Deciphering the Signaling Mechanisms of the Plant Cell Wall Degradation Machinery in Aspergillus oryzae . BMC Systems Biology. 2015. 9:77. doi: 10.1186/s12918-015-0224-5

  • K. Kang, J. Li, B.L. Lim, G. Panagiotou*. MESSI: metabolic engineering target selection and best strain identification tool . Database (Oxford). 2015 Vol. 2015: article ID bav076; doi:10.1093/database/bav076

  • D.B.R.K. Gupta Udatha, Karina Marie Madsen, Gianni Panagiotou*, Lisbeth Olsson. Multiple nucleophilic elbows leading to multiple active sites in a single module esterase from Sorangium cellulosum . Journal of Structural Biology. 2015. doi:10.1016/j.jsb.2015.04.009

  • 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

  • G. Udatha, S. Rasmussen, T. Sicheritz-Ponten, G. Panagiotou*. Targeted metabolic engineering analysis of single nucleotide polymorphisms (SNPs). Methods in Molecular Biology, 2013;985:409-28. doi: 10.1007/978-1-62703-299-5_20

  • Topakas, E. , G. Panagiotou & Christakopoulos, P. 2013. Characteristics, sources, production and applications. Xylanases. In: Bioprocessing Technologies in Biorefinery for Sustainable Production of Fuels, Chemicals, and Polymers. Yang, S-T., El Ensashy , H. & Thongchul, N. (eds.).Wiley ,Ch. 9 ,p. 147-169.23 p. ISBN (print) 978-0-470-54195-1.

  • 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.

  • M. Herrgård, G. Panagiotou*. Analyzing the genomic variation of microbial cell factories in the era of "New Biotechnology". Computational and Structural Biotechnology, Volume No: 3, Issue: 4, October 2012, e201210012,

  • D.B.R.K.G. Udatha, N. Sugaya, L. Olsson, G. Panagiotou*. How well do the substrates KISS the enzyme? Molecular docking program selection for feruloyl esterases. Scientific Reports (NPG), 2012. 2:323.

  • D.B.R.K.G. Udatha, V. Mapelli, G. Panagiotou, L. Olsson. Common and Distant Structural Characteristics of Feruloyl Esterase Families from Aspergillus oryzae. PLoS  One. 2012. 7(6):e39473.

  • G. Panagiotou*, O. Taboureau.  The impact of network biology in pharmacology and toxicology. SAR and QSAR in Environmental Research. 2012. 23(3-4):221-235.

  • G. Panagiotou, E. Topakas, M. Moukouli, P. Christakopoulos, L. Olsson. Studying the ability of Fusarium oxysporum and recombinant Saccharomyces cerevisae to efficiently cooperate in decomposition and ethanolic fermentation of wheat straw. Biomass and Bioenergy, 2011. 35(8), 3727-3732.

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

  • D.B.R.K.G. Udatha, I. Kouskoumvekaki, L. Olsson, G. Panagiotou*. The interplay of descriptor based computational analysis with pharmacophore modeling builds the basis for a novel classification scheme for feruloyl esterases. Biotechnology Advances, 2011. 29: 94-110.

  • J.M. Otero, M. Papadakis, D.B.R.K.G. Udatha, J. Nielsen, G. Panagiotou*. Yeast biological networks unfold the interplay of antioxidants, genome and phenotype and reveal a novel regulator of the oxidative stress response. PLoS One, 2010. 25:5, e13606.

  • R. Olivares-Hernández, Z. Yang, H. Sunner, J. Frisvad, J. Nielsen, L. Olsson, G. Panagiotou*. Substrate specificity with support vector classifiers reveals feruloyl esterase as a phylogenetically informative protein group. PLoS One2010, 22:5, e12781.

  • I. Kouskoumvekaki, G. Panagiotou*. Navigating the human metabolome for biomarker identification and the design of pharmaceutical molecules. Journal of Biomedicine and Biotechnology, 2010. doi:pii: 525497. 10.1155/2011/525497.

  • G. Panagiotou, E. Topakas, R. Olivares, P. Christakopoulos, L. Olsson. Feruloyl esterases as biosynthetic tools for the organic synthesis of nutraceutical compounds. Encyclopedia of Biotechnology in Agriculture and Food, Eds. Heldman and Bridges. 2010.

  • M.P. Salazar, W. Vongsangnak, G. Panagiotou, M.R. Andersen, J. Nielsen. Uncovering transcriptional regulation of glycerol metabolism in Aspergilli through genome-wide gene expression data analysis. Molecular Genetics and Genomics, 2009. 282, 571-576.

  • G. Panagiotou, J. Nielsen. Nutritional Systems Biology: definitions and approaches. Annual Review on Nutrition, 2009. 29, 329-339.

  • G. Panagiotou, T. Grotkjaer, G. Hofmann, P. Bapat, L. Olsson. Overexpression of a novel endogenous NADH kinase in Aspergillus nidulans enhances growth. Metabolic Engineering, 2009. 11, 31-39.

  • G. Panagiotou, M.R. Andersen, T. Grotkjaer, T. Regueira, J. Nielsen, L. Olsson. Studies of the production of polyketides in Aspergillus nidulans by using systems biology tools. Applied and Environmental Microbiology, 2009. 75, 2212-2220.

  • G. Panagiotou, M.R. Andersen, T. Grotkjaer, T. Regueira,G. Hofmann, J. Nielsen, L. Olsson. Systems analysis unfolds the growth effects of the phosphoketolase pathway in Aspergillus nidulans. PLoS One, 2008. 3, e3847.

  • G. Panagiotou*, M. Papadakis, E. Topakas, L. Olsson, P. Christakopoulos. Identification of NADH kinase activity in filamentous fungi; purification, kinetic characterization and structural modelling of the novel enzyme from Fusarium oxysporum. Process Biochemistry, 2008. 43, 1114-1120.

  • 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.

  • G. Panagiotou, F. Pachidou, D. Petroutsos, L. Olsson, P. Christakopoulos. Fermentation characteristics of Fusarium oxysporum grown on acetate. Bioresource Technology, 2008. 99, 7397-7401.

  • I. Kouskoumvekaki, Z. Yang, S.O. Jonsdottir, L. Olsson, G. Panagiotou*. Identification of biomarkers for genotyping Aspergilli using non-linear methods for clustering and classification. BMC Bioinformatics, 2008. 9, 1-11.  

  • G. Panagiotou, I. Kouskoumvekaki, S.O. Jonsdottir, L. Olsson. Monitoring novel metabolic pathways using metabolomics and machine learning; induction of the phosphoketolase pathway in Aspergillus nidulans cultivations. Metabolomics, 2007. 3, 503-516.

  • J.M Otero, G. Panagiotou, L. Olsson. Fueling Industrial Biotechnology Growth with Bioethanol. Advances in Biochemical/Biotechnology Engineering, 2007. 108,1-40.

  • G. Panagiotou, R. Olavarria, L. Olsson. Penicillium brasilianum as an enzyme factory; the essential role of feruloyl esterases fro the hydrolysis of plant cell wall. J. of Biotechnology, 2007. 139, 219-228.

  • S. Meijer, G. Panagiotou, L. Olsson, J. Nielsen. Physiological characterization of xylose metabolism in Aspergillus niger under oxygen limitation. Biotechnology and Bioengineering, 2007. 98, 462-475.

  • G. Panagiotou, L. Olsson. Effect of compounds released during pre-treatment of wheat straw on microbial growth and enzymatic hydrolysis rates. Biotechnology and Bioengineering, 2007. 96, 250-8. 

  • G. Panagiotou, P. Christakopoulos, T. Grotkjær, J. Nielsen, L. Olsson. Engineering of the redox imbalance of Fusarium oxysporum enables anaerobic growth on xylose. Metabolic Engineering. 2006. 8, 474-82.

  • G. Panagiotou, P. Granouillet, L. Olsson. Production and partial characterization of arabinoxylan-degrading enzymes by Penicillium brasilianum under solid state fermentation. Applied Microbiology and Biotechnology, 2006. 72, 1117-24.

  • G. Panagiotou, P. Christakopoulos, L. Olsson. The influence of different cultivation conditions on the metabolome of F. oxysporum. J. of Biotechnology, 2005. 108, 304-315.

  • G. Panagiotou, P. Christakopoulos, L. Olsson. Simultaneous saccharification and fermentation of cellulose by Fusarium oxysporum F3 – growth characteristics and metabolite profiling. Enzyme and Microbial Technology, 2005. 36, 693-699.

  • G. Panagiotou, S. G. Villas-Boas, P. Christakopoulos, J. Nielsen, L. Olsson. Intracellular metabolite profiling of Fusarium oxysporum converting glucose to ethanol. J. of Biotechnology, 2005. 115, 425-434.

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

  • G. Panagiotou, P. Christakopoulos. NADPH-dependent D-aldose reductases and xylose fermentation in Fusarium oxysporum. J. of Bioscience and Bioengineering, 2004. 97, 299-304.

  • G. Panagiotou, E. Topakas, L. Economou, D. Kekos, B.J. Macris, P. Christakopoulos. Induction, purification and characterization of two extracellular a-Larabinofuranisidases from F. oxysporum. Canadian Journal of Microbiology, 2003. 49, 639-644.

  • G. Panagiotou, D. Kekos, B. Makris, P. Christakopoulos. Production of cellulotic and xylanolytic enzymes by F. oxysporum grown on corn stover in solid state fermentation. Industrial Crops and Products, 2003. 01, 1-9.

  • G. Panagiotou, D. Kekos, B.J. Makris, P. Christakopoulos. Purification and characterization of xylitol dehydrogenase from Fusarium oxysporum. Biotechnology Letters, 2002. 24, 2089-2092. 

* indicates correspondence