Project INF

Integrated database and standardised analysis of experimental data

High-throughput data play a key role in modern life sciences and systems biology by measuring the abundances or activities or all molecules in a biological system. Thus, these data allow researchers to identify important genes, transcripts or proteins. Moreover, the data are used in modeling approaches, which help to understand complex systems and create hypotheses. As the CRC/TR FungiNet focuses on novel concepts in infection biology, which combine systems biology modeling with basic and applied research, it extensively makes use of high-throughput data. One big challenge is the huge amount of data gathered by those experiments. The major aim of the information and infrastructure project (INF) is the storage, archiving, and standardized analyses of experimental high-throughput data from the CRC/TR FungiNet, and thus, to connect the experimental groups with the systems biology groups.

During the first funding period, INF implemented and applied pipelines for the standardized analysis of transcriptomics, proteomics, and genomics data, as well as for network modeling. Moreover, INF created metadata templates for in detail description of high-throughput experiments and their analysis. These pipelines and templates will be further updated and adapted in the second funding period.

For sharing of unstructured data and knowledge (SOPs, presentations, posters, models, etc.), INF manages the platform FungiNet-SEEK. In addition, INF established the data warehouse FungiNetDB to share and visualize of expression data, both within the CRC/TR FungiNet and the public.

The aim of the second funding period is to pre-process and upload all expression data of both fungal pathogens Aspergillus fumigatus and Candida albicans, and their hosts, to FungiNetDB and thus establish the data warehouse as a major resource for fungal gene expression data. Moreover, INF will establish another data warehouse for fungal and host-pathogen gene regulatory networks as a central repository for network models. Visualization of expression data in the networks will be achieved by coloring of nodes.

Principal Investigator
Dr. Gianni Panagiotou
Dr. Gianni Panagiotou

Research Group Systems Biology and Bioinformatics

Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute

Author Year Title Journal Links
Patumcharoenpol P, Nakphaichit M, Panagiotou G, Senavonge A, Suratannon N, Vongsangnak W 2021 MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome. PLoS Computational Biology 17: e1008487 PubMed
Çakır T, Panagiotou G, Uddin R, Durmuş S 2020 Novel approaches for Systems Biology of metabolism-oriented pathogen-human interactions: A mini-review. Front Cell Infect Microbiol 10: 52 (Review) Frontiers
Dissanayake TK, Schäuble S, Mirhakkak M, Wu WL, Ng ACK, Yip CCY, López AG, Yeung ML, Chan KH, Yuen KY, Panagiotou G, To KKW 2020 Comparative transcriptomic analysis of Rhinovirus and Influenza virus infection. Front Microbiol 11: 1580 PubMed
Seelbinder B, Chen J, Brunke S, Uribe RV, Meyer AC, de Oliveira Lino FS, Chan KF, Loos D, Imamovic L, Tsang CC, Lam RPK, Sridhar S, Kang K, Hube B, Woo PCY, Sommer MOA, Panagiotou G 2020 Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria. Microbiome 8: 133 Microbiome
Machata S, Müller MM, Lehmann R, Sieber S, Panagiotou G, Carvalho A, Cunha C, Lagrou K, Maertens J, Slevogt H, Jacobsen ID 2020 Proteome analysis of bronchoalveolar lavage fluids reveals host and fungal proteins highly expressed during invasive pulmonary aspergillosis in mice and humans. Virulence 11: 1337-51 Virulence
Kämmer P, McNamara S, Wolf T, Conrad T, Allert S, Gerwien F, Hünniger K, Kurzai O, Guthke R, Hube B, Linde J, Brunke S 2020 Survival strategies of pathogenic Candida species in human blood show independent and specific adaptations. mBio 11: e02435-20 PubMed
Seelbinder B, Wallstabe J, Marischen L, Weiss E, Wurster S, Page L, Löffler C, Bussemer L, Schmitt A, Wolf T, Becker J, Kalinke U, Vogel J, Panagiotou G, Einsele H, Westermann A, Schäuble S, Loeffler J 2020 RNA-seq reveals synergy in a human virus-fungus co-infection model. Cell Rep 33: 108389 PubMed
Khaliq W, Großmann P, Neugebauer S, Kleyman A, Domizi R, Calcinaro S, Brealey D, Gräler M, Kiehntopf M, Schäuble S, Singer M, Panagiotou G, Bauer M 2020 Lipid metabolic signatures deviate in sepsis survivors compared to non-survivors. Comput Struct Biotechnol J 18: 3678-3691 Science direct
Barber A, Riedel J, Sae-Ong T, Kang K, Brabetz W, Panagiotou G, Deising H, Kurzai O 2020 Effects of agricultural fungicide use on Aspergillus fumigatus abundance, antifungal susceptibility, and population structure. mBio 11: e02213-20 PubMed
Zheng T, Li J, Ni Y, Kang K, Misiakou MA, Imamovic L, Chow BKC, Rode AA, Bytzer P, Sommer M, Panagiotou P 2019 Mining, analyzing and integrating viral signals from metagenomic data. Microbiome 7: 42 PubMed
Zoran T, Weber M, Springer J, White L, Bauer J, Schober A, Löffler C, Seelbinder B, Hünniger K, Kurzai O, Scherag A, Schäuble S, Morton CO, Einsele H, Linde J, Löffler J 2019 Treatment with etanercept and low monocyte concentration contribute to the risk of invasive aspergillosis in patients post allogeneic stem cell transplantation. Sci Rep 9: 17231 PubMed
Vlaic S, Conrad T, Tokarski-Schnelle C, Gustafsson M, Dahmen U, Reinhard Guthke R, Schuster S 2018 ModuleDiscoverer: Identification of regulatory modules in protein-protein interaction networks. Sci Rep 8: 433 PubMed
Sieber P, Voigt K, Kämmer P, Brunke S, Schuster S, Linde L 2018 Comparative study on alternative splicing in human fungal pathogens suggests its involvement during host invasion. Front Microbiol 9: 2313 Front Microbiol
Conrad T, Kniemeyer O, Henkel SG, Krüger T, Mattern DJ, Valiante V, Guthke R, Jacobsen ID, Brakhage AA, Vlaic S, Linde J 2018 Module-detection approaches for the integration of multilevel omics data highlight the comprehensive response of Aspergillus fumigatus to caspofungin. BMC Syst Biol 12: 88 PubMed
Dix A, Czakai K, Leonhardt I, Schäferhoff K, Bonin M, Guthke R, Einsele H, Kurzai O, Löffler J, Linde J 2017 Specific and novel microRNAs are regulated as response to fungal infection in human dendritic cells. Front Microbiol 8: 270 PubMed
Wolf T, Kämmer P, Brunke S, Linde J 2017 Two's company: Studying interspecies relationships with dual RNA-seq. Curr Opin Microbiol 42: 7-12 (Review) PubMed
Magnusson R, Mariotti GP, Köpsén M, Lövfors W, Gawel DR, Jörnsten R, Linde J, Nordling TEM, Nyman E, Schulze S, Nestor CE, Zhang H, Cedersund G, Benson M, Tjärnberg A, Gustafsson M 2017 LASSIM-A network inference toolbox for genome-wide mechanistic modeling. PLoS Comput Biol 13: e1005608 PubMed
Durmuş S, Çakır T, Guthke R 2016 Editorial: Computational systems biology of pathogen-host interactions. Front Microbiol 7: 21 PubMed
Böhringer M, Pohlers S, Schulze S, Albrecht-Eckardt D, Piegsa J, Weber M, Martin R, Hünniger K, Linde J, Guthke R, Kurzai O 2016 Candida albicans infection leads to barrier breakdown and a MAPK/NF-κB mediated stress response in the intestinal epithelial cell line C2BBe1. Cell Microbiol 18: 889-904 Cell Microbiol
Dix A, Czakai K, Springer J, Fliesser M, Bonin M, Guthke R, Schmitt AL, Einsele H, Linde J, Löffler J 2016 Genome-wide expression profiling reveals S100B as biomarker for invasive Aspergillosis. Front Microbiol 7: 320 PubMed
Dix A, Vlaic S, Guthke R, Linde J 2016 Use of systems biology to decipher host-microbial interaction networks and predict biomarkers. Clin Microbiol Infect 22: 600-6 PubMed
Guthke R, Gerber S, Conrad T, Vlaic S, Durmuş S, Çakır T, Sevilgen FE, Shelest E, Linde J 2016 Data-based reconstruction of gene regulatory networks of fungal pathogens. Front Microbiol 7: 570 PubMed
Schulze S, Schleicher J, Guthke R, Linde J 2016 How to predict molecular interactions between species? Front Microbiol 7: 442 PubMed
Czakai K, Leonhardt I, Dix A, Bonin M, Linde J, Einsele H, Kurzai O, Loeffler J 2016 Krüppel-like Factor 4 modulates interleukin-6 release in human dendritic cells after in vitro stimulation with Aspergillus fumigatus and Candida albicans Sci Rep 6: 27990 PubMed
Horn F, Linde J, Mattern DJ, Walther G, Guthke R, Scherlach K, Martin K, Brakhage AA, Petzke L, Valiante V 2016 Draft genome sequences of fungus Aspergillus calidoustus. Genome Announc 4: e00102-16 PubMed
Hebecker B, Vlaic S, Conrad T, Bauer M, Brunke S, Kapitan M, Linde J, Hube B, Jacobsen ID 2016 Dual-species transcriptional profiling during systemic candidiasis reveals organ-specific host-pathogen interactions. Sci Rep 6: 36055 PubMed
Gerwien F, Safyan A, Wisgott S, Hille F, Kaemmer P, Linde J, Brunke S, Kasper L, Hube B 2016 A novel hybrid iron regulation network combines features from pathogenic and nonpathogenic yeasts. mBio 7: e01782-16 PubMed
Schulze S, Henkel SG, Driesch D, Guthke R, Linde J 2015 Computational prediction of molecular pathogen-host interactions based on dual transcriptome data. Front Microbiol 6: 65 PubMed
Dix A, Hünniger K, Weber M, Guthke R, Kurzai O, Linde J 2015 Biomarker-based classification of bacterial and fungal whole-blood infections in a genome-wide expression study. Front Microbiol 6: 171 PubMed
Linde J, Schulze S, Henkel SG, Guthke R 2015 Data- and knowledge-based modeling of gene regulatory networks: An update. EXCLI J 14: 346-78 EXCLI Journal
Linde J, Duggan S, Weber M, Horn F, Sieber P, Hellwig D, Riege K, Marz M, Martin R, Guthke R, Kurzai O 2015 Defining the transcriptomic landscape of Candida glabrata by RNA-Seq. Nucleic Acids Res 43: 1392-406 PubMed
Priebe S, Kreisel C, Horn F, Guthke R, Linde J 2015 FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species. Bioinformatics 31: 445-6 PubMed
Horn F, Üzüm Z, Möbius N, Guthke R, Linde J, Hertweck C 2015 Draft genome sequences of symbiotic and nonsymbiotic Rhizopus microsporus Strains CBS 344.29 and ATCC 62417. Genome Announc 3: e01370-14 PubMed
Horn F, Habel A, Scharf DH, Dworschak J, Brakhage AA, Guthke R, Hertweck C, Linde J 2015 Draft genome sequence and gene annotation of the entomopathogenic fungus Verticillium hemipterigenum. Genome Announc 3: e01439-14 PubMed
Durmuş S, Çakır T, Özgür A, Guthke R 2015 A review on computational systems biology of pathogen-host interactions. Front Microbiol 6: 235 PubMed
Altwasser R, Baldin C, Weber J, Guthke R, Kniemeyer O, Brakhage AA, Linde J, Valiante V 2015 Network modeling reveals cross talk of MAP kinases during adaptation to caspofungin stress in Aspergillus fumigatus. PLoS One 10: e0136932 PubMed
Horn F, Linde J, Mattern DJ, Walther G, Guthke R, Brakhage AA, Valiante V 2015 Draft genome sequence of the fungus Penicillium brasilianum MG11. Genome Announc 3: e00724-15 PubMed
Schleicher J, Conrad T, Gustafsson M, Cedersund G, Guthke R, Linde J 2015 Facing the challenges of multiscale modelling of bacterial and fungal pathogen-host interactions. Brief Funct Genomics 16: 57-69 PubMed
Hillmann F, Linde J, Beckmann N, Cyrulies M, Strassburger M, Heinekamp T, Haas H, Guthke R, Kniemeyer O, Brakhage AA 2014 The novel globin protein fungoglobin is involved in low oxygen adaptation of Aspergillus fumigatus. Mol Microbiol 93: 539-53 PubMed
Horn F, Schroeckh V, Netzker T, Guthke R, Brakhage AA, Linde J 2014 Draft genome sequence of Streptomyces iranensis. Genome Announc 2: e00616-14 PubMed
Linde J, Schwartze V, Binder U, Lass-Flörl C, Voigt K, Horn F 2014 De Novo whole-genome sequence and genome annotation of Lichtheimia ramosa. Genome Announc 2: e00888-14 PubMed
Wartenberg A, Linde J, Martin R, Schreiner M, Horn F, Jacobsen ID, Jenull S, Wolf T, Kuchler K, Guthke R, Kurzai O, Forche A, d'Enfert C, Brunke S, Hube B 2014 Microevolution of Candida albicans in macrophages restores filamentation in a nonfilamentous mutant. PLoS Genet 10: e1004824 PubMed