Projects: A1, A2, A3, A4 (E), A5, A6, B1, B2, B4, B5, C2, C1, C3, C4 (E), C5, C6 (E), FungiNet A - Aspergillus projects, FungiNet B - Bioinformatics projects, FungiNet C - Candida projects, FungiNet total, INF, Z1, Z2, B3 (E), A7, A8, C7
Institutions: Leibniz-Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI)

Expertise: Systems Biology, Bioinformatics, Metabolic networks
Tools: Matlab, R, Python, Copasi, LaTeX, Systems biological modelling, Transcriptomics
Projects: B2, FungiNet total, B1
Institutions: Friedrich Schiller University Jena, Department of Bioinformatics, School for Biology and Pharmacy, Julius Maximilians University Würzburg, Biocenter, Department of Bioinformatics

Expertise: Mathematical Modelling, Systems Biology, Metabolic networks
Tools: Systems biological modelling, Matlab, Python, R, LaTeX
Projects: FungiNet B - Bioinformatics projects, FungiNet total, B1
Institutions: Friedrich Schiller University Jena, Department of Bioinformatics, School for Biology and Pharmacy
Expertise: Systems Biology
Principal investigator in B1. Full professor in bioinformatics at FSU Jena
I study the analysis of high-throughput transcriptom and genome data.
For transcritom data (RNA-Seq, microarrays), I perform preprocessing and statistics to identify differentially expressed genes, as well as their functional analysis. My main focus is the analysis of transcriptom data from human fungal pathogens in infection related conditions (f.e. nutrient limitation) as well as during the interaction with the host (dual RNA-seq). Experimental data is used to set up mathematical models for ...
Name Prof. Dr. Thomas Dandekar Position Professor and Chairman Affiliation Dept. of bioinformatics, Biocenter University of Würzburg Am Hubland 97074 Würzburg Phone 0931-318-4551 dandekar@biozentrum.uni-wuerzburg.de Born 23.07.1960
Career 1979-1986 Studies in medicine at the Ludwig Maximilians University of Munich 1982-1986 MD, Max Planck Inst. of Psychiatry, Dept. Neuropharmacology, Martinsried 1987-1988 Post-Doc, Institute Pasteur, Paris 1988- now Scientist at the European Molecular Biology ...
Institutions: BioControl Jena GmbH
Projects: Not specified
Institutions: Not specified
This model is a variant of the previously developed SBM of whole-blood infection assay. While in the previous model a spontaneous immune evasion mechanism (A) was implemented in this model immune evasion was caused by PMN molecule secretion (B).
Creators: Teresa Lehnert, Maria T. E. Prauße
Submitter: Sandra Timme
Model type: Not specified
Model format: Not specified
Environment: Not specified
Primary hepatocytes were exposed to a stimulus by exchanging culture medium, thereby simulating changes in the blood composition. The expression of genes at different time points was recorded. Differentially expressed genes were clustered using fuzzy c-means algorithm into five groups. The arcs of the possible network were identified using the NetGenerator algorithm under the restriction of biological knowledge. The analysis was restricted to the main metabolic pathways of hepatocytes. The reverse ...
Creators: Thomas Wolf, Wolfgang Schmidt-Heck, Reinhard Guthke
Submitter: Thomas Wolf
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Abstract (Expand)
Authors: R. Alonso-Roman, A. Last, M. H. Mirhakkak, J. L. Sprague, L. Moller, P. Grossmann, K. Graf, R. Gratz, S. Mogavero, S. Vylkova, G. Panagiotou, S. Schauble, B. Hube, M. S. Gresnigt
Date Published: 9th Jun 2022
Publication Type: Journal
PubMed ID: 35680868
Citation: Nat Commun. 2022 Jun 9;13(1):3192. doi: 10.1038/s41467-022-30661-5.
Abstract (Expand)
Authors: S. Allert, D. Schulz, P. Kammer, P. Grossmann, T. Wolf, S. Schauble, G. Panagiotou, S. Brunke, B. Hube
Date Published: 10th Feb 2022
Publication Type: Journal
PubMed ID: 35142597
Citation: Virulence. 2022 Dec;13(1):191-214. doi: 10.1080/21505594.2022.2026037.
Abstract (Expand)
Authors: M. H. Mirhakkak, X. Chen, Y. Ni, T. Heinekamp, T. Sae-Ong, L. L. Xu, O. Kurzai, A. E. Barber, A. A. Brakhage, S. Boutin, S. Schauble, G. Panagiotou
Date Published: 20th Jul 2023
Publication Type: Journal
PubMed ID: 37474497
Citation: Nat Commun. 2023 Jul 20;14(1):4369. doi: 10.1038/s41467-023-39982-5.
Abstract (Expand)
Authors: J. Pollmacher, S. Timme, S. Schuster, A. A. Brakhage, P. F. Zipfel, M. T. Figge
Date Published: 13th Jun 2016
Publication Type: Not specified
PubMed ID: 27291424
Citation: Sci Rep. 2016 Jun 13;6:27807. doi: 10.1038/srep27807.
Abstract (Expand)
Authors: J. Ewald, M. Bartl, C. Kaleta
Date Published: 30th Jul 2017
Publication Type: Not specified
PubMed ID: 28754658
Citation: Biochem Soc Trans. 2017 Jul 28. pii: BST20170137. doi: 10.1042/BST20170137.
Abstract (Expand)
Authors: J. Ewald, M. Bartl, T. Dandekar, C. Kaleta
Date Published: 18th Feb 2017
Publication Type: Not specified
PubMed ID: 28212377
Citation: PLoS Comput Biol. 2017 Feb 17;13(2):e1005371. doi: 10.1371/journal.pcbi.1005371. eCollection 2017 Feb.