Thomas Wolf

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About Thomas Wolf:

No description specified

SEEK ID: https://funginet.hki-jena.de/people/70

Location: Germany

ORCID: Not specified

Joined: 8th Mar 2016

Expertise: Bioinformatics, Data Management, Gene Regulatory Network Inference, Integrative Data Analysis, Transcriptional Regulation, Secondary Metabolites, Gene Clusters

Tools: R, Python, Perl, CASSIS, SMIPS, antiSMASH, MEME, FIMO, LaTeX

Their tags

Aspergillus fumigatus Bioinformatics Candida albicans compound treatment design database differential expression FungiNetDB INF Integrative Data Analysis Metadata Microarrays modelling network inference protein-protein interaction Regulatory Network RNA-seq sampling time point Seek Systems Biology

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Collaborative Research Center / Transregio 124 "Pathogenic fungi and their human host: Networks of Interaction - FungiNet"

The yeast Candida albicans and the filamentous fungus Aspergillus fumigatus are by far the most important causes of life-threatening invasive mycoses in Europe. Despite the increasing incidence of these infections, the current diagnosis is still difficult and often too late, and options for therapies are limited. Moreover, A. fumigatus and C. albicans have developed multiple sophisticated, specific and unique pathogenicity mechanisms. Many of these mechanisms are not well understood. Research on ...

Projects: FungiNet total, FungiNet A - Aspergillus projects, FungiNet B - Bioinformatics projects, FungiNet C - Candida projects, INF, A1, A2, A3, A4 (E), A5, B1, B2, B3 (E), B4, C1, C2, C3, C4 (E), C5, C6 (E), Z2, Z1, B5, A6, A7, A8, C7

Web page: http://www.funginet.de/home.html

Showing 5 out of a possible 24 Projects Advanced Projects list for this Person with search and filtering

INF: inactive since 2018-06-07

Integrated database for experimental data

Within the Collaborative Research Center / Transregio 124 “Pathogenic fungi and their human host: Networks of Interaction – FungiNet”, the INF project is responsible to analyse and share OMICS data. Databases help to foster the collaboration within FungiNet as an important point of the Collaborative Research Center. Therefore, we set-up two databases:

a) SEEK is a web-based platform to find, share and exchange unstructured data and knowledge, such as ...

Programme: Collaborative Research Center / Transregio 124 "Pathogenic fungi and their human host: Networks of Interaction - FungiNet"

Public web page: http://www.funginet.de/project-inf.html

Organisms: Aspergillus fumigatus, Candida albicans

FungiNet total: inactive since 2018-06-07

No description specified

Programme: Collaborative Research Center / Transregio 124 "Pathogenic fungi and their human host: Networks of Interaction - FungiNet"

Public web page: http://www.funginet.de/home.html

Organisms: Aspergillus fumigatus, Candida albicans

A6: inactive since 2018-06-07

Surface proteins of Lichtheimia corymbifera as virulence determinants

Programme: Collaborative Research Center / Transregio 124 "Pathogenic fungi and their human host: Networks of Interaction - FungiNet"

Public web page: https://www.funginet.de/project-a6.html

Organisms: Lichtheimia corymbifera

C4 (E): inactive since 2018-06-07

Mechanisms of adhesion and modulation of human immune cells by Candida albicans

Programme: Collaborative Research Center / Transregio 124 "Pathogenic fungi and their human host: Networks of Interaction - FungiNet"

Public web page: http://www.funginet.de/project-c4.html

Organisms: Candida albicans

C6 (E): inactive since 2018-06-07

Role of secreted Candida albicans proteins in immune evasion and pathogenicity

Programme: Collaborative Research Center / Transregio 124 "Pathogenic fungi and their human host: Networks of Interaction - FungiNet"

Public web page: http://www.funginet.de/project-c6.html

Organisms: Candida albicans

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Leibniz-Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI)

Country: Germany

City: 07745 Jena

Web page: http://www.hki-jena.de

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5th Joint Meeting IMIHM XII & CRC/TR 124

FungiNet total

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Programme

Creators: Thomas Wolf, Jürgen Löffler, Annika Tittelbach-Helmrich

Submitter: Thomas Wolf

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 7th Jun 2018 at 07:45, Last updated: 12th Jun 2018 at 11:31

Joint Meeting IMIHM XI & CRC/TRANSREGIO 124 Schedule 2017

FungiNet total

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Creators: Annika Tittelbach-Helmrich, Jürgen Löffler

Submitter: Thomas Wolf

Investigations: No Investigations

Studies: No Studies

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Created: 5th Sep 2017 at 11:22, Last updated: 27th Feb 2018 at 13:25

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[DEMO] Response of hepatocytes to rapid change in the medium composition (gene regulatory network): Model 1100 "freshMedia"

FungiNet total, FungiNet B - Bioinformatics projects

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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

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Created: 6th Jun 2017 at 07:38, Last updated: 27th Feb 2018 at 13:25

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Showing 5 out of a possible 8 Publications Advanced Publications list for this Person with search and filtering

Distinct transcriptional responses to fludioxonil in Aspergillus fumigatus and its DeltatcsC and Deltaskn7 mutants reveal a crucial role for Skn7 in the cell wall reorganizations triggered by this antifungal.

INF, A1

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BACKGROUND: Aspergillus fumigatus is a major fungal pathogen that causes severe problems due to its increasing resistance to many therapeutic agents. Fludioxonil is a compound that triggers a lethal …

Authors: S. Schruefer, A. Pschibul, S. S. W. Wong, T. Sae-Ong, T. Wolf, S. Schauble, G. Panagiotou, A. A. Brakhage, V. Aimanianda, O. Kniemeyer, F. Ebel

Date Published: 14th Nov 2023

Publication Type: Journal

PubMed ID: 37964194

Citation: BMC Genomics. 2023 Nov 14;24(1):684. doi: 10.1186/s12864-023-09777-5.

Created: 19th Jan 2024 at 12:02

Pathogen-specific innate immune response patterns are distinctly affected by genetic diversity.

INF, C2, C3

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Innate immune responses vary by pathogen and host genetics. We analyze quantitative trait loci (eQTLs) and transcriptomes of monocytes from 215 individuals stimulated by fungal, Gram-negative or …

Authors: A. Hader, S. Schauble, J. Gehlen, N. Thielemann, B. C. Buerfent, V. Schuller, T. Hess, T. Wolf, J. Schroder, M. Weber, K. Hunniger, J. Loffler, S. Vylkova, G. Panagiotou, J. Schumacher, O. Kurzai

Date Published: 5th Jun 2023

Publication Type: Journal

PubMed ID: 37277347

Citation: Nat Commun. 2023 Jun 5;14(1):3239. doi: 10.1038/s41467-023-38994-5.

Created: 17th Jan 2024 at 10:35

From environmental adaptation to host survival: Attributes that mediate pathogenicity of Candida auris.

INF, C1

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Candida species are a major cause of invasive fungal infections. While Candida albicans, C. glabrata, C. parapsilosis, and C. tropicalis are the most dominant species causing life-threatening candidiasis, …

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.

Created: 19th Jan 2024 at 12:15

Triple RNA-Seq Reveals Synergy in a Human Virus-Fungus Co-infection Model.

INF, A2, B5

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High-throughput RNA sequencing (RNA-seq) is routinely applied to study diverse biological processes; however, when performed separately on interacting organisms, systemic noise intrinsic to RNA extraction, …

Authors: B. Seelbinder, J. Wallstabe, L. Marischen, E. Weiss, S. Wurster, L. Page, C. Loffler, L. Bussemer, A. L. Schmitt, T. Wolf, J. Linde, L. Cicin-Sain, J. Becker, U. Kalinke, J. Vogel, G. Panagiotou, H. Einsele, A. J. Westermann, S. Schauble, J. Loeffler

Date Published: 17th Nov 2020

Publication Type: Not specified

PubMed ID: 33207195

Citation: Cell Rep. 2020 Nov 17;33(7):108389. doi: 10.1016/j.celrep.2020.108389.

Created: 10th Feb 2021 at 12:26, Last updated: 17th Jan 2024 at 10:24

Survival Strategies of Pathogenic Candida Species in Human Blood Show Independent and Specific Adaptations.

INF, B3 (E), C1, C3

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Only four species, Candida albicans, C. glabrata, C. parapsilosis, and C. tropicalis, together account for about 90% of all Candida bloodstream infections and are among the most common causes of invasive … fungal infections of humans. However, virulence potential varies among these species, and the phylogenetic tree reveals that their pathogenicity may have emerged several times independently during evolution. We therefore tested these four species in a human whole-blood infection model to determine, via comprehensive dual-species RNA-sequencing analyses, which fungal infection strategies are conserved and which are recent evolutionary developments. The ex vivo infection progressed from initial immune cell interactions to nearly complete killing of all fungal cells. During the course of infection, we characterized important parameters of pathogen-host interactions, such as fungal survival, types of interacting immune cells, and cytokine release. On the transcriptional level, we obtained a predominantly uniform and species-independent human response governed by a strong upregulation of proinflammatory processes, which was downregulated at later time points after most of the fungal cells were killed. In stark contrast, we observed that the different fungal species pursued predominantly individual strategies and showed significantly different global transcriptome patterns. Among other findings, our functional analyses revealed that the fungal species relied on different metabolic pathways and virulence factors to survive the host-imposed stress. These data show that adaptation of Candida species as a response to the host is not a phylogenetic trait, but rather has likely evolved independently as a prerequisite to cause human infections.IMPORTANCE To ensure their survival, pathogens have to adapt immediately to new environments in their hosts, for example, during the transition from the gut to the bloodstream. Here, we investigated the basis of this adaptation in a group of fungal species which are among the most common causes of hospital-acquired infections, the Candida species. On the basis of a human whole-blood infection model, we studied which genes and processes are active over the course of an infection in both the host and four different Candida pathogens. Remarkably, we found that, while the human host response during the early phase of infection is predominantly uniform, the pathogens pursue largely individual strategies and each one regulates genes involved in largely disparate processes in the blood. Our results reveal that C. albicans, C. glabrata, C. parapsilosis, and C. tropicalis all have developed individual strategies for survival in the host. This indicates that their pathogenicity in humans has evolved several times independently and that genes which are central for survival in the host for one species may be irrelevant in another.

Authors: P. Kammer, S. McNamara, T. Wolf, T. Conrad, S. Allert, F. Gerwien, K. Hunniger, O. Kurzai, R. Guthke, B. Hube, J. Linde, S. Brunke

Date Published: 6th Oct 2020

Publication Type: Not specified

PubMed ID: 33024045

Citation: mBio. 2020 Oct 6;11(5). pii: mBio.02435-20. doi: 10.1128/mBio.02435-20.

Created: 11th Feb 2021 at 08:45, Last updated: 17th Jan 2024 at 10:24

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Annual Meeting CRC/TR 124 FungiNet 2018

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Start Date: 19th Nov 2018

End Date: 20th Nov 2018

Event Website: Not specified

Country: Germany

City: Bad Staffelstein

Created: 20th Nov 2018 at 15:33, Last updated: 26th Nov 2018 at 13:18

Joint Meeting IMIHM XII & CRC/TR 124 2018-06

This year's 12th IMIHM meeting is held for the fifth time as a Joint Meeting together with scientists from the CRC TransRegio 124 (“Pathogenic fungi and their human host: Networks of interaction – FungiNet”). This collaborative Research Centre FungiNet is a network of scientists from Jena and Wuerzburg and is funded by the Deutsche Forschungsgemeinschaft. The Consortium collaborates to better understand complex invasive mycoses by investigating the pathobiology of fungi, the response of the immune ...

Start Date: 26th Jun 2018

End Date: 27th Jun 2018

Event Website: Not specified

Country: Germany

City: Würzburg

Created: 7th Jun 2018 at 07:45, Last updated: 26th Nov 2018 at 13:32

Joint Meeting IMIHM XI & CRC/TR 124 - September 2017

This year‘s 11 th IMIHM meeting is held for the fourth time as a Joint Meeting together with scientists from the CRC TransRegio 124 (“Pathogenic fungi and their human host: Networks of interaction – FungiNet”). This Collaborative Research Centre FungiNet is a network of scientists from Jena and Wuerzburg and is funded by the Deutsche Forschungsgemeinschaft. The Consortium collaborates to better understand complex invasive mycoses by investigating the pathobiology of fungi, the response of the ...

Start Date: 7th Sep 2017

End Date: 8th Sep 2017

Event Website: Not specified

Country: Germany

City: Würzburg

Created: 5th Sep 2017 at 11:24, Last updated: 27th Feb 2018 at 13:25

SFB FungiNet: Review Meeting in Würburg

No description specified

Start Date: 9th Feb 2017

End Date: 10th Feb 2017

Event Website: Not specified

Country: Germany

City: Würzburg

Created: 21st Feb 2017 at 15:56, Last updated: 27th Feb 2018 at 13:25

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