INF l HOFMANN, VON KARSTEDT & WESNER

INF - Research data management, analysis and bioinformatics support

Prof. Dr. Kay Hofmann

Institute for Genetics, University of Cologne

Contact: Kay.Hofmannuni-koeln.de
For more information visit: Hofmann lab

Prof. Dr. Silvia von Karstedt

Department of Translational Genomics, CECAD

Contact: s.vonkarstedtuni-koeln.de
For more information visit: von Karstedt Lab

Prof. Dr.-Ing. Stefan Wesner

IT Centre Cologne (ITCC), University of Cologne

Contact: wesneruni-koeln.de
For more information visit: ITTC

Abstract

This project is funded within the 2nd funding period of the SFB 1403, starting from 2024

Within the INF project, we aim to implement the infrastructural requirements to provide researchers with a set of standardized ontology, metadata templates, and teaching opportunities on FAIR data management. Moreover, we will closely cooperate with the IT department and core facilities to implement Data Integration Platforms (DIP) following the Investigation-Study-Assay concept requiring the storage of accompanying metadata to the raw data. The project aims to implement a user-friendly web application for exploring and analyzing proteomics data across funding periods.

Recent Publications

Project related Publications

2003 - 2023

Hermanns, T. and Hofmann, K. (2023). Bioinformatical Approaches to the Discovery and Classification of Novel Deubiquitinases. Methods Mol Biol 2591, 135-149.

Müller, F., Lim, J.K.M., Bebber, C.M., Seidel, E., Tishina, S., Dahlhaus, A., Stroh, J., Beck, J., Yapici, F.I., Nakayama, K., Torres Fernández, L., Brägelmann, J., Leprivier, G., and von Karstedt, S. (2022). Elevated FSP1 protects KRAS-mutated cells from ferroptosis during tumor initiation. Cell Death Differ, 30, 442-456

Bebber, C.M., Thomas, E.S., Stroh, J., Chen, Z., Androulidaki, A., Schmitt, A., Höhne, M.N., Stüker, L., Alves, C., de, P., Khonsari, A., Dammert, M.A., Parmaksiz, F., Tumbrink, H.L., Beleggia, F., Sos, M.L., Riemer, J., George, J., Brodesser, S., Thomas, R.K., Reinhardt, H.C., and von Karstedt, S. (2021). Ferroptosis response segregates small cell lung cancer (SCLC) neuroendocrine subtypes. Nature Commun. 12, 2048.

Seybold, D., Wesner, S., and Domaschka, J. (2020). King louie: reproducible availability benchmarking of cloud-hosted DBMS. In Proceedings of the 35th Annual ACM Symposium on Applied Computing, (New York, NY, USA: Association for Computing Machinery), pp. 144–153.

Pedrera, L., Espiritu, R.A., Ros, U., Weber, J., Schmitt, A., Stroh, J., Hailfinger, S., von Karstedt, S., and García-Sáez, A.J. (2020). Ferroptotic pores induce Ca 2+ fluxes and ESCRT-III activation to modulate cell death kinetics. Cell Death Differ 149,1–14.

Schanzel, B., Leznik, M., Volpert, S., Domaschka, J., Wesner, S. (2019). ‘Unified Container Environments for Scientific Cluster Scenarios’, in Proceedings of the 5^th bwHPC Symposium. bwHPC Symposium, Tübingen: Universität Tübingen. Doi:10.15496/3ataloguing-29052.

Hauser, C.B., Domaschka, J., and Wesner, S. (2018). Predictability of Resource Intensive Big Data and HPC Jobs in Cloud Data Centres. In 2018 IEEE International Conference on Software Quality, Reliability and Security Companion (QRS-C), pp. 358–365.

Hauser, C.B., and Wesner, S. (2018). Reviewing Cloud Monitoring: Towards Cloud Resource Profiling. In 2018 IEEE 11th International Conference on Cloud Computing (CLOUD), pp. 678–685.

Kajava, A.V., Klopffleisch, K., Chen, S., and Hofmann, K. (2014). Evolutionary link between metazoan RHIM motif and prion-forming domain of fungal heterokaryon incompatibility factor HET-s/HET-s. Sci Rep. 4, 7436.

Scheel, H., Tomiuk, S., and Hofmann, K. (2003). Elucidation of ataxin-3 and ataxin-7 function by integrative bioinformatics. Hum Mol Genet. 12, 2845–2852

UNIVERSITÄT ZU KÖLN

Sonderforschungsbereich 1403