Data Science

Prof. Dr. Folker Meyer

Folker Meyer is a Professor at the Department of Medicine and at the Computer Science Department of University of Duisburg-Essen.

The data science lab is part of the Institute for AI in medicine (IKIM), University Hospital Essen, Medical Faculty University of Duisburg-Essen. We are focused on efficient, reproducible and sustainable Data Science and Microbiome Analysis in the context of One Health. The group is affiliaed with the (Center for Water and the Environment](https://www.uni-due.de/zwu/start.php).

Data science brings together a number of disciplines and methods for the purpose of extracting knowledge from structured and unstructured data. It strives to achieve semantic integration of data from a variety of sources and disciplines, suitable technical platforms for integration are required to facilitate the process. Related to other disciplines like big data and machine learning, data science is part of the value-add chain from data to information to clinical and public health decision making.

Important aspects of data integration are suitable data exchange standards and data privacy, it is impossible to practice data science without good privacy and security concepts. The group aims for honor the principles of Data FAIRness as well as reproducible science via the use of workflow technology.

Microbiome and virome analysis presents an opportunity to assist with the rapid molecular characterization of infectious disease via DNA sequencing, It can also advance the early detection of life-threatening diseases e.g. sepsis, NEC, dysbiosis in patients with bone marrow transplants. Combined with a data science approach microbiome and virome analysis can provide vital clues for e.g. the detection of hospital borne infection, emergence of bacterial strains resistant to antibiotics and last but not least allow the establishment DNA base surveillance mechanism for the rapid and early detection of emerging DNA and RNA pathogens.

The group hosts the junior group MicrobiomeSepsisPred funded by the BMBF.

Wastewater based epidemiology (WBE) presents a unique opportunity to characterize the virome and microbiome of an entire community. WBE is a specialized form of environmental genomics and allows characterizing microbial and viral life in urban environments, integrating material from thousands of individuals. Using WBE we create preditive models of pathogens in the population and the environment. We also work towards the establishment of anomaly detection systems. The group routinely analyses samples from waste water treatments plants, the sewer system and the hospital environment.

The group runs a (meta-) genomic sequencing laboratory with both long and short read technology capabilities as well as robotic sample handling and library preparation facilities.

Contact

Girardethaus
Girardetstr. 8
House 8, 2nd floor
45131 Essen

Prof. Dr. Folker Meyer
Office

Projects

WBEready - Wastewater based epidemiology
Exploring and optimizing the use of wastewater for public health purposes
Detect and eliminate environmental origins of infectious disease
Optimizing detection of Pathogens in wastewater
MicrobiomSepsisPred
Prediction of Sepsis on the basis of microbiome sequence data

Recent Publications - see all...

Frank-Andreas Weber, J. Schoth, P. Jagemann, T. Schmidt, Marek Widera, Alexander Wilhelm, F. Meyer, Ricarda Schmithausen, Ivana Kraiselburd, S. Moebus, Dennis Schmiege, T. Wintgens, V. Linnemann, and J.-L Wolber. WBEready – Wastewater-based epidemiology and preparedness: research needs for an adaptive monitoring in the Public Health Service. Das Gesundheitswesen. 2024. [doi]

BibTeX

@inproceedings{webetal,
  author = {Weber, Frank-Andreas and Schoth, J. and Jagemann, P. and Schmidt, T. and Widera, Marek and Wilhelm, Alexander and Meyer, F. and Schmithausen, Ricarda and Kraiselburd, Ivana and Moebus, S. and Schmiege, Dennis and Wintgens, T. and Linnemann, V. and Wolber, J.-L},
  year = {2024},
  month = apr,
  pages = {},
  title = {WBEready – Wastewater-based epidemiology and preparedness: research needs for an adaptive monitoring in the Public Health Service},
  volume = {86},
  journal = {Das Gesundheitswesen},
  doi = {10.1055/s-0044-1781837}
}

S. Sachse, Olympia Anastasiou, Carina Elsner, R. Ross, S. Goretzki, S. Goer, R. Nagel, M. Koldehoff, Mykhailo Savin, Manuel Döhla, Nico Mutters, Alexander Thomas, Ivana Kraiselburd, F. Meyer, Ricarda Schmithausen, and Ulf Dittmer. From airport to school to hospital – the story of a rare SARS-CoV-2 virus variant import. Das Gesundheitswesen. 2024. [doi]

BibTeX

@inproceedings{Sachse24,
  author = {Sachse, S. and Anastasiou, Olympia and Elsner, Carina and Ross, R. and Goretzki, S. and Goer, S. and Nagel, R. and Koldehoff, M. and Savin, Mykhailo and Döhla, Manuel and Mutters, Nico and Thomas, Alexander and Kraiselburd, Ivana and Meyer, F. and Schmithausen, Ricarda and Dittmer, Ulf},
  year = {2024},
  month = apr,
  pages = {},
  title = {From airport to school to hospital – the story of a rare SARS-CoV-2 virus variant import},
  volume = {86},
  journal = {Das Gesundheitswesen},
  doi = {10.1055/s-0044-1781946}
}

Dennis Schmiege, Timo Haselhoff, Alexander Thomas, Ivana Kraiselburd, Folker Meyer, and Susanne Moebus. Small-scale wastewater-based epidemiology (WBE) for infectious diseases and antibiotic resistance: A scoping review. International Journal of Hygiene and Environmental Health. 2024. [doi] [url]

BibTeX

@article{SCHMIEGE2024114379,
  title = {Small-scale wastewater-based epidemiology (WBE) for infectious diseases and antibiotic resistance: A scoping review},
  journal = {International Journal of Hygiene and Environmental Health},
  volume = {259},
  pages = {114379},
  year = {2024},
  issn = {1438-4639},
  doi = {https://doi.org/10.1016/j.ijheh.2024.114379},
  url = {https://www.sciencedirect.com/science/article/pii/S1438463924000609},
  author = {Schmiege, Dennis and Haselhoff, Timo and Thomas, Alexander and Kraiselburd, Ivana and Meyer, Folker and Moebus, Susanne},
  keywords = {Antimicrobial resistance, Building, Neighborhood, Public health, Virus, Wastewater surveillance}
}

Alexander Thomas, Thomas Battenfeld, Ivana Kraiselburd, Olympia Anastasiou, Ulf Dittmer, Ann-Kathrin Dörr, Adrian Dörr, Carina Elsner, Jule Gosch, Vu Thuy Khanh Le-Trilling, Simon Magin, René Scholtysik, Pelin Yilmaz, Mirko Trilling, Lara Schöler, Johannes Köster, and Folker Meyer. UnCoVar: a reproducible and scalable workflow for transparent and robust virus variant calling and lineage assignment using SARS-CoV-2 as an example. BMC Genomics. 2024. [doi] [url]

BibTeX

@article{RN5113,
  author = {Thomas, Alexander and Battenfeld, Thomas and Kraiselburd, Ivana and Anastasiou, Olympia and Dittmer, Ulf and Dörr, Ann-Kathrin and Dörr, Adrian and Elsner, Carina and Gosch, Jule and Le-Trilling, Vu Thuy Khanh and Magin, Simon and Scholtysik, René and Yilmaz, Pelin and Trilling, Mirko and Schöler, Lara and Köster, Johannes and Meyer, Folker},
  title = {UnCoVar: a reproducible and scalable workflow for transparent and robust virus variant calling and lineage assignment using SARS-CoV-2 as an example},
  journal = {BMC Genomics},
  volume = {25},
  number = {1},
  pages = {647},
  issn = {1471-2164},
  doi = {10.1186/s12864-024-10539-0},
  url = {https://doi.org/10.1186/s12864-024-10539-0},
  year = {2024},
  type = {Journal Article}
}

Maxim Cherneha, Isabel Zydek, Peer Braß, Johannes Korth, Sarah Jansen, Stefan Esser, Christina B. Karsten, Folker Meyer, Ivana Kraiselburd, Ulf Dittmer, Monika Lindemann, Peter A. Horn, Oliver Witzke, Laura Thümmler, and Adalbert Krawczyk. Immunogenicity of the Monovalent Omicron XBB.1.5-Adapted BNT162b2 COVID-19 Vaccine in People Living with HIV (PLWH). Vaccines. 2024. [doi] [url]

BibTeX

@article{vaccines12070785,
  author = {Cherneha, Maxim and Zydek, Isabel and Braß, Peer and Korth, Johannes and Jansen, Sarah and Esser, Stefan and Karsten, Christina B. and Meyer, Folker and Kraiselburd, Ivana and Dittmer, Ulf and Lindemann, Monika and Horn, Peter A. and Witzke, Oliver and Thümmler, Laura and Krawczyk, Adalbert},
  title = {Immunogenicity of the Monovalent Omicron XBB.1.5-Adapted BNT162b2 COVID-19 Vaccine in People Living with HIV (PLWH)},
  journal = {Vaccines},
  volume = {12},
  year = {2024},
  number = {7},
  article-number = {785},
  url = {https://www.mdpi.com/2076-393X/12/7/785},
  issn = {2076-393X},
  doi = {10.3390/vaccines12070785}
}