Data Science

Prof. Dr. Folker Meyer

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.

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 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. Analyzing the environmental DNA (e.g. from wastewater treatment plants) allows the charaterization of microbial and viral life in the community at large.

Contact

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

Prof. Dr. Folker Meyer
Office

Projects

MicrobiomSepsisPred
Prediction of Sepsis on the basis of microbiome sequence data

Recent Publications - see all...

A. I. Tuns, T. Hartmann, S. Magin, R. C. Gonzalez, A. G. Henssen, S. Rahmann, A. Schramm, and J. Koster. Detection and Validation of Circular DNA Fragments Using Nanopore Sequencing. Front Genet. 2022. [doi] [url]

BibTeX

@article{RN1743,
  author = {Tuns, A. I. and Hartmann, T. and Magin, S. and Gonzalez, R. C. and Henssen, A. G. and Rahmann, S. and Schramm, A. and Koster, J.},
  title = {Detection and Validation of Circular DNA Fragments Using Nanopore Sequencing},
  journal = {Front Genet},
  volume = {13},
  pages = {867018},
  note = {Tuns, Alicia Isabell
  Hartmann, Till
  Magin, Simon
  Gonzalez, Rocio Chamorro
  Henssen, Anton George
  Rahmann, Sven
  Schramm, Alexander
  Koster, Johannes
  eng
  Switzerland
  2022/06/18
  Front Genet. 2022 May 30;13:867018. doi: 10.3389/fgene.2022.867018. eCollection 2022.},
  keywords = {algorithm
  cancer
  circular DNA
  nanopore sequencing
  snakemake},
  issn = {1664-8021 (Print)
  1664-8021 (Linking)},
  doi = {10.3389/fgene.2022.867018},
  url = {https://www.ncbi.nlm.nih.gov/pubmed/35711922},
  year = {2022},
  type = {Journal Article}
}

Manuel Döhla, Bianca Schulte, Gero Wilbring, Beate Mareike Kümmerer, Christin Döhla, Esther Sib, Enrico Richter, Patrick Frank Ottensmeyer, Alexandra Haag, Steffen Engelhart, and others. SARS-CoV-2 in environmental samples of quarantined households. Viruses. 2022. MDPI.

BibTeX

@article{dohla2022sars,
  title = {SARS-CoV-2 in environmental samples of quarantined households},
  author = {D{\"o}hla, Manuel and Schulte, Bianca and Wilbring, Gero and K{\"u}mmerer, Beate Mareike and D{\"o}hla, Christin and Sib, Esther and Richter, Enrico and Ottensmeyer, Patrick Frank and Haag, Alexandra and Engelhart, Steffen and others},
  journal = {Viruses},
  volume = {14},
  year = {2022},
  publisher = {MDPI}
}

Ramona Dolscheid-Pommerich, Eva Bartok, Marcel Renn, Beate M Kümmerer, Bianca Schulte, Ricarda M Schmithausen, Birgit Stoffel-Wagner, Hendrik Streeck, Sandra Saschenbrecker, Katja Steinhagen, and others. Correlation between a quantitative anti-SARS-CoV-2 IgG ELISA and neutralization activity. Journal of medical virology. 2022.

BibTeX

@article{dolscheid2022correlation,
  title = {Correlation between a quantitative anti-SARS-CoV-2 IgG ELISA and neutralization activity},
  author = {Dolscheid-Pommerich, Ramona and Bartok, Eva and Renn, Marcel and K{\"u}mmerer, Beate M and Schulte, Bianca and Schmithausen, Ricarda M and Stoffel-Wagner, Birgit and Streeck, Hendrik and Saschenbrecker, Sandra and Steinhagen, Katja and others},
  journal = {Journal of medical virology},
  volume = {94},
  year = {2022}
}

Mykhailo Savin, Gabriele Bierbaum, Ricarda Maria Schmithausen, Céline Heinemann, Judith Kreyenschmidt, Silvia Schmoger, Inna Akbaba, Annemarie Käsbohrer, and Jens Andre Hammerl. Slaughterhouse wastewater as a reservoir for extended-spectrum β-lactamase (ESBL)-producing, and colistin-resistant Klebsiella spp. and their impact in a “One Health” perspective. Science of The Total Environment. 2022. Elsevier.

BibTeX

@article{savin2022slaughterhouse,
  title = {Slaughterhouse wastewater as a reservoir for extended-spectrum $\beta$-lactamase (ESBL)-producing, and colistin-resistant Klebsiella spp. and their impact in a “One Health” perspective},
  author = {Savin, Mykhailo and Bierbaum, Gabriele and Schmithausen, Ricarda Maria and Heinemann, C{\'e}line and Kreyenschmidt, Judith and Schmoger, Silvia and Akbaba, Inna and K{\"a}sbohrer, Annemarie and Hammerl, Jens Andre},
  journal = {Science of The Total Environment},
  volume = {804},
  year = {2022},
  publisher = {Elsevier}
}

Mykhailo Savin, Gabriele Bierbaum, Nico T Mutters, Ricarda Maria Schmithausen, Judith Kreyenschmidt, Isidro Garcı́a-Meniño, Silvia Schmoger, Annemarie Käsbohrer, and Jens Andre Hammerl. Genetic characterization of carbapenem-resistant Klebsiella spp. from municipal and slaughterhouse wastewater. Antibiotics. 2022. MDPI.

BibTeX

@article{savin2022genetic,
  title = {Genetic characterization of carbapenem-resistant Klebsiella spp. from municipal and slaughterhouse wastewater},
  author = {Savin, Mykhailo and Bierbaum, Gabriele and Mutters, Nico T and Schmithausen, Ricarda Maria and Kreyenschmidt, Judith and Garc{\'\i}a-Meni{\~n}o, Isidro and Schmoger, Silvia and K{\"a}sbohrer, Annemarie and Hammerl, Jens Andre},
  journal = {Antibiotics},
  volume = {11},
  year = {2022},
  publisher = {MDPI}
}