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}
}

Philipp Carl Hackstein, Jasper Spitzer, Konstantinos Symeonidis, Helena Horvatic, Tanja Bedke, Babett Steglich, Lisa Assmus, Alexandru Odainic, Nina Kessler, Sabine Klein, and others. Suppression of systemic T cell immunity to viral infection during liver injury is prevented by inhibition of interferon and IL-10 signaling. bioRxiv. 2022. Cold Spring Harbor Laboratory.

BibTeX

@article{hackstein2022suppression,
  title = {Suppression of systemic T cell immunity to viral infection during liver injury is prevented by inhibition of interferon and IL-10 signaling},
  author = {Hackstein, Philipp Carl and Spitzer, Jasper and Symeonidis, Konstantinos and Horvatic, Helena and Bedke, Tanja and Steglich, Babett and Assmus, Lisa and Odainic, Alexandru and Kessler, Nina and Klein, Sabine and others},
  journal = {bioRxiv},
  year = {2022},
  publisher = {Cold Spring Harbor Laboratory}
}

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}
}

Ashraf Mahgoub, Paul C Wood, Subrata Mitra, Folker Meyer, Somali Chaterji, and Saurabh Bagchi. IRIS: Online Reconfiguration of Distributed NoSQL Databases for Dynamic Workloads. 2022.

BibTeX

@article{mahgoub2022iris,
  title = {IRIS: Online Reconfiguration of Distributed NoSQL Databases for Dynamic Workloads},
  author = {Mahgoub, Ashraf and Wood, Paul C and Mitra, Subrata and Meyer, Folker and Chaterji, Somali and Bagchi, Saurabh},
  year = {2022}
}

Kerstin U Ludwig, Ricarda M Schmithausen, David Li, Max L Jacobs, Ronja Hollstein, Katja Blumenstock, Jana Liebing, Mikolaj Slabicki, Amir Ben-Shmuel, Ofir Israeli, and others. LAMP-Seq enables sensitive, multiplexed COVID-19 diagnostics using molecular barcoding (vol 39, pg 1556, 2021). NATURE BIOTECHNOLOGY. 2022.

BibTeX

@article{ludwig2022lamp,
  title = {LAMP-Seq enables sensitive, multiplexed COVID-19 diagnostics using molecular barcoding (vol 39, pg 1556, 2021)},
  author = {Ludwig, Kerstin U and Schmithausen, Ricarda M and Li, David and Jacobs, Max L and Hollstein, Ronja and Blumenstock, Katja and Liebing, Jana and Slabicki, Mikolaj and Ben-Shmuel, Amir and Israeli, Ofir and others},
  journal = {NATURE BIOTECHNOLOGY},
  year = {2022}
}