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 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.

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.

Contact

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

Prof. Dr. Folker Meyer
Office

Projects

Recent Publications - see all...

  1. Dennis Schmiege, Ivana Kraiselburd, Timo Haselhoff, Alexander Thomas, Adrian Doerr, Jule Gosch, Jens Schoth, Burkhard Teichgräber, Susanne Moebus, and Folker Meyer. Analyzing community wastewater in sub-sewersheds for the small-scale detection of SARS-CoV-2 variants in a German metropolitan area. Science of The Total Environment. 2023. [doi] [url]
    BibTeX
    @article{SCHMIEGE2023165458,
      title = {Analyzing community wastewater in sub-sewersheds for the small-scale detection of SARS-CoV-2 variants in a German metropolitan area},
      journal = {Science of The Total Environment},
      volume = {898},
      pages = {165458},
      year = {2023},
      issn = {0048-9697},
      doi = {https://doi.org/10.1016/j.scitotenv.2023.165458},
      url = {https://www.sciencedirect.com/science/article/pii/S0048969723040810},
      author = {Schmiege, Dennis and Kraiselburd, Ivana and Haselhoff, Timo and Thomas, Alexander and Doerr, Adrian and Gosch, Jule and Schoth, Jens and Teichgräber, Burkhard and Moebus, Susanne and Meyer, Folker},
      keywords = {COVID-19, Public health, Small-scale, Single nucleotide variants (SNVs), Wastewater surveillance, Whole genome sequencing}
    }
    
  2. Maren Bormann, Leonie Brochhagen, Mira Alt, Mona Otte, Laura Thümmler, Lukas van de Sand, Ivana Kraiselburd, Alexander Thomas, Jule Gosch, Peer Braß, Sandra Ciesek, Marek Widera, Sebastian Dolff, Ulf Dittmer, Oliver Witzke, Folker Meyer, Monika Lindemann, Andreas Schönfeld, Hana Rohn, and Adalbert Krawczyk. Immune responses in COVID-19 patients during breakthrough infection with SARS-CoV-2 variants Delta, Omicron-BA.1 and Omicron-BA.5. Frontiers in Immunology. 2023. [doi] [url]
    BibTeX
    @article{10.3389/fimmu.2023.1150667,
      author = {Bormann, Maren and Brochhagen, Leonie and Alt, Mira and Otte, Mona and Thümmler, Laura and van de Sand, Lukas and Kraiselburd, Ivana and Thomas, Alexander and Gosch, Jule and Braß, Peer and Ciesek, Sandra and Widera, Marek and Dolff, Sebastian and Dittmer, Ulf and Witzke, Oliver and Meyer, Folker and Lindemann, Monika and Schönfeld, Andreas and Rohn, Hana and Krawczyk, Adalbert},
      title = {Immune responses in COVID-19 patients during breakthrough infection with SARS-CoV-2 variants Delta, Omicron-BA.1 and Omicron-BA.5},
      journal = {Frontiers in Immunology},
      volume = {14},
      year = {2023},
      url = {https://www.frontiersin.org/articles/10.3389/fimmu.2023.1150667},
      doi = {10.3389/fimmu.2023.1150667},
      issn = {1664-3224}
    }
    
  3. Sultan Imangaliyev, Jörg Schlötterer, Folker Meyer, and Christin Seifert. Diagnosis of Inflammatory Bowel Disease and Colorectal Cancer through Multi-View Stacked Generalization Applied on Gut Microbiome Data. Diagnostics. 2022. [doi]
    BibTeX
    @article{imangaliyevDiagnosisInflammatoryBowel2022,
      title = {Diagnosis of {{Inflammatory Bowel Disease}} and {{Colorectal Cancer}} through {{Multi-View Stacked Generalization Applied}} on {{Gut Microbiome Data}}},
      author = {Imangaliyev, Sultan and Schl{\"o}tterer, J{\"o}rg and Meyer, Folker and Seifert, Christin},
      year = {2022},
      month = oct,
      journal = {Diagnostics},
      volume = {12},
      number = {10},
      pages = {2514},
      issn = {2075-4418},
      doi = {10.3390/diagnostics12102514},
      langid = {english}
    }
    
  4. Tomislav Cernava, Daria Rybakova, François Buscot, Thomas Clavel, Alice Carolyn McHardy, Fernando Meyer, Folker Meyer, Jörg Overmann, Bärbel Stecher, Angela Sessitsch, Michael Schloter, Gabriele Berg, Paulo Arruda, Thomas Bartzanas, Tanja Kostic, Paula Iara Brennan, Bárbara Bort Biazotti, Marie-Christine Champomier-Verges, Trevor Charles, Mairead Coakley, Paul Cotter, Don Cowan, Kathleen D’Hondt, Ilario Ferrocino, Kristina Foterek, Gema Herrero-Corral, Carly Huitema, Janet Jansson, Shuang-Jiang Liu, Paula Malloy, Emmanuelle Maguin, Lidia Markiewicz, Ryan Mcclure, Andreas Moser, Jolien Roovers, Matthew Ryan, Inga Sarand, Bettina Schelkle, Annelein Meisner, Ulrich Schurr, Joseph Selvin, Effie Tsakalidou, Martin Wagner, Steve Wakelin, Wiesław Wiczkowski, Hanna Winkler, Juanjuan Xiao, Christine J. Bunthof, Rafael Soares Correa de Souza, Yolanda Sanz, Lene Lange, Hauke Smidt, and The MicrobiomeSupport Team. Metadata Harmonization–Standards Are the Key for a Better Usage of Omics Data for Integrative Microbiome Analysis. Environmental Microbiome. 2022. [doi]
    BibTeX
    @article{cernavaMetadataHarmonizationStandards2022,
      title = {Metadata Harmonization\textendash{{Standards}} Are the Key for a Better Usage of Omics Data for Integrative Microbiome Analysis},
      author = {Cernava, Tomislav and Rybakova, Daria and Buscot, Fran{\c c}ois and Clavel, Thomas and McHardy, Alice Carolyn and Meyer, Fernando and Meyer, Folker and Overmann, J{\"o}rg and Stecher, B{\"a}rbel and Sessitsch, Angela and Schloter, Michael and Berg, Gabriele and Arruda, Paulo and Bartzanas, Thomas and Kostic, Tanja and Brennan, Paula Iara and Biazotti, B{\'a}rbara Bort and {Champomier-Verges}, Marie-Christine and Charles, Trevor and Coakley, Mairead and Cotter, Paul and Cowan, Don and D'Hondt, Kathleen and Ferrocino, Ilario and Foterek, Kristina and {Herrero-Corral}, Gema and Huitema, Carly and Jansson, Janet and Liu, Shuang-Jiang and Malloy, Paula and Maguin, Emmanuelle and Markiewicz, Lidia and Mcclure, Ryan and Moser, Andreas and Roovers, Jolien and Ryan, Matthew and Sarand, Inga and Schelkle, Bettina and Meisner, Annelein and Schurr, Ulrich and Selvin, Joseph and Tsakalidou, Effie and Wagner, Martin and Wakelin, Steve and Wiczkowski, Wies{\l}aw and Winkler, Hanna and Xiao, Juanjuan and Bunthof, Christine J. and {de Souza}, Rafael Soares Correa and Sanz, Yolanda and Lange, Lene and Smidt, Hauke and {The MicrobiomeSupport Team}},
      year = {2022},
      month = jun,
      journal = {Environmental Microbiome},
      volume = {17},
      number = {1},
      pages = {33},
      issn = {2524-6372},
      doi = {10.1186/s40793-022-00425-1}
    }
    
  5. 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}
    }
    

Team

Photo of Folker Meyer

Prof. Dr. Folker Meyer

folker.meyer@uni-due.de
Phone: +4920172377802

Photo of Ivana Kraiselburd

Dr. Ivana Kraiselburd

ivana.kraiselburd@uni-due.de
Interests: Bacterial Diversity, Sepsis, and Machine learning & Prediction

Administration

Photo of Kerstin Bornemann

Kerstin Bornemann

kerstin.bornemann@uk-essen.de
Phone: +492017237883

Researchers

Photo of Ricarda Schmithausen

PD Dr. Dr. Ricarda Schmithausen

ricarda.schmithausen@uni-due.de

Photo of Simon Magin

Dr. Simon Magin

simon.magin@uk-essen.de

Research Assistants

Photo of Katharina Block

M.Sc. Katharina Block, Ph.D. Candidate

katharina.block@uk-essen.de

Photo of Adrian Doerr

M.Sc. Adrian Doerr, Ph.D. Candidate

adrian.doerr@uk-essen.de

Photo of Alexander Thomas

M.Sc. Alexander Thomas, Ph.D. Candidate

alexander.thomas@uk-essen.de

Photo of Josefa Welling

M.Sc. Josefa Welling, Ph.D. Candidate

josefa.welling@uk-essen.de
Interests: antibiotic resistances and ML

Photo of Ann-Kathrin Brüggemann

M.Sc. Ann-Kathrin Brüggemann, Ph.D. Candidate

Ann-Kathrin.Brueggemann@uk-essen.de
Interests: Time Series Data and 16s rDNA

Tech

Photo of Jule Gosch

Jule Gosch

jule.gosch@uk-essen.de

Photo of Ryan Aydelott

Ryan Aydelott, Experimental/HPC Systems Specialist

ryan.aydelott@uk-essen.de