Hasso-Plattner-Institut
Prof. Dr. Bernhard Renard
 

Postdoctoral Researcher

 Phone:+49 (0)331 5509 - 4973
 E-mail:jakub.bartoszewicz(at)hpi.de
 Organization:Hasso Plattner Institute, University of Potsdam
 Address:Prof.-Dr.-Helmert-Str. 2-3, 14482 Potsdam, Germany
 Room:HPI Campus II, K.E-11

Research Interests

  • Deep learning
  • Interpretability
  • Pathogen detection & (meta)genomics
  • AI in synthetic biology & biomolecule design
  • Biosecurity & biosafety

Research

Interpretable deep learning for novel pathogen detection from DNA sequences

Regular emergence of novel pathogens is one of the greatest threats to global health, and synthetic DNA must be screened for potential threats. However, standard approaches for pathogen detection can only recognize agents that are already known. We solve this problem by training deep neural networks that predict if a DNA read originates from potential human pathogens (bacteria, viruses or fungi) or viruses and microbes that do not infect humans. [Read more...]

Publications

  • 1.
    Bartoszewicz, J.M., Nasri, F., Nowicka, M., Renard, B.Y.: Detecting DNA of novel fungal pathogens using ResNets and a curated fungi-hosts data collection. Bioinformatics. 38, ii168-ii174 (2022).
     
  • 2.
    Bartoszewicz, J.M., Seidel, A., Renard, B.Y.: Interpretable detection of novel human viruses from genome sequencing data. NAR Genomics and Bioinformatics. 3, (2021).
     
  • 3.
    Bartoszewicz, J.M., Genske, U., Renard, B.Y.: Deep learning-based real-time detection of novel pathogens during sequencing. Briefings in Bioinformatics. 22, bbab269 (2021).
     
  • 4.
    Bartoszewicz, J.M., Seidel, A., Rentzsch, R., Renard, B.Y.: DeePaC: predicting pathogenic potential of novel DNA with reverse-complement neural networks. Bioinformatics. 36, 81–89 (2020).