Ewa Szczurek

Research Interests

  • Computational Biology, focus: Computational Oncology
  • Statistical data analysis and machine learning

Current projects

  • Modeling epidemic spread. I am involved in two projects modeling COVID-19 dynamics in Poland: SEIR-based COVID-19 model and microsimulation-based MOCOS (MOdeling COronavirus spread) model.
  • Drawing the genealogical trees of tumors. Which cancer mutations come first? How do metastases occur? How does drug resistance appear in cancer? Is tumor evloution neutral, or is it driven by selection? These and many more questions about the family history of tumor cells I find very exciting! Find out more on our CONTRA (Computational ONcology TRaining Alliance) website.
    Types of methods to be developed in this project: probabilistic graphical models, mathematical models
  • Working out the bottleneck of metastasis initiation. Cancer makes astronomic numbers of trials to set up metastatic colonies. Only a few succeed. We figure out why.
    Methods developed: mathematical models
  • Who talks with whom in cellular networks? I study cellular signaling pathways by kicking their members out and observing what happens. And of course, we model cancer pathways!
    Methods developed: probabilistic graphical models
  • Fighting cancer with its own weapons. I am analyzing the phenomenon of synthetic lethality between cancer genes. We can use synthetic lethality for cancer treatment. Once one gene is mutated, we can target its synthetic lethal target in order to kill cancer cells. Learn more on our project website.
    Methods developed: statistical tests, survival analysis methods
  • Deep Pathologist! Can deep learning algorithms scale the work of pathologists? We train a deep pathologist on colorectal cancer histological images to recognize eight tissue types.
    Methods developed: deep learning models
  • Modeling efficacy of drugs and drug combinations. Together with colleagues from the Oncology Bioinformatics department at Merck, Germany, we try to understand and predict how drugs work on cancer cell lines.
    Methods developed: statistical models, optimization algorithms

Open positions

  • Oct 2020. We invite applications for a research project, related to modeling copy number evolution in tumors. Requirements: programming in c, c++, knowledge in Bayesian statistics. To apply, please contact per email, sending your CV.
  • Oct 2020. We invite applications for a research project, related to modeling copy number evolution in tumors. Requirements: expertise in Bayesian statistics. To apply, please contact per email, sending your CV.
  • Oct 2020. We invite applications for a research project in computational oncology. Requirements: expertise in machine learning, in particular gaussian processes. To apply, please contact per email, sending your CV.
  • Oct 2020. We invite applications for a research project in computational oncology, related to generative models of antimicrobial peptides. Requirements: python programming, keras programming, knowledge of machine learning, in particular variational autoencoders. To apply, please contact per email, sending your CV.
  • Oct 2020. We invite applications for a research project in computational oncology, related to generative models of antimicrobial peptides. Requirements: python programming, PyTorch programming, knowledge of machine learning, in particular variational autoencoders. To apply, please contact per email, sending your CV.
  • Oct 2020. We invite applications for a research project in computational oncology, related to generative models of antimicrobial peptides. Requirements: Expertise in machine learning, in particular variational autoencoders. To apply, please contact per email, sending your CV.

Past position announcements

  • Aug 2020. We invite applications for a research project, related to spatial transcriptomics data analysis. To apply, please contact per email, sending your CV.
  • June 2020. We invite applications for a research project, related to single cell copy number variant analysis. To apply, please contact per email, sending your CV.
  • June 2020. We invite applications for a research project, related to drug sensitivity modeling. To apply, please contact per email, sending your CV.
  • Jan 2020. We invite applications for a research project, related to single cell copy number variant analysis. To apply, please contact per email, sending your CV.
  • Jan 2020. We invite applications for a research project, related to immune cell types and spatial transcriptomics analysis. To apply, please contact per email, sending your CV.
  • Aug 2019. We invite applications for a research project, in the area of modeling cancer drug action. To apply, please contact per email, please contact per email, sending your CV.
  • Dec 2017 ESR 9: Evolution of drug resistance on genetic and phenotypic levels.
  • Dec 2017 ESR 5:Evolutionary history of circulating tumour cells and distant metastases.
  • June 2017 Announcement leaflet in pdf.

Teaching

Winter semester
  • Statistical data analysis 2 (in English), materials available for students at Moodle
Summer semester Previous courses

Organized seminars

Past organized conferences

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