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Center for Data and Simulation Science

Interests of Prof. Dr. Bozek lie in machine learning-based representation learning and complex data analysis in biology. Her previous work was applied in the study of HIV drug resistance and human evolution, currently her research focuses on developing new machine learning methods to analyze biological image and video data. This research direction is motivated by the rise of deep learning methods for image analysis and language processing. The new set of computational tools enable a broader, data-driven approach to using visual data in biomedical research via learning of their representations dedicated to quantifying specific signals of interest. The computational and analytical solutions developed in her group are applied to questions in cancer and aging research.

We combine different types of large-scale biological information such as sequence data, protein levels and also importantly visual information. Using machine learning we build quantitative representations of image data which allows to perform integrative analysis of the highly diverse biological information combining morphological and dynamic aspects of systems with the underlying molecular states of tissues.

Selected publications

  1. Bozek K, Hebert L, Portugal Y, Mikheyev AS, Stephens GJ. Pixel personality for dense object tracking in a 2D honeybee hive. https://arxiv.org/abs/1812.11797
  2. Bozek K, Hebert L, Mikheyev AS, Stephens GJ. Towards dense object tracking in a 2D honeybee hive Computer Vision and Pattern Recognition 2018
  3. Bozek K, Wei Y, Yan Z, Liu X, Xiong J, Sugimoto M, Tomita M, Pääbo S, Sherwood CC, Hof PR, Ely JJ, Li Y, Steinhauser D, Willmitzer L, Giavalisco P, Khaitovich P. Organization and evolution of brain lipidome revealed by large-scale analysis of human, chimpanzee, macaque and mouse tissues. Neuron 2015 Feb 18;85(4):695-702.
  4. Bozek K, Wei Y, Yan Z, Liu X, Xiong J, Sugimoto M, Tomita M, Pääbo S, Pieszek R, Sherwood CC, Hof PR, Ely JJ, Steinhauser D, Willmitzer L, Bangsbo J, Hansson O, Call J, Giavalisco P, Khaitovich P. Exceptional evolutionary divergence of human muscle and brain metabolomes parallels human cognitive and physical uniqueness. PLoS Biol 2014 May 27;12(5):e1001871.
  5. Bozek K, Lengauer T, Sierra S, Kaiser R, Domingues FS. Analysis of physicochemical and structural properties determining HIV-1 coreceptor usage. PLoS Comput Biol. 2013;9(3):e1002977
  6. Bozek K, Lengauer T. Positive selection of HIV host factors and the evolution of lentivirus genes. BMC Evol Biol. 2010 Jun 18;10:186.