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Simulation of the cell type-specific three-dimensional structure of the genome of a given species

The project was executed with the professional participation of UD-GenoMed Kft. (spin-off company of the Institute of Biochemistry and Molecular Biology of the University of Debrecen).

GenomAtlas makes it possible to predict the three-dimensional structure of the genome, based on the connection matrices obtained by processing sequencing data of a particular cell type by bioinformatic transformations.

With the help of the artificial intelligence algorithms, the visualization of the three-dimensional structure can be performed efficiently and in a user-friendly way. The application is therefore able to visualize the structure of the genome in space and perform simulations. The display is interactive, which allows users to perform various geometric transformations in a three-dimensional space with just a few clicks (zoom-out, rotate, etc.).

The developed application will also help us to get closer to understanding how different cell types, such as macrophages, can adapt to a changing environment and to examine what role the cell type-specific three-dimensional chromatin structure plays in this. The results of this research and development project provides a basis for analyzing the pathomechanisms of high blood pressure, obesity, cancer or other so-called multifactorial diseases.

The system can be characterized by the following main usecases:

  • Uploading and organizing raw data produced by the sequencing agent.
  • Generating so-called connection matrices from raw sequencing files based on a user-friendly session.
  • Prediction of the three-dimensional structure based on the interface matrix using the discovered artificial intelligence algorithms.
  • Viewing the generated 3D object and performing interactive transformations.
  • Region-specific study of the object, during which existing genomic databases can be projected onto the given structure.

The InnovITech project entitled; “ Three-dimensional display of cell type-specific genomes belonging to a given species” was supported by the Hungarian State and the European Union with a financial subsidy of HUF 129.98 million. Project ID number: GINOP-2.1.7-15-2016-01487