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Bioinformatics of Pathogens (Invited Talk)

Author Tomáš Vinař

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Subject Classification

ACM Subject Classification
  • Applied computing → Bioinformatics
Keywords
  • sequence analysis
  • genome assembly
  • neural networks
  • probabilistic modeling

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Abstract

Genomic sequencing has become an important tool in identification and surveillance of human pathogens. Compared to large organisms, where our goal is to obtain high-quality sequences for detailed analysis, in pathogen sequencing the emphasis is often on optimization of cost and time. Consequently, sequencing of pathogens creates interesting computational challenges and development of new methods has a potential to significantly enhance applicability of the results in epidemiology and clinical practice. In my talk, I will give two examples: plasmid identification in bacterial isolates and genomic surveillance of wastewater for SARS-CoV-2. In both cases, application of better algorithms and modeling helps to improve the quality of analysis of very noisy data.

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Tomáš Vinař. Bioinformatics of Pathogens (Invited Talk). In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 1:1-1:2, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024) https://doi.org/10.4230/LIPIcs.WABI.2024.1

Author Details

Tomáš Vinař
  • Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Slovakia

Funding

EU Horizon 2020 project number 872539 (PANGAIA), VEGA grant agency 1/0538/22, Slovak Research and Development Agency APVV-22-0144.

Acknowledgements

These results are joint work with Broňa Brejová, Cedric Chauve, Janik Sielemann, Katharina Sielemann, Mattia Sgro, Paola Bonizzoni, Askar Gafurov, Jozef Nosek, Boris Klempa, and Kristína Boršová.

References

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