LIPIcs.WABI.2024.1.pdf
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Bioinformatics of Pathogens (Invited Talk)
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Tomáš Vinař 
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24th International Workshop on Algorithms in Bioinformatics (WABI 2024)
Series: Leibniz International Proceedings in Informatics (LIPIcs)
Conference: International Workshop on Algorithms in Bioinformatics (WABI) - License:
Creative Commons Attribution 4.0 International license
- Publication Date: 2024-08-26
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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.
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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
https://doi.org/10.4230/LIPIcs.WABI.2024.1
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.
Subject Classification
ACM Subject Classification
- Applied computing → Bioinformatics
Keywords
- sequence analysis
- genome assembly
- neural networks
- probabilistic modeling
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References
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