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PhD or postdoc in Computational Phylogenetics with Applications to Virus Evolution, Wädenswil
Client:
Zurich University of Applied Sciences (ZHAW)
Location:
Wädenswil
Job Category:
Other
Job Reference:
15e22f1e4aa7
Job Views:
10
Posted:
21.01.2025
Expiry Date:
07.03.2025
Job Description:
Job tasks include describing the evolutionary history of molecules using phylogenetic trees inferred from genomic sequences. Phylogenies are essential for testing biological hypotheses in fields ranging from medicine to ecology. This role involves developing methods to enhance the reliability of phylogenetic analyses, addressing circularity issues, and applying a likelihood-based method for joint inferences. The project aims to create a new maximum likelihood method for scalable joint inference of evolutionary history, including alignment, tree, and ancestral sequences, under models accommodating multiple residue insertions and deletions. Practical application of these methods will involve real data, specifically from the Swiss HIV Cohort. The project is funded by the Swiss National Science Foundation.
The positions are based at the Institute of Computational Life Sciences, Zurich University of Applied Sciences (ZHAW Wädenswil), with the PhD student also enrolled at the University of Zurich. The research group collaborates with the Swiss Institute of Bioinformatics, offering additional training and networking opportunities.
Relevant Articles:
1. Maiolo M, Zhang X, Gil M, Anisimova M. "Progressive multiple sequence alignment with indel evolution" BMC Bioinformatics. 2018. 19(1):331. doi: 10.1186/s12859-018-2357-1.
2. Pečerska, J., Gil, M. and Anisimova, M. “Joint alignment and tree inference” bioRxiv, 2021. pp.2021-09. doi: 10.1101/2021.09.28.462230.
3. Jowkar, G., Pečerska, J., Maiolo, M., Gil, M., & Anisimova, M. “ARPIP: Ancestral sequence Reconstruction with insertions and deletions under the Poisson Indel Process” Systematic biology. 2022. syac050-syac050. doi: 10.1093/sysbio/syac050
Profile Requirements:
* Strong background in computational science, algorithms, programming, statistics, stochastic modeling, or similar;
* Working knowledge of C++ and/or Rust;
* Some knowledge of phylogenetics and molecular evolution is an advantage.
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