PhD Student in Plant Genomics with Deep Learning Focus
2 months ago
Advances in high-throughput DNA sequencing technologies have led to the production of large genome assemblies, including those of conifers, wheat, axolotl salamanders, and giant lungfish. Genome annotation, particularly the identification of transposable elements (TEs), presents a significant challenge in analyzing these large genomes. Deep learning models, which can encode high-dimensional genome sequences into vectors and learn to resolve sequence complexity, offer promising solutions for efficient TE identification.
Research ObjectivesThis PhD project focuses on plant genomics and the development of deep learning-driven computational tools. The objectives are to:
- Develop new deep learning-driven TE identification tools to reduce computational demand for large genome analysis.
- Construct a comprehensive TE dataset to capture sequence diversity by collecting genome data from hundreds of plant species.
- Predict TE insertion profiles from genome sequences to gain insights into TE movement and evolution.
To be eligible for this position, applicants must have a strong academic background in plant biology, machine learning, bioinformatics, or a related field. Required skills and knowledge include:
- Experience in standard molecular biological techniques or machine learning.
- Excellent written and oral English language skills.
- Proficiency in working with computers and programming, including Linux Shell, R, Python, or Julia.
To be admitted to the PhD program, applicants must meet the general entry requirements for third-cycle studies, including a completed degree at the second-cycle level or equivalent qualifications. Specific requirements for the PhD program in Plant Science at Umeå Plant Science Centre include completion of 90 ECTS relevant to the doctoral thesis project, with at least 30 ECTS in a subject closely related to the research topic.
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Umeå, Västerbotten, Sweden Umeå University Full timeProject OverviewAs a PhD student in plant science, you will contribute to the development of deep-learning driven computational tools for efficient identification of transposable elements in large plant genomes. This project aims to advance our understanding of the complexities of transposable elements in plant genomes and their impact on genome...
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Umeå, Västerbotten, Sweden Umeå University Full timeProject OverviewAs part of our ongoing research in plant genomics, we are seeking a highly motivated PhD student to join our team at Umeå University. The successful candidate will work on developing deep-learning driven computational tools for efficient identification of transposable elements (TEs) in large plant genomes.Research ObjectivesDevelop new...
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Umeå, Västerbotten, Sweden Umeå University Full timeProject OverviewWe are seeking a highly motivated and skilled PhD student to join our team at Umeå University in the field of deep-learning conifer genomics. The successful candidate will be involved in the development of novel deep-learning driven computational tools for efficient identification of transposable elements in large plant genomes.Research...
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Umeå, Västerbotten, Sweden Umeå University Full timeProject OverviewHigh-throughput DNA sequencing technologies have led to the production of large genome assemblies, including those of conifers, wheat, axolotl salamanders, and giant lungfish. Genome annotation, particularly the identification of transposable elements (TEs), presents a significant challenge in analyzing these large genomes. Deep-learning...
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Umeå, Västerbotten, Sweden Umeå University Full timeProject OverviewThe project focuses on plant genomics and the development of deep-learning driven computational tools. The goal is to develop new deep-learning driven transposable elements (TEs) identification tools to further decrease the computational demand for large genome analysis.Key ObjectivesDevelop a comprehensive TE dataset to capture the sequence...
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