PhD Student in Plant Genomics with Deep Learning Focus

2 months ago


Umeå, Västerbotten, Sweden Umeå University Full time
Project Overview

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 Objectives

This 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.
Requirements and Qualifications

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.
Admission Requirements

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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