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PhD student in plant science with focus on deep-learning conifer genomics
The Department of Plant Physiology (Umeå University, Umeå Plant Science Centre, Sweden) invites applicants for a PhD position in plant science. The expected starting date is November 1, 2024 or according to agreement. Application deadline is September 2, 2024.
Umeå Plant Science Centre (UPSC) is one of the strongest research environments for basic plant research in Europe. Research at UPSC covers a wide range of disciplines in plant biology including ecology, computational biology, genetics, physiology, biochemistry, cell biology and molecular biology (see www.upsc.se). A PhD student position is open at the Department of Plant Physiology, which is part of Umeå Plant Science Centre.
Project description
Ever advancing high-throughput DNA sequencing technologies continue to produce genome assemblies of larger genome sizes, such as conifers (10-40 Gb, 3-15x of human genome), wheat (15 Gb, 5x), axolotl salamander (32 Gb, 11x), and giant lungfish (43 Gb, 14x). Genome annotation (identifying various functional sequence elements) presents one big challenge in analyzing large genomes, for example, to identify transposable elements (TEs), major component of most plant genomes especially those large genomes. Deep-learning models (currently used for computer vision and natural language processing), which can encode high-dimensional genome sequences into vectors and learn and resolve the sequence complexity, offer promising solutions for efficient identifying sequence elements (such as TEs) from genome sequences.
The PhD project focuses on plant genomics and the development of deep-learning driven computational tool. (1) This project aims to develop new deep-learning driven TEs identification tools to further decrease the computational demand for large genome analysis. (2) To develop such an efficient computational tool, this project will first construct a comprehensive TE dataset to capture the sequence diversity of TEs by collecting genome data from hundreds of plant species. (3) This project will also look into TEs integration profile by predicting TE insertion from genome sequences. This project will potentially develop a set of new analytical tools and reveal a more insightful picture of TE movement and evolution.
This PhD position is focused on developing and applying deep-learning driven methods to advance our understanding of complexities of TE in large plant genome. The successful candidate will work at the interface of machine-learning, computational biology, and molecular biology and will have the opportunity to collaborate with experimentalists and computational scientists across a wide range of disciplines.
Admission requirements
To fulfil the general entry requirements for studies at third-cycle level the applicant must have qualifications equivalent to a completed degree at second-cycle level or completed course requirements of at least 240 ECTS credits including at least 60 ECTS credits at second-cycle level. To fulfil the specific entry requirements to be admitted for studies at third-cycle level in Plant Science at Umeå Plant Science Centre, the successful candidate must have completed 90 ECTS relevant to the doctoral thesis project. Out of this, at least 30 ECTS have to be in a subject closely related to the research topic of the graduate program. Applicants who have acquired equivalent skills in some other educational system in Sweden or abroad are also eligible.
For this position, we are looking for a person interested in plant biology and machine-learning. You should have an academic background in plant biology, machine-learning, bioinformatics or a related field. The following achievements, skills and/or knowledge are also required:
Experience in standard molecular biological techniques or in machine-learning.
Very good written and oral English language skills.
Proficiency in working with computers and programming, e.g. in Linux Shell, R, Python, Julia, etc.
The PhD student is expected to play an active role in developing this doctoral project and in the department. In addition, the PhD student is expected to have a scientific, structured, flexible and result-oriented approach to their work. The assessments of the applicants are based on their qualifications and presumed ability to take part in doctoral education.
The application
Applications must be submitted electronically using the e-recruitment system of Umeå University. Log in and apply via the button at the bottom of the page. All documents should be written in English (preferably) or Swedish and uploaded in pdf format. The deadline for applications is September 2nd, 2024.
A complete application must include:
A cover letter summarizing your qualifications, scientific interests and motives for applying (max two pages)
A Curriculum Vitae
Certified copies of relevant degree certificate(s) translated to English or Swedish.
Master theses work or equivalent and copy of other relevant publications (if any)
Transcripts with grades, with English or Swedish translation.
Contact information to two reference persons
More information
For further information contact the Principal Investigator of the project, Associate Professor Jian-Feng Mao, jianfeng.mao@umu.se
Umeå University wants to offer an equal environment where open dialogue between people with different backgrounds and perspectives lay the foundation for learning, creativity and development. We welcome people with different backgrounds and experiences to apply for the current employment.
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