PhD in structural and functional protein bioinformatics - Hiring in process/Finished, not possible to apply

Background

In the Atkinson lab we are interested in making exciting discoveries about the evolution of protein function and structure. We work mainly with bioinformatic methods, developing our own tools and taking advantage of the wealth of available genome and predicted proteome sequences. The Atkinson lab is based in the Department of Experimental Medical Sciences in the Biomedical Centre (BMC) in Lund. You can read more about our group on our lab website here: https://atkinson-lab.com/, and about the department here: https://www.medicine.lu.se/faculty-medicine-lund-university/departments/department-experimental-medical-science

One of our main research directions concerns toxin-antitoxin (TA) systems of bacteria and bacteriophages, which has led to papers in PNAS(1) and Molecular Cell(2) on toxSAS enzymes that dramatically inhibit bacterial growth though producing poisonous nucleotides, or modifying tRNA, as well as a more recent preprint on the hyper promiscuous antitoxin domain that we have named Panacea(3). Our work on toxin-antitoxins, and their evolution, structure, function and biotechnological applications was recently supported by a generous grant from the Knut and Alice Wallenberg foundation (see https://kaw.wallenberg.org/en/research/bacterias-emergency-stop-buttons). As a mechanism of defence against bacteriophages, TAs have significance for developing new biotechnological tools, as well as understanding and eventually overcoming natural barriers to phage therapy for treating antibiotic resistant infections.

References

1. Jimmy, S. et al. Proc Natl Acad Sci U S A 117, 10500-10510, (2020).
2. Kurata, T. et al. Mol Cell 81, 3160-3170 e3169, (2021).
3. Kurata, T.et al. Proc Natl Acad Sci U S A (in press) and bioRxiv, https://www.biorxiv.org/content/10.1101/2021.1105.1107.442387v442381, (2021).

In our group, we strive for a supportive, respectful and stimulating working environment that promotes personal and professional development for all members.

We are looking for a PhD student to continue the lab’s high impact work, driving new directions in toxin-antitoxin system research. A significant part of the project will be the use of deep learning methods for structural prediction such as AlphaFold2. The employment is for 4 years at full time and the start date is by agreement.

Responsibilities

In this PhD project you will be using and developing computational tools to predict the structure and biological function of toxin-antitoxin systems of bacteria and bacteriophages. Bioinformatic predictions that come out of this project will be verified experimentally through our collaborative network. Much of the project will focus on toxin-antitoxin systems, but you will also have opportunities to broaden your horizons to other molecular systems. You will have the opportunity to attend and present your work at international meetings.

Qualifications

Required qualifications:

• Coding skills (preferably in Python)
• Experience in structural bioinformatics
• Proficiency in spoken and written English
• Background understanding of, and interest in molecular biology and evolution of microbes

Desirable qualifications:

• Experience in creating pipelines for use with high performance computing clusters
• Competence in large dataset handling
• Previous use of machine learning or artificial intelligence methods, especially for structural prediction such as AlphaFold2 or RosettaFold

Eligibility
Students with basic eligibility for third-cycle studies are those who- have completed a second-cycle degree- have completed courses of at least 240 credits, of which at least 60 credits are from second-cycle courses, or- have acquired largely equivalent knowledge in some other way, in Sweden or abroad.

The employment of doctoral students is regulated in the Swedish Code of Statues 1998: 80. Only those who are or have been admitted to PhD-studies may be appointed to doctoral studentships. When an appointment to a doctoral studentship is made, the ability of the student to benefit from PhD-studies shall primarily be taken into account. In addition to devoting themselves to their studies, those appointed to doctoral studentships may be required to work with educational tasks, research and administration, in accordance with specific regulations in the ordinance.

Type of employment
Limit of tenure, four years according to HF 5 kap 7§.

Include the following documents in your application:

1. A cover letter (maximum 1 page) with the following sections:

a) Motivation

 (explain your interest in the project, motivation for applying, and what you hope to learn)

b) Eligibility and experience

(explain how you fulfil the eligibility and qualification requirements, describe your previous relevant experience and outline how you will contribute to the research group)

2. A CV (maximum 2 pages) with contact details of two referees

3. Bachelors and Masters certificates