[SocBiN] PhD in structural and functional protein bioinformatics

Tue Dec 7 16:49:25 CET 2021

 Department of Experimental Medical Science

https://lu.varbi.com/en/what:job/jobID:456054

Lund University was founded in 1666 and is repeatedly ranked among the
world’s top 100 universities. The University has around 44 000 students and
more than 8 000 staff based in Lund, Helsingborg and Malmö. We are united
in our efforts to understand, explain and improve our world and the human
condition.

Lund University welcomes applicants with diverse backgrounds and
experiences. We regard gender equality and diversity as a strength and an
asset.

*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

The Faculty of Medicine is a part of Lund University, and is responsible
for education and research within medicine and healthcare. Our academic
programs are closely linked with the healthcare system and are firmly
anchored in the faculty’s strong research tradition. Our research spans a
broad field within experimental preclinical research, near-patient clinical
research and health sciences research. The Faculty of Medicine, with its
1,800 employees and 2,700 students in Lund and Malmö, is a
knowledge-intensive meeting place for students, teachers and researchers
from all over the world.

We kindly decline all sales and marketing contacts.
Type of employment Temporary position longer than 6 months
First day of employment 220301
Salary Monthly salary
Number of positions 1
Working hours 100
City Lund
County Skåne län
Country Sweden
Reference number PA2021/3992
Contact

   - Gemma Atkinson, 046-2220000

Union representative

   - OFR/ST:Fackförbundet ST:s kansli, 046-222 93 62
   - SACO:Saco-s-rådet vid Lunds universitet, 046-222 93 64
   - SEKO: Seko Civil, 046-222 93 66

Published 07.Dec.2021
Last application date 09.Jan.2022 11:59 PM CET

Yours

Arne

-----------------------------------------
  Arne Elofsson                  Science for Life Laboratory
  Tel:+46-(0)70 695 1045   Stockholm University
  http://bioinfo.se/               Box 1031,
  Email: arne at bioinfo.se   17121 Solna, Sweden
  Twitter:   https://twitter.com/arneelof
  Zoom: https://stockholmuniversity.zoom.us/my/arneelof/
  Scholar: http://scholar.google.se/citations?user=s3OCM3AAAAAJ
  ORCID: 0000-0002-7115-9751 <https://orcid.org/0000-0002-7115-9751>
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