Post-doctoral scholarship in bioinformatics

Link to the ad on the Lund University website, and PDF

Lund University is one of Europe’s leading universities. Here, history and tradition lay the
ground for the study and research environments of tomorrow. We offer education and research
within engineering, science, law, social sciences, economics and management, humanities,
theology, fine art, music and theatre. Through interaction with business and the community we
ensure that knowledge and innovations benefit society. The University has 47 000 students and
7 200 staff from all over the world, based mainly in Lund, Malmö and Helsingborg. We work
with 680 partner universities in more than 50 countries.


Lund University invites applications for the following position:
Post-doctoral scholarship in bioinformatics
Placement: Department of Experimental Medical Science
Ref No: V2021/2101
Duration: The scholarship can be drawn for a total of two years, with each contract being of
six months duration.
Starting time: By agreement
Last day for applying:
October 18th 2021


Description
In the Atkinson lab our aim is to make fundamental discoveries about the evolution of protein function and structure. We work mainly with bioinformatic methods, developing our own tools and taking advantage of the huge amounts of available genome and predicted proteome sequences. One of our main research directions concerns toxin-antitoxin (TA) systems of bacteria and bacteriophages. Our studies of toxSAS TA enzymes that dramatically inhibit bacterial growth though producing poisonous nucleotides, or modifying tRNA have recently been recently published in PNAS [1] and Molecular Cell [2], respectively, and our recent discovery of a hyperpromiscuous antitoxin domain that we have named Panacea is currently in revision [3]. 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. 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.

The post-doctoral scholarship will be an opportunity for scientific development in protein bioinformatics and skill acquisition in coding and web development. Building on the success of our gene-neighbourhood analysis Python tool FlaGs (www.webflags.se) [4], you will be participating in the development of bioinformatic methods for the discovery of new exciting biology. The bioinformatic predictions will be tested experimentally in our group and through our collaborative network.

References

  1. Jimmy, S. et al. Proc Natl Acad Sci U S A 117, 10500-10510 (2020).
  2. Kurata, T. et al. Molecular Cell 81(15): 3160-3170 (2021)
  3. Kurata, T. et al. bioRxiv, 2021.2005.2007.442387 (2021).
  4. Saha, C. K., Sanches Pires, R., Brolin, H., Delannoy, M. & Atkinson, G. C. Bioinformatics
    37, 1312-1314 (2021).


    Qualifications
    Expertise: Required
  • Coding skills (preferably in Python)
  • Background understanding of, and strong interest in molecular biology and evolution

    Expertise: Experience in any of the following is desirable but not essential:
  • Web tool development
  • Machine learning methods
  • Phylogenetic sequence analysis
  • Handling of large data sets of genomes and proteomes

    Eligible candidates must have obtained their PhD within the last three years, and must not have
    held positions at Lund University within the last two years.

    The application should contain:
  • Cover letter explaining your motivation for applying for the scholarship
  • Curriculum vitae with contact details of two referees
  • PhD Diploma

    Appointment procedure:
    Applications with CV is to be sent to Gemma C. Atkinson via e-mail:
    gemma.atkinson@med.lu.se
    Ref. No V2021/2101 shall be indicated on the application.

    Information regarding post doc scholarships at Lund University
    • The scholarship amounts are paid quarterly.
    • The scholarship follows the regulations laid down by the University Vice-Chancellor (LS
    2010/68, A13).
    • The scholarship is intended for the holder’s own education/professional development and
    does not constitute remuneration for work or other service that has been carried out or will be
    carried out on behalf of the University.
    • The scholarship does not give any entitlement to sickness benefit, parental allowance, holiday
    pay or pension.
    • The host faculty/department and the scholarship holder shall draw up in writing an agreed
    plan for the studies/development.
    • The Scholarship holder is to be informed about the length of the stay, assured social
    conditions, and continual review of the scholarship holder’s development.
    • The Scholarship holder is to be informed about insurance covering the scholarship holder and
    the need to check his/her own insurance requirements.
    • The scholarship holder is to be treated equally to students/researchers in the same situation but
    with different sources of funding.
    • The scholarship holder is to be assured and to contribute to a good working environment.
    • The Scholarship holder is to be informed about the risk of possible retrospective taxation in
    Sweden in cases where the scholarships are administered and paid out by LU and the
    scholarship holder gains employment at LU shortly after the period of the scholarship.
    • There may be a risk of the scholarship holder being taxed in his/her home country; the
    scholarship holder should investigate this before the period of the scholarship.

Information:
Dr. Gemma C. Atkinson: gemma.atkinson@med.lu.se