[SocBiN] Phd position in Stockholm
Arne Elofsson
arne.elofsson at gmail.com
Tue Jun 3 15:08:04 CEST 2025
PhD Position at Stockholm University in "Using Deep Learning to Understand
Protein Structure Evolution".
https://su.varbi.com/en/what:job/jobID:830925/
[image: Logo for Stockholms universitet] <https://su.varbi.com/>
PhD student in Bioinformatics
To apply you must first logout from your company account
*The Department of Biochemistry and Biophysics*
SciLifeLab (SciLifeLab <https://www.scilifelab.se/>) is a national center
for molecular biosciences with a focus on health and environmental
research. The center combines frontline technical expertise with advanced
knowledge of translational medicine and molecular bioscience. SciLifeLab is
a national resource hosted by Karolinska Institutet, KTH Royal Institute of
Technology, Stockholm University and Uppsala University. The center
also collaborates with several other universities.
The employment will be placed at the Department of biochemistry and
biophysics, at Stockholm university.
More information about us, please visit: the Department of Biochemistry and
Biophysics <http://www.dbb.su.se/>.
Project description
Your studies in Bioinformatics will be in the project: "Using Deep Learning
to Understand Protein Structure Evolution”.
We have studied domain evolution and observed that structural change is
roughly linear with sequence change. However, larger structural changes
might also occur within a domain during evolution, particularly within
transporters3. Further, domains can be combined to create multi-domain
proteins. Most domain architectures arise from adding or removing a single
domain at the N- or C-terminal regions, while certain repeat-domain
families undergo more internal duplications. We also demonstrated that
eukaryotic proteins harbour substantially more disordered and linker
regions, which expand more rapidly than globular domains. Most phylogenetic
studies of proteins, including ours, have primarily focused on changes in
the amino-acid sequences. Today, accurate structural models from AlphaFold
make it possible to integrate structure into large-scale phylogenetic and
sequence analyses. Therefore, in this application, we propose revisiting
earlier studies, scaling them up, and adding structural information to the
analysis. This study will provide a detailed structural understanding of
changes within domains, how novel protein architectures emerge, and why
certain domains and architectures continue expanding and diversifying in
specific lineages. We believe this study will provide fundamental insights
into protein structure evolution and how evolutionary mechanisms and
selective pressures have shaped proteins. Together, the three aims of this
project will reveal how domain changes their structure and how
rearrangements shape structural protein diversity across the tree of life.
The Elofsson group is located at the Science for Life Laboratory. Elofsson
has worked on protein structure predictions and evolution for over two
decades. He has worked on various techniques using machine learning and
other computational techniques. Our most important contributions to this
work are the methods he has developed to identify the quality of protein
models, Pcons, and various versions of ProQ. The group comprises 5 PhD
students, one postdoc, and one senior researcher.
Qualification requirements
In order to be admitted to postgraduate education, the applicant must have
the general and specific entry requirements. The qualification requirements
must be met by the deadline for applications.
You meet *general entry requirements* if you have completed a second-cycle
degree, or completed courses equivalent to at least 240 higher education
credits, of which 60 credits must be in the second cycle, or have otherwise
acquired equivalent knowledge in Sweden or elsewhere.
In order to meet *the specific entry requirements*, for acceptance in the
Biochemistry, especially Bioinformatics, program the applicant must have
passed courses within the first and second cycles of at least 90 credits in
either, a) Chemistry/Molecular Biology/Biotechnology, or b) Computer
Science/Mathematics/Physics and at the second cycle level, 60 credits in
Life Science, Computer Science Mathematics, Physics or Bioinformatics
including a 30 credit Degree Project (thesis).
Selection
The selection amongst the eligible candidates will be based on their
capacity to successfully complete the program. Important criteria when
assessing this capacity are; documented knowledge and skill in the field of
the thesis project, written and oral proficiency in English, the capacity
for analytical thinking, the ability to collaborate, as well as creativity,
initiative, and independence. The assessment will be based on previous
experience and grades, the quality of the degree project, references,
relevant experience, interviews and the candidate’s written motivation for
seeking the position.
Admission Regulations for Doctoral Studies at Stockholm University.
<https://medarbetare.su.se/en/our-su/governance/rules--regulations/education/admission-regulations-for-third-cycle-study-programmes>
About the post
We offer a fixed-term employment as a doctoral student according to Chapter
5 of the Higher Education Ordinance (1993:100). The period of employment
may not be longer than what corresponds to full-time doctoral education for
four years. As a doctoral student, you should primarily devote yourself to
your own doctoral education, but the employment may include work with
education, research and administration to a limited extent (maximum 20 %).
A new employment as a doctoral student is for a maximum of one year, the
employment is then renewed for a maximum of two years at a time.
Stockholm University strives to be a workplace free from discrimination and
with equal opportunities for all.
Contact
For more information, please contact Professor Arne Elofsson,
arne.elofsson at dbb.su.se.
Application
Apply for the PhD student position at Stockholm University's recruitment
system. Attach a personal letter and CV as well as the attachments
requested in the application form. It is the responsibility of the
applicant to ensure that the application is complete in accordance with the
instructions in the job advertisement, and that it is submitted before the
deadline.
The instructions for applicants are available at: How to apply for a
position
<https://www.su.se/english/about-the-university/work-at-su/how-to-apply-for-a-position>
.
Stockholm University contributes to the development of sustainable
democratic society through knowledge, enlightenment and the pursuit of
truth.
Type of employment Temporary position
Contract type Full time
Salary Fixed salary
Number of positions 1
Full-time equivalent 100 %
City Stockholm
County Stockholms län
Country Sweden
Reference number SU FV-2178-25
Union representative
- ST/OFR, st at st.su.se
- Saco-S, saco at saco.su.se
- Seko, seko at seko.su.se
Published 23.May.2025
Last application date 13.Jun.2025
To apply you must first logout from your company account
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
Bluesky: @bioinfo.se
Twitter/X: @arneelof
Mastodon: @arneelof at fediscience.org
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>
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
Bluesky: @bioinfo.se
Twitter/X: @arneelof
Mastodon: @arneelof at fediscience.org
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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