From anukuk at utu.fi Wed Jul 2 13:34:23 2025 From: anukuk at utu.fi (Anu Kukkonen-Macchi) Date: Wed, 2 Jul 2025 11:34:23 +0000 Subject: [SocBiN] Open position in scientific IT support role at Turku Medical Bioinformatics Centre, Finland Message-ID: <674b1a6a431c480cbe5221276e7049fc@utu.fi> Project researcher/ Project specialist for scientific IT support to Turku Medical Bioinformatics Centre The Medical Bioinformatics Centre (MBC) is looking for an IT professional to join our team in new role and contribute to the growth and development of our bioinformatics core facility. MBC is part of the national Biocenter Finland research infrastructure and the European-wide ELIXIR infrastructure. As a core facility of Turku Bioscience Centre, MBC supports high-quality research by providing bioinformatics support to academic research units and healthcare organizations, among others, and scientific IT support to researchers. MBC also conducts internationally high-level research, and develops and applies computational data analysis tools for interpreting large molecular and clinical datasets in medical research, in close collaboration with leading medical research groups and biobanks. We are looking for an expert in information technology to join our team and take responsibility of the development of scientific IT support services targeted for life science researchers across Finland. The position is part of the national Biocenter Finland infrastructure, aiming to enhance efficient utilization of the IT infrastructures and resources provided by CSC, ELIXIR, and the Biocenter Finland host universities. Interested? Read full description here: https://ats.talentadore.com/apply/projektiasiantuntija-projektitutkija-it-painotteiseen-bioinformatiikan-tehtavaan/mMN397?lang=en Leave your application by August 28, 2025. Position starts in September 2025 or as agreed. The position is for a fixed term until the end of the year 2027 with possibility for extension. -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne.elofsson at gmail.com Thu Jul 3 05:09:06 2025 From: arne.elofsson at gmail.com (Arne Elofsson) Date: Thu, 3 Jul 2025 10:09:06 +0700 Subject: [SocBiN] Fwd: Karolinska Institutet is recruiting 20 assistant professors In-Reply-To: References: Message-ID: > Dear all, Karolinska Institutet is recruiting 20 assistant professors. Generous startup offers. Link to the call: https://ki.se/en/about-ki/jobs-at-ki/join-a-global-community-of-excellence with direct links to perhaps the most relevant positions in terms of cryo-EM here: https://ki.varbi.com/what:job/jobID:839971/ and here https://ki.varbi.com/what:job/jobID:839804/ For electron microscopy, the 3D-EM core facility is equipped with an Aquilos 2, a cold-FEG Krios G3i (with BioQuantum K3), a Talos 120 kV, a Leica ICE high-pressure freezer, and a Leica cryo-confocal SP8 for cryo-CLEM. https://ki.se/en/research/research-infrastructure-and-environments/core-facilities-for-research/3d-em-core-facility/3d-em-our-offer Deadline September 2. Best regards, Martin *När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. *Här finns information om hur KI behandlar personuppgifter . *Sending email to Karolinska Institutet (KI) will result in KI processing your personal data.* You can read more about KI’s processing of personal data here . -- You received this message because you are subscribed to the Google Groups "all_users_cryoem" group. To unsubscribe from this group and stop receiving emails from it, send an email to all_users_cryoem+unsubscribe at scilifelab.se. To view this discussion visit https://groups.google.com/a/scilifelab.se/d/msgid/all_users_cryoem/MM0P280MB0373E668428DE28FE92D3BD9F840A%40MM0P280MB0373.SWEP280.PROD.OUTLOOK.COM . For more options, visit https://groups.google.com/a/scilifelab.se/d/optout. -------------- next part -------------- An HTML attachment was scrubbed... URL: From erik.sonnhammer at scilifelab.se Sat Jul 19 22:52:29 2025 From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer) Date: Sat, 19 Jul 2025 22:52:29 +0200 Subject: [SocBiN] Bioinformatics industry PhD position in Stockholm "Deep learning modeling of spatial biology data for expression profile based drug repurposing" Message-ID: <65fc4016-9419-46d7-9e1f-5c439ae81371@scilifelab.se> DDLS Industry PhD studentship in bioinformatics: Deep learning modeling of spatial biology data for expression profile based drug repurposing A new exciting opportunity is combining spatial biology with AI-driven modeling of gene expression responses to drug treatment in the field of drug repurposing. Drug repurposing involves identifying new therapeutic uses for existing medications, a strategy that can significantly reduce the time and cost required to bring a drug to market. The project will use AI models such as CycleGANs, that by learning from complex spatial gene expression profiles and cellular heterogeneity within tissues can predict how existing drugs might act on previously uncharacterized disease mechanisms or cellular subtypes. These models will be employed to translate spatial gene expression profiles from healthy tissues to disease states, and vice versa. This capability allows researchers to simulate the effects of drug treatments on spatially resolved gene expression without the need for extensive experimental data. By learning the underlying mappings between these domains, synthetic data will be generated that reflects potential drug responses, thereby enhancing the predictive power of our models. This is an Industry PhD Project which is a collaboration between Stockholm University and Merck AB. The PhD student will be employed by Merck AB but registered and accepted to the PhD program at Stockholm University. The project will have a base in the Sonnhammer group at Science for Life Laboratory in Stockholm, Sweden, which is a strong research environment for large-scale life science research, and a joint physical center for a number of computational and life science groups at Stockholm University, KTH, and Karolinska Institutet. The research project will be supervised by Professor Erik Sonnhammer and Dr. Dimitri Guala. Data-driven life science (DDLS) uses data, computational methods and artificial intelligence to study biological systems and processes at all levels, from molecular structures and cellular processes to human health and global ecosystems. The SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS) aims to recruit and train the next generation of data-driven life scientists and to create globally leading computational and data science capabilities in Sweden. The program is funded with a total of 3.3 billion SEK (about 290 M USD) over 12 years from the Knut and Alice Wallenberg (KAW) Foundation. In 2025 the DDLS Research School will be expanded with the recruitment of 19 academic and 7 industrial PhD students. During the DDLS program more than 260 PhD students and 200 postdocs will be part of the Research School. The DDLS program has four strategic research areas: cell and molecular biology, evolution and biodiversity, precision medicine and diagnostics, epidemiology and biology of infection. For more information, please see scilifelab.se/data-driven/ddls-research-school/ The future of life science is data-driven. Will you be part of that change? Then join us in this unique program! See ad at https://sonnhammer.org/download/ads/open.html Deadline August 15 To apply, follow the instructions on https://careers.merckgroup.com/global/en/job/288421/Industrial-PhD-student-in-Bioinformatics. Thanks for spreading to potentially interested persons. Best Regards, ___________________________________ Erik Sonnhammer, Ph.D. Professor of Bioinformatics DBB, Stockholm University Science for Life Laboratory Stockholm, Sweden Email: Erik.Sonnhammer at scilifelab.se https://sonnhammer.org https://x.com/eriksonnhammer -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Sun Jul 20 10:46:02 2025 From: arne at bioinfo.se (Arne Elofsson) Date: Sun, 20 Jul 2025 10:46:02 +0200 Subject: [SocBiN] =?utf-8?q?Phd_position_in_Using_Deep_Learning_to_Underst?= =?utf-8?q?and_Protein_Structure_Evolution=E2=80=9D=2E?= Message-ID: https://su.varbi.com/what:job/jobID:830925/where:4/ 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). 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: @arneelof.bsky.social 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From bjorn.nystedt at scilifelab.se Wed Jul 30 09:36:39 2025 From: bjorn.nystedt at scilifelab.se (=?utf-8?Q?Bj=C3=B6rn_Nystedt?=) Date: Wed, 30 Jul 2025 09:36:39 +0200 Subject: [SocBiN] =?utf-8?q?Bioinformatician/Data_Scientist_position_at_NB?= =?utf-8?q?IS/SciLifeLab=2C_Ume=C3=A5=2C_Sweden?= Message-ID: Dear all, National Bioinformatics Infrastructure Sweden (NBIS), a part of SciLifeLab, has a Staff scientist in Bioinformatics and Data Science position out in Umeå, Sweden. This is a permanent staff scientist positions focusing on support to Swedish researchers (it is NOT a post doc position). Please see the link below for more information and how to apply. We only accept applications through the application system, not by email. Staff scientist in Bioinformatics and Data Science. https://www.umu.se/en/work-with-us/open-positions/staff-scientist-in-bioinformatics-and-data-science_838707/ Application deadline: Aug 31st, 2025. Best regards, Björn Nystedt National Bioinformatics Infrastructure Sweden at SciLifeLab ------------------------------------------------ Bjorn Nystedt, PhD National Bioinformatics Infrastructure Sweden at SciLifeLab www.nbis.se, www.scilifelab.se/units/nbis/ Phone: 018 - 471 4413 E-mail: bjorn.nystedt at scilifelab.se ------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: