From marcel.tarbier at scilifelab.se Mon Aug 4 08:53:20 2025 From: marcel.tarbier at scilifelab.se (Marcel Tarbier) Date: Mon, 4 Aug 2025 08:53:20 +0200 Subject: [SocBiN] multiOmics Postdoc and PhD positions in Riga, Lavia - DL 08.08.25 Message-ID: Hi all, Nikolay Oskolkov is starting a computational lab on multiOmics topics at LIOS, Riga, Latvia, and is going to recruit a few people to my Metabolic Research Group within the TARGETWISE project https://targetwise.osi.lv/overview/. If you are interested in working with him as a postdoc, there are two vacancies, please apply here: https://euraxess.ec.europa.eu/jobs/358375 https://euraxess.ec.europa.eu/jobs/358370 Two PhD positions in his group will be announced later, please contact him at nikolay.oskolkov at scilifelab.se for more information. He can highly recommend Riga, it is a beautiful city with very good living conditions. Contact info: ****************************************************************** Nikolay Oskolkov, PhD Bioinformatician, Lund University, NBIS SciLifeLab https://www.biology.lu.se/nikolay-oskolkov https://nikolay-oskolkov.com/ https://scholar.google.ca/citations?user=0DnwWQIAAAAJ&hl=en Biology Department, Lund University Sölvegatan 35 , 22362 Lund Phone: 0761463349 E-mail: nikolay.oskolkov at scilifelab.se ************************************************ -------------- next part -------------- An HTML attachment was scrubbed... URL: From nikolay.oskolkov at scilifelab.se Mon Aug 4 19:39:38 2025 From: nikolay.oskolkov at scilifelab.se (Nikolay Oskolkov) Date: Mon, 4 Aug 2025 19:39:38 +0200 Subject: [SocBiN] Two postdoc positions in metabolic research group Message-ID: Dear colleagues, I am starting a computational lab on multiOmics topic at LIOS, Riga, Latvia, and going to recruit a few people to my Metabolic Research Group. Please DM at nikolay.oskolkov at scilifelab.se if you are interested in a postdoc or PhD position in my group. I can highly recommend Riga, it is a beautiful and comfortable city. Best, Nikolay ****************************************************************** Nikolay Oskolkov, PhD Bioinformatician, Lund University, NBIS SciLifeLab https://www.biology.lu.se/nikolay-oskolkov https://nikolay-oskolkov.com/ https://scholar.google.ca/citations?user=0DnwWQIAAAAJ&hl=en Biology Department, Lund University Sölvegatan 35 , 22362 Lund Phone: 0761463349 E-mail: nikolay.oskolkov at scilifelab.se ****************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From nikolay.oskolkov at scilifelab.se Mon Aug 4 19:41:45 2025 From: nikolay.oskolkov at scilifelab.se (Nikolay Oskolkov) Date: Mon, 4 Aug 2025 19:41:45 +0200 Subject: [SocBiN] Two postdoc positions in metabolic research group Message-ID: Dear colleagues, I am starting a computational lab on multiOmics topic at LIOS, Riga, Latvia, and going to recruit a few people to my Metabolic Research Group. Please DM at nikolay.oskolkov at scilifelab.se if you are interested in a postdoc or PhD position in my group. I can highly recommend Riga, it is a beautiful and comfortable city. Best, Nikolay ****************************************************************** Nikolay Oskolkov, PhD Bioinformatician, Lund University, NBIS SciLifeLab https://www.biology.lu.se/nikolay-oskolkov https://nikolay-oskolkov.com/ https://scholar.google.ca/citations?user=0DnwWQIAAAAJ&hl=en Biology Department, Lund University Sölvegatan 35 , 22362 Lund Phone: 0761463349 E-mail: nikolay.oskolkov at scilifelab.se ****************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From daniele.raimondi at igmm.cnrs.fr Mon Aug 11 11:48:31 2025 From: daniele.raimondi at igmm.cnrs.fr (Daniele Raimondi) Date: Mon, 11 Aug 2025 11:48:31 +0200 Subject: [SocBiN] open phd position in bioinformatics / machine learning in Montpellier Message-ID: <9d8a0e0d-50d3-42ec-b872-2e46aca1d6d3@igmm.cnrs.fr> *_Please feel free to share this offer for a PHD position at IGMM in Montpellier_ Project:*DNA large language models for end to end genome interpretation _*Motivation*_ Interpreting the genome means modeling the relationship between genotype and phenotype, which is the fundamental goal of biology. Achieving this would revolutionize genetics, medicine, and agro-tech. In clinical genetics, it could lead to personalized treatments tailored to each patient's genome, enabling precision medicine. _*Objectives*_ This project fuses quantitative genetics with bioinformatics and cutting-edge Artificial Intelligence, using the latest Deep Learning Large Language Models for DNA to advance our ability to predict the phenotypes deriving from the observed genotypes. This project is based on the previous work of Dr. Raimondi on Genome Interpretation (GI) for the prediction of clinically relevant phenotypes in humans. Dr. Raimondi previous works focused on encoding Whole-Exome/Whole-Genome Sequencing (WES/WGS) data into compact, machine-readable features, while reducing overfitting caused by high-dimensional genomic data. However, to limit complexity, we had to rely on coarse gene-level summaries, such as mutational burden per gene, which sacrificed fine-grained genetic detail. The goal of this project is to move beyond these gene-centric encodings by building neural network architectures that operate directly at the nucleotide level. To achieve this, we propose integrating pre-trained DNA LLMs as unsupervised feature extractors within GI models. These models, trained using self-supervised learning on entire genomes, capture rich patterns of DNA dependencies and can produce information-dense latent representations. DNA LLMs have shown strong performance in various functional genomics tasks, such as identifying regulatory elements and variant effects. This project will evaluate whether their latent representations can improve phenotype prediction. The new DNA LLM methods will be prototyped on A.thaliana, which is a well known model organism. Later developments will be translated to the disease risk prediction of Inflammatory Bowel Disease (IBD). Unlike DNA LLM research, this work applies LLMs to the interpretation of individual-level WES/WGS data for disease risk, marking a novel use of these models in human genetic prediction. _*Candidate profile*_ We are looking for a *motivated*and *curious*candidate, with a strong passion for science and for scientific discovery through the use and creation of new data science and Machine Learning methods. Bioinformatics and Genome Interpretation are multi-disciplinary and rapidly evolving fields. Therefore, the candidate is expected to 1) be eager to continuously *learn*new skills, methods and concepts, and 2) to *enjoy*finding new solutions in the face of new and unforeseen difficulties. The ideal candidate has *very good*1) python programming skills, 2) understanding of *the mathematical foundations and principles*of Machine Learning, Linear Algebra (vectorial and matricial operations, optimization), with a particular focus on *Neural Networks*, 3) *problem solving*skills, 4) familiarity with GNU/Linux environment and 5) ability to *multi-task*across different projects. A good understanding of the basic concepts of Bioinformatics is not necessary but welcome. The project will be based on the development of *un-orthodox Neural Network*models with *Pytorch*. B2 level of English is *required*. The offer provides an initial 6-month contract, with possibility of renewal to 2 years. This project can be extended to 3 years and offers the opportunity to obtain a PhD. _*Research environment*___ The recruited person will join the “AI for Genome Interpretation” team led by Dr. Daniele Raimondi at IGMM. The work will be conducted in an international (English-speaking) and interdisciplinary environment. The Institute of Molecular Genetics of Montpellier (IGMM) is a joint research unit affiliated with the CNRS and the University of Montpellier. It comprises around 200 members, organized into 18 research groups, 9 shared support services and 9 technological and scientific platforms. IGMM is a multidisciplinary institute whose research has both fundamental and translational impact in molecular and cellular biology at the international level. _*Qualifications*_ The ideal candidate has *very good*1) python programming skills, 2) understanding of *the mathematical foundations and principles*of Machine Learning, Linear Algebra (vectorial and matricial operations, optimization), with a particular focus on *Neural Networks*, 3) *problem solving*skills, 4) familiarity with GNU/Linux environment and 5) ability to *multi-task*across different projects. A good understanding of the basic concepts of Bioinformatics is not necessary but welcome. The project will be based on the development of *un-orthodox Neural Network*models with *Pytorch*. B2 level of English is required. Familiarity with scientific computing and libraries such as numpy, scikit-learn, scipy, pytorch. *HOW TO APPLY:* https://umontpellier.nous-recrutons.fr/poste/7sqwj9n4vg-ingenieur-en-calcul-scientifique-ou-ingenieur-en-ingenierie-logicielle-fh/ -- Daniele Raimondi, PhD Chaire de Professeur Junior CNRS AI for Genome Interpretation group Institut de Génétique Moléculaire de Montpellier (IGMM) 1919 Route de Mende 34090 Montpellier, France -obscurum per obscurius- -------------- next part -------------- An HTML attachment was scrubbed... URL: From par.engstrom at scilifelab.se Fri Aug 15 14:12:42 2025 From: par.engstrom at scilifelab.se (=?utf-8?B?UMOkciBFbmdzdHLDtm0=?=) Date: Fri, 15 Aug 2025 14:12:42 +0200 Subject: [SocBiN] Bioinformatician positions at NBIS, SciLifeLab Stockholm Message-ID: <8F90926C-E050-4846-878A-E4709AE4D29A@scilifelab.se> Dear all, National Bioinformatics Infrastructure Sweden (NBIS) is looking for 1-2 bioinformatics experts to join us at SciLifeLab Stockholm. This time we are specifically interested in candidates with experience of spatial omics and/or advanced biostatistics and machine learning. These are permanent staff scientist positions (i.e. not postdoc positions) focusing on supporting Swedish researchers with bioinformatics. The employment will be at Stockholm University. More information and how to apply: https://su.varbi.com/en/what:job/jobID:847098/ (deadline Friday September 5th) NBIS also has several other openings currently in Uppsala, Umeå and Linköping, for bioinformaticans, system developers, project managers and other experts: https://nbis.se/about/work-with-us Welcome to apply! Pär -- Pär Engström Co-head of Bioinformatics Support, Infrastructure and Training Unit National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory Department of Biochemistry and Biophysics, Stockholm University http://www.nbis.se, http://www.scilifelab.se/platforms/nbis From arne.elofsson at gmail.com Sat Aug 16 08:26:15 2025 From: arne.elofsson at gmail.com (Arne Elofsson) Date: Sat, 16 Aug 2025 08:26:15 +0200 Subject: [SocBiN] Fwd: [MLSB @ NeurIPS 2024] MLSB 2025 Submissions are Open! In-Reply-To: References: Message-ID: Hi everyone, Great news! Submissions for Machine Learning in Structural Biology (MLSB 2025), co-located with NeurIPS 2025 in San Diego, are now officially open. We're bringing together folks working at the exciting intersection of machine learning and structural biology to share the latest and greatest research. MLSB 2025 is a non-archival venue, so feel free to send us your work-in-progress or papers you've submitted elsewhere! Mark your calendars: - Submission Deadline: Friday, September 26, 2025 - Decisions Sent Out: October 15, 2025 - CMT submission site: https://cmt3.research.microsoft.com/MLSB2025 - Call for papers instructions: https://www.mlsb.io/call-for-papers We're looking for submissions on a broad range of topics around structural biology, like generative models for biomolecule design, new frontiers in structure prediction, biological language models, and much more. Excited to see what you've been working on! Cheers, The MLSB 2025 Organizers -- You received this message because you are subscribed to the Google Groups "Machine Learning in Structural Biology" group. To unsubscribe from this group and stop receiving emails from it, send an email to workshopmlsb+unsubscribe at googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.a.a.nylander at gmail.com Mon Aug 18 11:13:27 2025 From: j.a.a.nylander at gmail.com (Johan Nylander) Date: Mon, 18 Aug 2025 11:13:27 +0200 Subject: [SocBiN] Bioinformatician with expertise in genome data analysis, NRM, Stockholm Message-ID: Title: Bioinformatician with expertise in genome data analysis Deadline for application: 8 September 2025 Employer: Swedish Museum of Natural History (https://www.nrm.se), Stockholm, Sweden. Type of employment: Permanent or fixed-term employment Description: The Swedish Museum of Natural History is looking for a bioinformatician to join the staff at the Department of Bioinformatics and Genetics (https://www.nrm.se/engelska/in-english/about-us/organisation/research-division/department-of-bioinformatics-and-genetics). Duties: Most of the time (about 70-80%) will be spent assisting and facilitating (long-term and daily) researchers from the Swedish Museum of Natural History who want to conduct collection-based genetic research. In order to be at the forefront of science, part of the working time (about 20-30%) is expected to be devoted to own research, which includes publishing research articles and applying for external funding. Full description and How to Apply at Arbetsförmedlingen (use the Translate link for English version): https://arbetsformedlingen.se/platsbanken/annonser/29793822 From marcel.tarbier at scilifelab.se Thu Aug 21 11:14:17 2025 From: marcel.tarbier at scilifelab.se (Marcel Tarbier) Date: Thu, 21 Aug 2025 11:14:17 +0200 Subject: [SocBiN] Permanent bioinformatics position (genomics) @ NRM Stockholm Message-ID: ---------- Forwarded message --------- From: José Cerca Date: Wed, Aug 20, 2025 at 11:57 AM Subject: [Evolgen-at-lists.su.se] Permanent bioinformatics position @ NRM To: evolgen at lists.su.se Cc: Knud Jønsson Hi again Evol-gen folks, The Naturhistoriska Riksmuseet is seeking a full time bioinformatician. Permanent position, 70-80% of the time should be dedicated to supporting day-to-day activities and long-term research of research groups. 20-30% time for one's own research. Come join the museum-side of the force; Happy to answer any questions you may have! https://arbetsformedlingen.se/platsbanken/annonser/29793822 Best, José -------------- next part -------------- An HTML attachment was scrubbed... URL: