October 2025 - BBClist - maillist.psb.ugent.be

[mlcsb.cosi] Fwd: [Bioinf] PhD in GenAI for Scientific Workflow Reconstruction and FAIR Publication at VU Amsterdam
by BeNeLux bioinformaticians forum 24 Oct '25

24 Oct '25

-------- Forwarded Message -------- Subject: [Bioinf] New Phd position Date: Fri, 24 Oct 2025 08:59:45 +0000 From: Işik, Z. (Zerrin) <z.isik(a)vu.nl> To: bio-plus.few(a)listserver.vu.nl <bio-plus.few(a)listserver.vu.nl> Dear all, I want to share a new PhD opportunity, which is a joint position in Bioinformatics (Dr. Zerrin Isik) and User Centric Data Science (Dr. Ronald Siebes) research groups at VU Amsterdam. Please feel free to forward it in your network. https://workingat.vu.nl/vacancies/phd-in-genai-for-scientific-workflow-reco… Thank you in advance! Best, Zerrin ------------------------------------------------- Dr. Zerrin Isik Assistant Professor for Bioinformatics Department of Computer Science Vrije Universiteit Amsterdam Email: z.isik(a)vu.nl -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1111 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +312059 87783 - skype: kafeenstra - room NU 12A31| | |Feenstra(a)few.vu.nl -www.few.vu.nl/~feenstra/ | | | "Wicky-wicky Wa-wild West" (Will Smith) | |_____________|_______________________________________________________|

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Open PhD position TUDelft-LUMC
by BeNeLux bioinformaticians forum 21 Oct '25

21 Oct '25

PhD Position Study Genetic Impacts on Brain Cells Using Single-Cell and Spatial ML Techniques Join us to decode how genetic variation reprograms brain cells and disrupts their communication using AI Job description We are looking for a PhD student to work at the intersection of machine learning, single-cell genomics, and neurogenetics. Your project will focus on developing new methods to understand how genetic variants affect not only individual brain cells but also change the way cells interact and communicate — insights that are essential for understanding the cellular origins of brain disorders. Despite major progress in genetics research, we still don’t know how genetic risk factors for brain disorders like schizophrenia, alzheimer, and depression disrupt brain function. Genetic discoveries point to thousands of disease-associated SNPs, but most of them act in subtle and cell type–specific ways, and their downstream biological effects remain poorly understood. This project tackles this fundamental gap — by building computational models that simulate what goes wrong in the brain, one cell (and one cell–cell interaction) at a time. You will work with large-scale single-cell and spatial transcriptomics data to develop and apply single-cell foundation models — generative machine learning models that represent the structure and variation of cell states. These models act as virtual cells simulating how perturbing the expression of genes altered by genetic variants affects the cell’s identity, behavior, and trajectory. You will extend these models to understand how genetic risk factors alter cell–cell communication networks. Spatial transcriptomics datasets will be used to anchor these models in real tissue context, revealing how spatially organized cell communities rewire under genetic perturbation. Key challenges * Use and improve single-cell foundation models to predict SNP-driven shifts in cell state and cell fate. * Integrate spatial transcriptomics data to anchor these predictions in tissue context. * Develop machine learning methods (e.g. graph neural networks, variational or diffusion models) to model cell–cell communication dynamics under genetic perturbation. * Investigate how local interactions between perturbed and unperturbed cells reshape signaling networks and tissue states. * Closely collobarate with neuroscientists in the BRAINSCAPES consortium to link model predictions to experimental and clinical relevance. Benefits * Shape next-generation models for understanding brain disease mechanisms. * Work in a collaborative, interdisciplinary, and dynamic environment with leading experts in machine learning, computational biology, and neurogenomics. * Access cutting-edge datasets, infrastructure, and computational and experimental facilities. * Receive support for professional development and participation in international conferences. Job requirements * A Master’s degree in computational biology, machine learning, bioinformatics, AI, or a related field. * Strong background in machine learning and data analysis. * Interest in single-cell omics, spatial data, or systems neuroscience. * Intellectual curiosity, independence, and motivation to tackle open-ended problems with real-world impact. * Strong analytical thinking and problem-solving skills. * A passion for using AI to answer fundamental questions in biology and medicine. * Ability to work independently and as part of a multidisciplinary team. * Strong interpersonal communication and collaboration abilities * Strong communication skills and proficiency in English. To apply go to: https://careers.tudelft.nl/job/Delft-PhD-Position-Study-Genetic-Impacts-on-… TU Delft (Delft University of Technology) Delft University of Technology is built on strong foundations. As creators of the world-famous Dutch waterworks and pioneers in biotech, TU Delft is a top international university combining science, engineering and design. It delivers world class results in education, research and innovation to address challenges in the areas of energy, climate, mobility, health and digital society. For generations, our engineers have proven to be entrepreneurial problem-solvers, both in business and in a social context. At TU Delft we embrace diversity as one of our core values<https://www.tudelft.nl/en/strategy/integrity-policy/tu-delft-code-of-conduct> and we actively engage<https://www.tudelft.nl/en/strategy/diversity-inclusion> to be a university where you feel at home and can flourish. We value different perspectives and qualities. We believe this makes our work more innovative, the TU Delft community more vibrant and the world more just. Together, we imagine, invent and create solutions using technology to have a positive impact on a global scale. That is why we invite you to apply. Your application will receive fair consideration. Challenge. Change. Impact! Faculty of Electrical Engineering, Mathematics and Computer Science The Faculty of Electrical Engineering, Mathematics and Computer Science (EEMCS) brings together three scientific disciplines. Combined, they reinforce each other and are the driving force behind the technology we all use in our daily lives. Technology such as the electricity grid, which our faculty is helping to make completely sustainable and future-proof. At the same time, we are developing the chips and sensors of the future, whilst also setting the foundations for the software technologies to run on this new generation of equipment – which of course includes AI. Meanwhile we are pushing the limits of applied mathematics, for example mapping out disease processes using single cell data, and using mathematics to simulate gigantic ash plumes after a volcanic eruption. In other words: there is plenty of room at the faculty for ground-breaking research. We educate innovative engineers and have excellent labs and facilities that underline our strong international position. In total, more than 1000 employees and 4,000 students work and study in this innovative environment. Click here<https://www.tudelft.nl/ewi/> to go to the website of the Faculty of Electrical Engineering, Mathematics and Computer Science. BRAINSCAPES BRAINSCAPES is a prestigious, nationally funded 10-year scientific program dedicated to mapping the biological mechanisms underlying multiple brain disorders. While genetic discovery studies have provided unprecedented insight into the genes associated with these disorders, the critical next step is to translate this knowledge into mechanistic understanding. BRAINSCAPES develops innovative analytical and experimental approaches to investigate how risk genes affect the function of specific cell types, neural circuits, and ultimately behavior. By uncovering the molecular and cellular basis of complex brain disorders, the program aims to pave the way for the development of novel, targeted treatments. Learn more about BRAINSCAPES at brainscapes.nl<https://careers.tudelft.nl/job/Delft-PhD-Position-Study-Genetic-Impacts-on-…>. Conditions of employment Doctoral candidates will be offered a 4-year period of employment in principle, but in the form of 2 employment contracts. An initial 1,5 year contract with an official go/no go progress assessment within 15 months. Followed by an additional contract for the remaining 2,5 years assuming everything goes well and performance requirements are met. Salary and benefits are in accordance with the Collective Labour Agreement for Dutch Universities , increasing from €3059 - €3881 gross per month, from the first year to the fourth year based on a fulltime contract (38 hours), plus 8% holiday allowance and an end-of-year bonus of 8.3%. As a PhD candidate you will be enrolled in the TU Delft Graduate School. The TU Delft Graduate School provides an inspiring research environment with an excellent team of supervisors, academic staff and a mentor. The Doctoral Education Programme is aimed at developing your transferable, discipline-related and research skills. The TU Delft offers a customisable compensation package, discounts on health insurance, and a monthly work costs contribution. Flexible work schedules can be arranged. Will you need to relocate to the Netherlands for this job? TU Delft is committed to make your move as smooth as possible! The HR unit, Coming to Delft Service<https://www.tudelft.nl/en/about-tu-delft/working-at-tu-delft/coming-to-the-…>, offers information on their website to help you prepare your relocation. In addition, Coming to Delft Service organises events to help you settle in the Netherlands, and expand your (social) network in Delft. A Dual Career Programme<https://www.tudelft.nl/en/about-tu-delft/working-at-tu-delft/coming-to-the-…> is available, to support your accompanying partner with their job search in the Netherlands. Additional information This PhD position is positioned within the Delft Bioinformatics Lab, part of the Computer Science department of the Delft University of Technology under supervision of Prof. Marcel Reinders, m.j.t.reinders(a)tudelft.nl<mailto:m.j.t.reinders@tudelft.nl>, and Ahmed Mahfouz from the Leiden University Medical Center, a.mahfouz(a)lumc.nl<mailto:a.mahfouz@lumc.nl>, in close collaboration with BRAINSCAPES scientists across the Netherlands. Application procedure Are you interested in this vacancy? Please apply no later than 16 November 2025 via the application button and upload the following documents: * An up-to-date and detailed curriculum vitae. * Copies of relevant academic transcripts. * A cover letter, which should summarize (1) why the applicant wants the position, (2) why the project is of interest to the applicant, (3) evidence of suitability for the job, and (4) what the applicant hopes to gain from the position. You can address your application to Marcel Reinders and Ahmed Mahfouz. Doing a PhD at TU Delft requires English proficiency at a certain level to ensure that the candidate is able to communicate and interact well, participate in English-taught Doctoral Education courses, and write scientific articles and a final thesis. For more details please check the Graduate Schools Admission Requirements<https://www.tudelft.nl/onderwijs/opleidingen/phd/admission>. Please note: * You can apply online. We will not process applications sent by email and/or post. * As part of knowledge security, TU Delft conducts a risk assessment during the recruitment of personnel. We do this, among other things, to prevent the unwanted transfer of sensitive knowledge and technology. The assessment is based on information provided by the candidates themselves, such as their motivation letter and CV, and takes place at the final stages of the selection process. When the outcome of the assessment is negative, the candidate will be informed. The processing of personal data in the context of the risk assessment is carried out on the legal basis of the GDPR: performing a public task in the public interest. You can find more information about this assessment on our website about knowledge security.<https://www.tudelft.nl/over-tu-delft/strategie/kennisveiligheid> * Please do not contact us for unsolicited services.

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VAIA collaboration: online introductory "Machine learning in biomedical research" course
by BeNeLux bioinformaticians forum 18 Oct '25

18 Oct '25

Dear all, As a collaboration of researchers in Belgium, VAIA announces this online course with a self-paced start and subsequent online short classes: https://www.vaia.be/nl/opleidingen/introduction-to-ai-and-machine-learning-… Please check out the course program and register before 18th of November. Best regards, Alex

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Symposium "Present and Future of Bioinformatics and Systems Biology" Oct 22 14-17h - Registration for Online participation
by BeNeLux bioinformaticians forum 17 Oct '25

17 Oct '25

Dear all, I'm very happy to be able to announce the upcoming symposium "Present and Future of Bioinformatics and Systems Biology" which we're organising at the Vrije Universiteit Amsterdam Wednesday October 22 from 14.00-17.00h. *Online registration (free): https://forms.gle/AaXHQne25r9Bz7Vt8 * Zoom link will be distributed by email to registered online participants closer to the event *Programme:* * Dr. Andreas Gisel, International Institute of Tropical Agriculture, Nigeria and Italian Research Council, Italy *"Bioinformatics goes to farmers' fields in Africa”* * Dr. Ana Tereza Ribeiro de Vasconcelos, Head of the Bioinformatics Laboratory, National Laboratory for Scientific Computing LNCC/MCTI, Brazil *”Precision Medicine through AI, Genomics, and Metagenomics.”* * Dr. K. Anton Feenstra, Programme director Master Bioinformatics and Systems Biology, VU and UvA Amsterdam, The Netherlands. *"Understanding life through protein interactions"* * Professor Erik Bongcam-Rudloff, Head of Bioinformatics at Department of Animal Sciences, SLU, Sweden *"Living the Future: How Biotechnologies and Bioinformatics are Quietly Changing Our World”* * Dr. Senanayake Kanchana, University of Colombo, Colombo, Sri Lanka *“Cracking the Code: Bioinformatics and the Fight Against Tropical Diseases – The Setaria Genome Case”* * * Professor Jaap Heringa, emeritus, Integrative Bioinformatics, VU Amsterdam, The Netherlands. *"Science, Infrastructure and the future of computational biology"* *Online registration (free): https://forms.gle/AaXHQne25r9Bz7Vt8 * This symposium is organised by EMBnet www.embnet.it <http://www.embnet.it> On behalf of the organising team, I hope to meet many of you at our symposium! Groetjes, Anton. -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1111 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +312059 87783 - skype: kafeenstra - room NU 12A31| | |Feenstra(a)few.vu.nl -www.few.vu.nl/~feenstra/ | | | "You could give Aristotle a tutorial. And you could | | | thrill him to the core of his being. Such is the | | | privilege of living after Newton, Darwin, Einstein, | | | Planck, Watson, Crick and their colleagues." (Richard | | | Dawkins) | |_____________|_______________________________________________________|

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18 months POST-DOCTORAL position in bioinformatics / machine learning in Montpellier
by BeNeLux bioinformaticians forum 11 Oct '25

11 Oct '25

Dear colleagues, please feel free to share the offer below for a 18 months post-doc in Bioinformatics/Machine Learning at the IGMM (CNRS) in Montpellier (France). ** *Postdoctoral Position – Mixed Effects Neural Networks for Genome Interpretation* * We are looking for a motivated postdoctoral researcher to join the AI for Genome Interpretation (AI4GI <https://www.igmm.cnrs.fr/team/ia-pour-linterpretation-du-genome/>) group at the IGMM (CNRS, Montpellier) for 18 months. The project is a collaboration between IGMM and IMAG, at the interface of genetics, bioinformatics, statistics, machine learning and deep learning. The projectInterpreting the genome means modeling the relationship between genotype and phenotype, which is the fundamental goal of biology. Achieving this could revolutionize genetics, medicine, and agricultural technology, leading for example to the development of better crops, able to face the challenges posed by global warming._Objectives:_ This project is an interdisciplinary effort at the frontier between Biology (Genetics, Genomics), Bioinformatics, Artificial Intelligence (Neural Networks) and Statistics (LMMs). The aim is to join the Bioinformatics expertise of Dr. Raimondi on the development of GI NN methods and their application to relevant biological problems with the expertise of Dr. Bry and Dr. Trottier on the statistical inference of Linear Mixed Models (LMMs). The project’s goal is to develop a new breed of Mixed Effects Neural Networks (MENN) for Genome InterpretationI that take the best from both worlds, merging the flexibility and power of NNs with the ability of LMMs to robustly learn from structured and noisy (non i.i.d.) data, applying them on the prediction of both plantsand humanphenotypes. These models will combine the flexibility of neural networks with the statistical robustness of linear mixed models to tackle one of biology’s most fundamental questions: how do genetic variants determine phenotypes? The postdoc will: * Start by familiarizing with existing research and methods for genome interpretation (GI NNs, LMMs, GWAS). * Familiarize with the sequencing data * Develop and benchmark MENN prototypes on sequencing datasets (WES/WGS), starting first from model organisms and then working on disease risk prediction in humans. _Candidate profile:_We are looking for a motivatedand curious candidate, with a strong passion for scienceand for scientific discovery through the use and creation of new neural networks 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 learnnew skills, methods and concepts, and 2) to enjoy finding new solutionsin 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/Linuxenvironment. A good understanding of the basic concepts of Bioinformatics is not necessary but welcome. The project will consist in developing un-orthodox Neural Network models with Pytorch. At least the B2 level of English is required. Skills requiredWe are looking for someone with: * Strong backgroundin neural networks, machine learning, linear algebra and an understanding of statistics. * Solid programming skills in Pythonand in scientific computing(PyTorch, scikit-learn, numpy, etc). * Familiarity with GNU/Linux. * Problem solving skills. * Good communication and teamwork skills. * Knowledge of linear/mixed models is a plus. * Familiarity with GWAS, population genetics, or bioinformatics pipelines are a plus. * Experience with the processing of genomic biological data (whole exome or genome sequencing) is a plus _Practical details_ * Location: IGMM, Montpellier (with joint supervision at IMAG). * Duration: 18 months. * Starting date: flexible, but the candidate must be selected beforethe end of 2025. If you’re interested in working at the crossroads of AI, statistics, and genomics—and in developing new methods rather than just applying existing ones—we’d like to hear from you. You can apply from this link * emploi.cnrs.fr Portail Emploi CNRS - Offre d'emploi - Postdoctoral Researcher – Mixed-Effects Neural Networks for Genome Interpretation (M/F) 🔗 https://emploi.cnrs.fr/Offres/CDD/UMR5535-SARADE-091/Default.aspx?lang=EN <https://emploi.cnrs.fr/Offres/CDD/UMR5535-SARADE-091/Default.aspx?lang=EN>

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Manager of Greenhouse and Climate-Controlled Facilities
by BeNeLux bioinformaticians forum 10 Oct '25

10 Oct '25

Dear all, At Wageningen University & Reseach we have the following job vacancy: https://www.wur.nl/en/vacancy/manager-of-greenhouse-and-climate-controlled-… Wageningen University & Research (WUR) is looking for a Greenhouse & Climate Room Operations Manager for Klima/NPEC — a unique opportunity to shape the future of plant science infrastructure at Unifarm, our state-of-the-art research facility. In this role, you will: - Lead operations in greenhouses, climate rooms, and growth cabinets - Guide and coach a skilled technical team - Ensure top-quality facility performance and technical innovation - Work closely with researchers, educators, and students - Manage planning, budgeting, and project administration You combine leadership and technical expertise with a solid background in Plant Sciences, Agrotechnology, or a related field. Fluency in Dutch (spoken and written) is required. We offer: - A dynamic position in a leading research environment - Excellent employment conditions and work-life balance - A gross monthly salary between €3,708 and €5,538 (scale 9–10, CAO-NU) - Development and growth opportunities at one of the world’s top universities in agricultural sciences For more details and how to apply: https://www.wur.nl/en/vacancy/manager-of-greenhouse-and-climate-controlled-… Best, Sven

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Re: Bioinformatician BSc/MSc position at Erasmus MC Rotterdam
by BeNeLux bioinformaticians forum 06 Oct '25

06 Oct '25

Dear BBC list, Maybe you forgot about my email below. Please share the text below, as I did not receive the message via the bbc mailing list. All the best, Harmen van de Werken From: Harmen van de Werken Sent: 1 October, 2025 10:54 To: 'bbclist(a)psb.ugent.be' <bbclist(a)psb.ugent.be> Subject: Bioinformatician BSc/MSc position at Erasmus MC Rotterdam Do you want to work with cutting-edge genomics technologies at one of Europe's leading biomedical institutions? The Erasmus MC Genomics Core Facility is looking for a talented and motivated (bio)informatician to join our dynamic team. For more information, please see: https://www.werkenbijerasmusmc.nl/en/vacancy/1213873/bioinformatician-1940 All the best, Harmen van de Werken

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Research Software Engineer (full-stack) @ University of Antwerp
by BeNeLux bioinformaticians forum 05 Oct '25

05 Oct '25

The Adrem Data Lab at the University of Antwerp (Prof. Dr. Wout Bittremieux) is recruiting a Research Software Engineerto help build AI tools for the analysis of mass spectrometry-based proteomics data. You will help design modern, user-friendly scientific web applications, build and maintain back-end services, and assist with deployment on research servers and cloud environments. The ideal candidate has strong experience in front-end development and is comfortable with back-end technologies. Experience with cloud or containerization is a plus. This position offers the opportunity to contribute to open-source software used by researchers worldwide, work in an interdisciplinary international team, and benefit from flexible working conditions and generous leave. Location: Campus Middelheim, University of Antwerp Contract: Full-time, one year (renewable) Application deadline: 27 October 2025 Ideal for creative developers with strong front-end (React/TypeScript) and back-end (Python/Node) skills; cloud or container experience is a plus. More information and application link: https://www.uantwerpen.be/en/jobs/vacancies/administrative-and-technical/?q… Questions: wout.bittremieux(a)uantwerpen.be<mailto:wout.bittremieux@uantwerpen.be>

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Postdoc Position: Crop Genomics and Machine Learning
by BeNeLux bioinformaticians forum 02 Oct '25

02 Oct '25

Dear All, Join a transformative project at RIBES, Radboud University, that will utilize machine learning and genomics to overcome linkage drag and accelerate crop breeding by design. We are looking for a postdoctoral researcher who will build models, analyse new sequencing data, and optimise strategies for combining multiple advantageous traits. Contribute to groundbreaking research shaping the future of sustainable agriculture! For more information, you can check the link below. The deadline for the application is Nov. 16, 2025. https://www.ru.nl/en/working-at/job-opportunities/postdoc-position-crop-gen… Cheers, Roven Rommel Fuentes Assistant Professor of Crop Genomics & Engineering | RIBES | Radboud University HG 02.022 Heyendaalseweg 135, 6525 AJ Nijmegen [cid:7d54afed-1439-405a-968f-d8cfb445bc8f]

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Bioinformatician BSc/MSc position at Erasmus MC Rotterdam
by BeNeLux bioinformaticians forum 01 Oct '25

01 Oct '25

Do you want to work with cutting-edge genomics technologies at one of Europe's leading biomedical institutions? The Erasmus MC Genomics Core Facility is looking for a talented and motivated (bio)informatician to join our dynamic team. For more information, please see: https://www.werkenbijerasmusmc.nl/en/vacancy/1213873/bioinformatician-1940 All the best, Harmen van de Werken

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