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2026.1 VIB course opportunities. Invest in your career !!!
by BeNeLux bioinformaticians forum 16 Dec '25

16 Dec '25

[cid:image002.png@01DC6B71.8C7C8700] Chose the next training and invest in your career! * PROGRAMMING Programming in Python: master your first project Click for registration<https://training.vib.be/all-trainings/programming-python-master-your-first-…>, Online 14 Jan 2026, 4 half days * DATA ANALYSIS OMICS Assess protein dynamics & post-translational modifications Click for registration<https://training.vib.be/all-trainings/assess-protein-dynamics-post-translat…>, FREE (ELIXIR funded), Gent 19 Jan 2026, 1 day Genome assembly using long-reads Click for registration<https://training.vib.be/all-trainings/genome-assembly-using-long-reads>, Gent 23 Jan 2026, 1 day Variant analysis using long-reads Click for registration<https://training.vib.be/all-trainings/variant-analysis-using-long-reads>, Gent 30 Jan 2026, 1 day IMAGING QuPath: quantitative pathology & bioimage analysis software Click for registration<https://training.vib.be/all-trainings/qupath-quantitative-pathology-bioimag…>, Leuven 23 Jan 2026, 1 day Basic image processing using Fiji, Click for registration<https://training.vib.be/all-trainings/basic-image-processing-using-fiji-8> Leuven 30 Jan 2026, 1 day REPRODUCIBILITY Micro-credential - Reproducible Data Analysis: an Essential Capability in Modern Science Click for registration<https://studiekiezer.ugent.be/2026/micro-credential-reproducible-data-analy…>, 9 days spread between April and June Follow the micro-credential to have the A-Z view of reproducible data analysis. Or follow the individual courses bellow. 1. Discussing reproducibility real-life cases Click for registration<https://training.vib.be/all-trainings/discussing-reproducibility-real-life-…>, Gent 20 Apr 2026, 1 day 2. Versioning code and documentation with Git & GitHub Click for registration<https://training.vib.be/all-trainings/versioning-code-and-documentation-git…>, Gent 27 Apr 2026, 2 days 3. Containerise data analysis with Docker & Apptainer Click for registration<https://training.vib.be/all-trainings/containerise-data-analysis-docker-app…>, Gent 11 May 2026, 2 days Pre-requisite FREE registration<https://training.vib.be/all-trainings/using-high-performance-computing-infr…>: Using High Performance Computing infrastructure 4. Nextflow for reproducible and automated data analysis Click for registration<https://training.vib.be/all-trainings/nextflow-reproducible-and-automated-d…>, Leuven 04 Jun 2026, 2 days Pre-requisite FREE registration<https://training.vib.be/all-trainings/using-high-performance-computing-infr…>: Using High Performance Computing infrastructure * GENERAL RESEARCH SKILLS Strategic use of generative AI Click for registration<https://training.vib.be/all-trainings/strategic-use-generative-ai-1>, Antwerp 23 Feb 2026, 1 day Click for registration<https://training.vib.be/all-trainings/strategic-use-generative-ai-2>, Gent 27 Mar 2026, 1 day Research Data Management (RDM) in life sciences: essentials Click for registration<https://training.vib.be/all-trainings/research-data-management-rdm-life-sci…>, Antwerp 13 Mar 2026, 1 day Click for registration<https://training.vib.be/all-trainings/research-data-management-rdm-life-sci…>, Gent31 Mar 2026, 1 day Check all trainings and conferences that are open for registration in our website<https://www.vibtrainingandconferences.be/#/>! VIB Training & Conferences Technologiepark-Zwijnaarde 75, 9052 Ghent – Belgium vibtrainingandconferences.be<https://www.vibtrainingandconferences.be/#/> | elixir-belgium.org/training<https://www.elixir-belgium.org/training> [Graphical user interface Description automatically generated]<https://vib.be/en/technology>

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Vacancy bioinformatician be.Prepared project (pathogen WGS capacity)
by BeNeLux bioinformaticians forum 15 Dec '25

15 Dec '25

Dear all, The Bioinformatics Platform at the Belgian Institute of Health (www.sciensano.be<http://www.sciensano.be>) currently has a vacancy for a bioinformatician in the context of the be.Prepared project to help setting up a Belgian Whole Genome Sequencing (WGS) bioinformatics infrastructures and capacities to respond to infectious diseases in order to increase pathogen outbreak/pandemic preparedness and response capacity. More info and applications are available on our job site: https://jobs.sciensano.be/front/nl/vacancies/3532/ Sincerely, K Kevin Vanneste, PhD Senior scientist - Lead Bioinformatics Platform Transversal activities in Applied Genomics (TAG) T + 32 2 642 50 65 [cid:image001.jpg@01DC6DB7.F6D1F570] Rue Juliette Wytsmanstraat 14 * 1050 Brussels www.sciensano.be<http://www.sciensano.be/> P Please consider the environment before printing this e-mail

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DSB 2026: Call for Abstracts and Participation
by BeNeLux bioinformaticians forum 15 Dec '25

15 Dec '25

Dear BBC community, The 12th edition of the 2-days workshop “Data Structures in Bioinformatics” (DSB) will take place in Venice (Italy) on February 18-19th, 2026: https://dsb-meeting.github.io/DSB2026/ The workshop "Data Structures in Bioinformatics" is an annual scientific meeting at the crossroads of computer science and biology. It is a unique forum to discuss compact data structures and algorithms in the context of data processing for the life sciences. Topics include string algorithms and combinatorics, data structures, algorithms for genome/pangenome/metagenome/transcriptome/... analysis. More details on DSB at https://dsb-meeting.github.io/ **REGISTRATION** HERE: https://forms.gle/V9yrUXYvAsTPpq6J7 Registrations will be open until January 31st, 2026. **ABSTRACT SUBMISSION** HERE: https://forms.gle/baHkDCZW1Lvx1xZT6 Submissions of abstracts for an oral presentation are open until January 2nd, 2026. DSB 2026 is organized by the RAVEN<https://raven-laboratory.github.io/> (Research on Algorithms VENice) research group at Ca' Foscari University of Venice. Looking forward to seeing you in Venice! The DSB 2026 organizing team

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postdoc in bioinformatics at the University of Montpelier
by BeNeLux bioinformaticians forum 10 Dec '25

10 Dec '25

Hello, We are recruiting a postdoctoral researcher in bioinformatics for a project focused on developing machine learning approaches to study disordered proteins. The position is fully funded for one year, with the possibility of extension. You will find the full description of the position and the application guidelines in the attached document. Best regards, Gabriele

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Postdoctoral Position – Deep Learning models to predict phenotypes from genomics data
by BeNeLux bioinformaticians forum 05 Dec '25

05 Dec '25

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Fwd: job offers -- ERC advanced project BindingShadows
by BeNeLux bioinformaticians forum 04 Dec '25

04 Dec '25

Dear all, there's some job openings in a great group here in Jena! See below. Best, Bas ---------- Forwarded message --------- From: Sebastian Böcker <sebastian.boecker(a)uni-jena.de> Date: Thu, Dec 4, 2025 at 12:03 PM Subject: job offers -- ERC advanced project BindingShadows To: Bas E. Dutilh <bedutilh(a)gmail.com> https://bio.informatik.uni-jena.de/mitarbeiterin-erc-bindingshadows/ The Chair for Bioinformatics, Institute of Computer Science at the Friedrich-Schiller-University Jena offers the following positions: Multiple postdocs and PhD students as research associates (Wissenschaftliche Mitarbeiterin) These positions are part of the ERC advanced project BindingShadows, funded by the European Union through the European Research Council. Liquid Chromatography Mass Spectrometry (LC-MS) is the predominant experimental techniques in untargeted metabolomics and related areas. To give a ballpark estimate: There are 2.2 million scientific studies that use mass spectrometry for the analysis of small molecules, whereas DNA sequencing is mentioned in 2.8 million studies. Our group has made substantial progress to support the annotation of small molecules: SIRIUS (Dührkop et al., Nature Methods 2019) is used by thousands of scientists submitting more than a million compound queries per day; CANOPUS (Dührkop et al., Nature Biotechnology 2021) allows to assign compound classes even for compounds that are unknown to mankind; and, the COSMIC confidence score (Hoffmann et al., Nature Biotechnology 2022) will assign a confidence to all annotations done by CSI:FingerID (Dührkop et al., PNAS 2015). The project BindingShadows will take these ideas to the next level: We will develop machine learning models that predict bioactivity (toxicity, antifungal activity etc.) as well as protein binding, solely from the mass spectral data of a small molecule, but without establishing its identity. The molecular structure of the query small molecule is unknown; it is unknown to the machine learning models, to the scientist doing the experiment, and potentially even to mankind. Elucidating the structure of the small molecule is not the focus of the project, and may be postponed until after experimental confirmation of bioactivity. Our models will not predict one particular bioactivity or protein binding, but rather tens in parallel. Evolution has, through variation and selection, optimized the structure of small molecules for tasks such as communication and warfare, and the pool of natural products is enriched with bioactive compounds. BindingShadows will allow us to harvest this information. We will then apply models at a repository scale, screening millions of tandem MS spectra in thousands of datasets for small molecules that are most likely to have bioactivity or to bind. Furthermore, we will make all methods available through the SIRIUS platform, allowing users to en passant screen for bioactive compounds. If you want to know more, watch our videos or read our papers. We offer: Challenging, interesting and highly relevant questions from machine learning, bioinformatics and computer science; an international network of cooperation partners in method development and application of our methods. Our faculty is moving into a brand new building in Oct 2026. BindindShadows will have a dedicated compute server with 10+ Hopper GPU cards, to be bought beginning of 2026. We are looking for: Applicants for this project must have or be about to obtain a Master’s degree or a qualification equivalent to the German Diploma in bioinformatics, computer science, chemoinformatics, or mathematics. The project combines machine learning, bioinformatics, statistics and combinatorics, so proven interest in one or more of these fields is a must. For the postdocs, we expect experience in developing machine learning models for small molecules (say, bioactivity prediction) or protein folding, or in developing computational methods for (small molecule) mass spectrometry. Introductory course level knowledge in biology and molecular biology and good programming skills are required. Willingness to visit our cooperation partners in Helsinki, München, Saarbrücken, San Diego, and Zürich is assumed. Salary is according to Entgeltgruppe 13 TV-L and between 65% and 100% (postdocs). Positions are temporary appointments; running time of the project are five years. Handicapped applicants will be given preference in case of equal qualifications. Project start is early 2026. Please send your application with the usual documents (CV, copies of certificates, publication lists, suggested contacts for references) via email and ASAP to: sekretariat.bioinformatik(a)uni-jena.de Friedrich-Schiller-Universität Jena Institut für Informatik Lehrstuhl für Bioinformatik Ernst-Abbe-Platz 2 07743 Jena, Germany -- Prof. Dr. Sebastian Boecker, Lehrstuhl fuer Bioinformatik Institut fuer Informatik, Friedrich-Schiller-Universitaet Jena Ernst-Abbe-Platz 2, 07743 Jena, Germany Office 3405, Phone +49 (0)3641 9-46451, Fax +49 (0)3641 9-46452 http://bio.informatik.uni-jena.de/ -- Prof. Dr. Bas E. Dutilh <http://tbb.bio.uu.nl/dutilh> Viral Ecology and Omics Group <https://www.veo.uni-jena.de/> | Metagenomics Group Microverse Cluster <https://microverse-cluster.de/en/> | Theoretical Biology and Bioinformatics <https://tbb.bio.uu.nl/> European Virus Bioinformatics Centre <http://evbc.uni-jena.de/> | Utrecht Bioinformatics Center <https://ubc.uu.nl/> Friedrich Schiller University Jena <https://www.uni-jena.de/en/> | Utrecht University <https://www.uu.nl/>

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CFP OLA'2026 Int. Conf. Optimization & Learning @Creta (Greece)
by BeNeLux bioinformaticians forum 02 Dec '25

02 Dec '25

Apologies for cross-posting. Appreciate if you can distribute this CFP to your network. **************************************************************************************** OLA'2026 International Conference on Optimization and Learning 28-30 April 2026 Chania, Crete, Greece http://ola2026.sciencesconf.org/ SCOPUS Springer Proceedings **************************************************************************************** OLA is a conference focusing on the future challenges of optimization and/or machine learning methods and their applications. The conference OLA'2026 will provide an opportunity to the international research community in optimization and learning to discuss recent research results and to develop new ideas and collaborations in a friendly and relaxed atmosphere. OLA'2026 welcomes presentations that cover any aspects of optimization and/or machine learning research such as big optimization and learning, optimization for learning, learning for optimization, optimization and learning under uncertainty, deep learning, new high-impact applications, parameter tuning, 4th industrial revolution, computer vision, hybridization issues, optimization-simulation, meta-modeling, high-performance computing, parallel and distributed optimization and learning, surrogate modeling, multi-objective optimization ... Submission papers: We will accept two different types of submissions: - S1: Extended abstracts of work-in-progress and position papers of a maximum of 3 pages - S2: Original research contributions of a maximum of 12 pages - S3: High-quality manuscripts that have recently, within the last year, been submitted or accepted for journal publication Important dates: =============== Paper submission deadline extension Dec 19, 2025 Proceedings: Accepted papers in categories S1 and S2 will be published in the proceedings. A SCOPUS and DBLP indexed Springer book will be published for accepted long papers. Proceedings will be available at the conference. -- *********************************************************************** OLA'2026 10th International Conference on Optimization and Learning (SCOPUS, Springer) April 28-30, 2026, Creta, Greece, https://ola2026.sciencesconf.org *********************************************************************** Prof. El-ghazali TALBI Polytech'Lille, University Lille - INRIA CRISTAL - CNRS

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postdoc position University of Amsterdam
by BeNeLux bioinformaticians forum 28 Nov '25

28 Nov '25

Dear all, We are looking for a postdoc to work on integrating plant microbiome and omics data. See om https://www.academictransfer.com/en/jobs/356519/postdoc-in-integrating-plan… if you are interested. Best, Aalt-Jan University of Amsterdam

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postdoctoral position in machine learning and bioinformatics in Montpellier
by BeNeLux bioinformaticians forum 20 Nov '25

20 Nov '25

*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> On 9/29/25 12:55, Matteo Pallocca wrote: > > caro Daniele > > puoi usare la funzione submit news del sito > o mandarci l'annuncio a questa mail provvederemo alla pubblicazione > grazie > MP > > Il giorno gio 25 set 2025 alle ore 14:09 Daniele Raimondi > <daniele.raimondi(a)igmm.cnrs.fr> ha scritto: > > Gent Bits, > > mi chiamo Daniele Raimondi e ho recentemente aperto il mio gruppo di > bioinformatica all'istituto di genetica molecolare di Montpellier > (IGMM). Vorrei sapere come posso pubblicizzare le offerte di lavoro > (phd, postdocs) che saranno disponibili nel mio gruppo sul vostro > sito. > > Al momento, per esempio, sto cercando un postdoc per 18 mesi. > > grazie, > > Daniee > > -- > 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- > -- 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-

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PhD Positions in Computational Research, Data Science and AI at the German Cancer Research Center (DKFZ)
by BeNeLux bioinformaticians forum 14 Nov '25

14 Nov '25

Wenn dieser Newsletter nicht richtig angezeigt wird, klicken Sie bitte hier.<https://t24acb3b8.emailsys1a.net/mailing/276/8754640/0/f4781b87b9/index.html> Dear Colleagues, THE APPLICATION FOR THE 2025/26 DKFZ PHD WINTER SELECTION IS NOW OPEN PLEASE FORWARD THIS MESSAGE TO POTENTIAL CANDIDATES AT YOUR INSTITUTIONS. [https://c.emailsys1a.net/mailingassets/06186b46ab4b4b73a8556e15f259663c555c…] PHD POSITIONS IN COMPUTATIONAL RESEARCH, DATA SCIENCE AND ARTIFICIAL INTELLIGENCE Are you interested in solving fascinating biological or medical questions computationally? At the German Cancer Research Center (DKFZ), Germany´s largest biomedical research institute with its core site in Heidelberg, computational scientists work at the forefront of artificial intelligence and cancer research. They combine interdisciplinary approaches from computer science, medical informatics, physics, biology, bioinformatics and statistics to analyze and understand complex biological and medical data. Research activities include: * Development and application of machine learning and computational methods for multi-modal data integration, including integrative analysis of genomic, epigenomic, transcriptomic, proteomic, metabolomic and radiomic imaging data * Development of methods for modeling and simulation of biological and medical processes * Medical informatics * DNA mutation analysis and machine learning to decipher cancer genome variation * Application and development of state-of-the-art technologies for single-cell omics and life cell imaging * Computer-assisted radiology and surgery * Biostatistical evaluation of experimental and clinical data For more information about the groups and their research visit www.dkfz.de/research<https://t24acb3b8.emailsys1a.net/c/276/8754640/0/0/0/29073/d8ba95ef0b.html?…>. Apply now: www.dkfz.de/phd<https://t24acb3b8.emailsys1a.net/c/276/8754640/0/0/0/29074/890f8c6e7b.html?…> Deadline: 15 December 2025 We support and value diversity and encourage applications from individuals from underrepresented groups. If you require assistance during the application process, please contact phd(a)dkfz.de<mailto:phd@dkfz.de> PhD Program Office DKFZ International PhD Program German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 280 69120 Heidelberg Germany [https://c.emailsys1a.net/mailingassets/37318665b3834adcf8b31be95514ff8a933d…] phd(a)dkfz.de<mailto:phd@dkfz.de> www.dkfz.de/phd<http://www.dkfz.de/phd> Management Board: Prof. Dr. med. Dr. h.c. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 If you do not want to receive these kind of messages in the future, please write "unsubscribe" to phd(a)dkfz.de<mailto:phd@dkfz.de>

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