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

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

1 0

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-

1 0

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>

1 0

VIB courses December 2025: Scywalker for long-read single cell RNAseq || Generative AI for Research
by BeNeLux bioinformaticians forum 05 Nov '25

05 Nov '25

Dear all, I’ like to share with you the invitation to two training courses in December 2025. The first free 1/2-day training introduces Scywalker, a tool for processing long-read single-cell RNA-Seq data (e.g., ONT or PacBio) to enable full-length transcript analysis. Please register at: https://training.vib.be/all-trainings/scywalker-processing-long-read-single… The second one is an introduction to Generative AI for Research in Leuven - the workshop is designed for support staff and researchers who are new to using generative AI tools in their regular practise. Considering the high versatility of this new technology, the class is designed as an interdisciplinary initiative and is open to all researchers and support staff regardless of their field. This course does not cover the use of coding or other potential automation tasks. Please register at: https://training.vib.be/all-trainings/strategic-use-generative-ai-0 Best regards, Alex Dr. Alexander Botzki VIB Training & Conferences | Suzanne Tassierstraat 1 | 9052 Ghent | Belgium ELIXIR Belgium | Suzanne Tassierstraat 1 | 9052 Ghent | Belgium Tel. +32 9 244 66 11<tel:+3292446611> VIB has flexible working hours, so while it suits me to send this e-mail now, please note that I do not expect a reply or action outside of your working hours. Website<https://www.vibtrainingandconferences.be/> | LinkedIn<https://www.linkedin.com/showcase/vibtrainconf/> | Bluesky<https://bsky.app/profile/vibtrainconf.bsky.social> [Image]<https://www.vibtrainingandconferences.be/> [Hx1KyM2Q09lnAAAAAElFTkSuQmCC]

1 0

Call for Participation: 1st Bioinformatics and Computational Biology Developer Room at FOSDEM 2026
by BeNeLux bioinformaticians forum 05 Nov '25

05 Nov '25

Dear Benelux Bioinformatics Conference community, I'd like to share with you our Call for Participation: 1st Bioinformatics and Computational Biology Developer Room at FOSDEM 2026 ([Link to CfP](https://fosdem-bioinformatics.github.io/cfp.html)) The Bioinformatics and Computational Biology FOSDEM community is pleased to announce the 1st edition of our DevRoom and invite participants to submit proposals for talks for the event. It will take place on January, 31st in Belgium, at the Université Libre de Bruxelles (ULB) in the afternoon. General Information about FOSDEMhttps://fosdem-bioinformatics.github.io/cfp.html#general-information-about-fosdem FOSDEM is a free and non-commercial two-day weekend event organized annually in Brussels, Belgium. It brings together 8000+ open source developers and enthusiasts from around the world. No registration or payment is necessary. FOSDEM provides a unique opportunity for developers and communities to meet, share knowledge, and promote the development and benefits of open source solutions. Bioinformatics & Computational Biologyhttps://fosdem-bioinformatics.github.io/cfp.html#bioinformatics-amp-computational-biology Over the past two decades, biology has been transformed by high-throughput technologies that generate vast amounts of data. This revolution created demand for efficient algorithms, parallel computing infrastructures (GPUs, HPC, cloud platforms), and sophisticated software tools. Open-source software is integral to this landscape. Bioinformatics bridges engineering, computer science, and biology. We define it broadly to encompass: - Genomics - Medical imaging (ie Radiology, digital Pathology) - AI-driven protein research - Medical informatics and med-tech - ... Any field at the intersection of the Life Sciences and technology that has a FOSS angle The Devroomhttps://fosdem-bioinformatics.github.io/cfp.html#the-devroom Following a successful Birds of a Feather session at FOSDEM 2025 that drew dozens of attendees from diverse backgrounds, we're launching a dedicated Bioinformatics & Computational Biology devroom. It focuses on sharing and collaboration in the life sciences, covering: - Best practices and emerging approaches - FOSS projects and tools - Workflow Management & HPC - Reproducibility and open science - Software Engineering and UX - AI & Machine Learning applications - Visualization and interactive tools Call for presentationshttps://fosdem-bioinformatics.github.io/cfp.html#call-for-presentations Submission deadline: November 30, 2025 We invite proposals from developers, researchers, and any enthusiasts working with open source tools in the life sciences. Whether you're from academia, industry, or the public sector, we want to hear about: - Technical presentations on FOSS bioinformatics tools and projects - Tutorials and demos of workflows, pipelines, infrastructure or software - Best practices in reproducibility, performance optimization, or collaboration - Experience reports from production systems or large-scale deployments - Technologies like ML/AI We especially encourage submissions that: - Address practical challenges with real-world solutions - Cover the biological context driving computational choices - Showcase cross-disciplinary collaboration - Highlight lessons learned from FOSS development in life sciences We have several talk Formats: - Standard talks: 20 minutes + 5 minutes Q&A - Short talks: 10 minutes + 5 minutes Q&A - Lightning talks: 5 minutes "Your project in 1 slide" (perfect for introducing new tools, seeking collaborators, or sparking discussions which can be continued in the hallway) Note: All talks will be live-streamed and recorded (audio+video). By submitting, you agree to being recorded and that your content will be published under a Creative Commons (CC-BY) license. How to submit a talkhttps://fosdem-bioinformatics.github.io/cfp.html#how-to-submit-a-talk - Go to [FOSDEM pretalx](https://pretalx.fosdem.org/fosdem-2026/cfp) website. - Indicate the duration in the title (20min, 10min or 5 min) - Select ‘Bioinformatics and Computational Biology’ from the ‘Track’ field. Note: Organizers may request shorter talk formats if we receive more submissions than we can accommodate. If you cannot use Pretalx for any reason, contact us via the mailing list (https://framagroupes.org/sympa/info/bioinfo-fosdem) or in our Matrix space. Join our communityhttps://fosdem-bioinformatics.github.io/cfp.html#join-our-community - Matrix room: https://matrix.to/#/#fosdem-bioinfo:matrix.org - Mailing list: https://framagroupes.org/sympa/info/bioinfo-fosdem We look forward to your submissions and to seeing you at FOSDEM 2026! The Bioinformatics & Computational Biology Devroom Teamhttps://fosdem-bioinformatics.github.io/cfp.html#the-bioinformatics-amp-computational-biology-devroom-team - Alexis Praga - Medical Doctor, Ph.D in HPC - Freek van Hemert - Next-Generation Sequencing & Data Infrastructure - Jim Procter - Computational Scientist, FOSS Community - Elena Grassi - Computational Biologist, Bioconductor/Bioconda contributor - Alessandro Pilotti - Open Source Cloud Computing and Bioinformatics

1 0