- BBClist - maillist.psb.ugent.be

PhD & ML engineer positions in AI & Bioinformatics – University of Antwerp (deadline: March 3, 2025)
by BeNeLux bioinformaticians forum 04 Feb '25

04 Feb '25

Dear colleagues, Our lab at the University of Antwerp is hiring for positions in AI-driven bioinformatics and computational mass spectrometry: * PhD position(s) – Develop cutting-edge deep learning models for molecular data analysis, with applications in proteomics, immunopeptidomics, and metabolomics. Details & apply<https://www.uantwerpen.be/en/jobs/vacancies/academic-staff/?q=3822>. * Machine learning engineer – Build scalable ML software, translate research into high-impact bioinformatics tools, and optimize HPC infrastructure. Details & apply<https://www.uantwerpen.be/en/jobs/vacancies/administrative-and-technical/?q…>. Join our lab! * World-class research environment: Collaborate with experts in AI, bioinformatics, and life sciences in a dynamic and internationally connected research community. * High quality of life: Affordable living, rich cultural heritage, and a thriving international atmosphere in the heart of Europe. * Strong academic ecosystem: Work in a top research university with access to cutting-edge computational resources and interdisciplinary collaboration. 📅 Application deadline: March 3, 2025. Please share with strong candidates! Best, Wout Bittremieux Assistant Professor University of Antwerp

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nf-core hackathon - Amsterdam site!
by BeNeLux bioinformaticians forum 03 Feb '25

03 Feb '25

Hi everyone, My name is Rayan, and I am part of the Data Team (Joep de Ligt’s team) at the Hartwig Medical Foundation in Amsterdam. >From March 24th to 26th, in collaboration with Google, we will be hosting a local site in Amsterdam at the Google offices for the March edition of the nf-core hackathon! This event is open to everyone who wants to get together in an informal setting work on Nextflow and nf-core related things. Interested? Here’s the registration information https://nf-co.re/events/2025/hackathon-march-2025 Spread the news: https://shorturl.at/DTlpI I hope you can join us! With kind regards, Rayan Hassaïne, MSc Bioinformatician, Data Team [Hartwig Medical Foundation] [signature_129242794]<http://www.ccg2025.eu/> A Science Park 408, 1098 XH Amsterdam T +31 (0)20 226 9700<tel:+31202269700> | +31 (0)6 2391 4885<tel:+31623914885> W hartwigmedicalfoundation.nl<https://www.hartwigmedicalfoundation.nl/> | oncoact.nl<https://oncoact.nl/> N Subscribe to our newsletter<https://mailchi.mp/475bfde5c6f3/nieuwsbrieven-hartwig-medical-foundation> [LinkedIn][Instagram][YouTube][Facebook] It is our mission to realize that every cancer patient with metastatic cancer receives a personalized treatment using a complete DNA test

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Master RNA-Seq & Single-Cell RNA-Seq Data Analysis – In-Person & Online Courses
by BeNeLux bioinformaticians forum 03 Feb '25

03 Feb '25

Dear all, Are you working with RNA-Seq or Single-Cell RNA-Seq data? Gain the skills and confidence to analyse your transcriptomics datasets with our expert-led training courses at Edinburgh Genomics. We offer both in-person and onlineoptions to suit your needs. 🔬 RNA-Seq Data Analysis 📍 In-Person: 17–20 February 2025 (Details & Registration<https://genomics.ed.ac.uk/event/rna-seq-data-analysis-3/>) 💻 Online: 16–19 June 2025 (Details & Registration<https://genomics.ed.ac.uk/event/rna-seq-data-analysis-4/>) Learn how to process and analyse bulk RNA sequencing data, from quality control to differential expression analysis, using widely adopted bioinformatics workflows. 🧬 Single-Cell RNA-Seq Data Analysis 📍 In-Person: 24–26 February 2025 (Details & Registration<https://genomics.ed.ac.uk/event/single-cell-rna-seq-data-analysis/>) 💻 Online: 23–25 June 2025 (Details & Registration<https://genomics.ed.ac.uk/event/single-cell-rna-seq-data-analysis-3/>) Explore cutting-edge single-cell transcriptomics analysis, covering pre-processing, clustering, and interpretation of complex datasets. Why join our courses? ✅ Expert-led instruction from experienced bioinformaticians ✅ Hands-on exercises with real-world datasets ✅ Small class sizes for personalised learning ✅ Flexible in-person and online formats These courses are ideal for researchers, bioinformaticians, and students looking to develop their skills in RNA sequencing data analysis. Spaces are limited—register now to secure your place! For any questions, feel free to get in touch. Best regards, Dr Kathryn Campbell Genomics and Bioinformatics Training Coordinator - Edinburgh Genomics School of Biological Sciences University of Edinburgh Email: kcampb2(a)ed.ac.uk [C0537FE1-6FA3-49DE-BC61-6312CF32C502.png] ======================================================== Edinburgh Genomics' Privacy Notice can be viewed at: http://genomics.ed.ac.uk/about-us/privacy-notice This email and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. ======================================================== The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

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Extended deadline ECCO'2025 Combinatorial Optimization @Marrakech
by BeNeLux bioinformaticians forum 01 Feb '25

01 Feb '25

************************************************************************************* ECCO'2025 38th Conference of the European Chapter on Combinatorial Optimization 8-10 May 2025 Marrakech, Morocco https://ecco2025.sciencesconf.org ************************************************************************************* The 38th Conference of the European Chapter on Combinatorial Optimization will be held in Marrakech (Morocco) from 8 till 10 May 2025. AIMS The ECCO annual meetings aim to bring together researchers in Combinatorial Optimization to present their work, share experiences, and discuss recent advances in theory and applications. CALL FOR ABSTRACTS We invite all researchers, practitioners, and students interested in the following subject areas to submit an abstract: - Theory and applications of combinatorial optimization - Optimal solution methods, approximation algorithms and metaheuristics for combinatorial optimization problems - Integer programming, global optimization, stochastic integer programming, multi-objective programming, mixed optimization, graph theory and network flows - Application domains include, but are not limited to, logistics and supply chain optimization, manufacturing, energy production and distribution, land consolidation, telecommunications, bioinformatics, finance, discrete tomography, discrete and hybrid dynamical systems. IMPORTANT DATES Extended deadline for abstract submission 28 Feb 2025 Notification of acceptance 14 March 2025 Deadline for early registration 28 March 2025 ABSTRACT SUBMISSION Abstracts must be written in English and contain no more than 1,500 characters in plain text format (no formulas are allowed). Please note that the submission MUST be done by the person who will present the paper. For each submitted paper, ONE unique registration must be submitted (e.g., for two submitted papers, two separate registrations must be submitted). SOCIAL EVENTS Conference Dinner: Friday 9 May at Chez Ali PUBLICATIONS Book of Abstracts Special Issue: A special issue of the Journal of Combinatorial Optimization will be devoted in papers presented in the conference. All articles will be refereed according to the high standards of the journal. Details of the process will be given during the conference. COMMITTEES Conference chair El-Ghazali Talbi (chair), University of Lille, France Program and steering committee Jacek Blazewicz, Poznań University of Technology, Poland Bo Chen, University of Warwick, UK Van-Dat Cung, Université Grenoble Alpes, France Alain Hertz, Polytechnique Montréal, Canada Silvano Martello, Università di Bologna, Italy Greet Vanden Berghe, KU Leuven, Belgium El-Ghazali Talbi (chair), University of Lille and INRIA, France Paolo Toth, Università di Bologna, Italy CONTACT Prof. El-ghazali Talbi email: ecco2025(a)sciencesconf.org -- *********************************************************************** OLA'2025 International Conference on Optimization and Learning (SCOPUS, Springer) April 23-25, 2025, Dubai, https://ola2025.sciencesconf.org *********************************************************************** ********************************************************************** ECCO'2025 EURO Conference on the European Chapter of Combinatorial Optimization May 8-10, 2025, Marrakech, Morocco, http://ecco2025.sciencesconf.org *********************************************************************** Prof. El-ghazali TALBI Polytech'Lille, University Lille - INRIA CRISTAL - CNRS

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Genome Assembly and Annotation Online Course - Few Spaces Remaining
by BeNeLux bioinformaticians forum 27 Jan '25

27 Jan '25

Genome Assembly and Annotation Online Course *NEW* Date: 10-12 February 2025 Time: 10am-3pm Register here<https://genomics.ed.ac.uk/event/genome-assembly-and-annotation/> We have a few spaces left on our exciting Genome Assembly and Annotation Course, taking place online from 10–12 February 2025. If you’ve been considering attending, this is your chance—spaces are filling up, and registration closes soon! This hands-on workshop is perfect for anyone working with long-read sequencing technologies like PacBio or Oxford Nanopore, offering practical skills and insights to advance your research. Key Benefits: * Hands-on learning: Master tools for genome assembly, polishing, and annotation. * Hi-C data integration: Learn techniques to boost genome completeness. * Tailored instruction: Explore both prokaryotic and eukaryotic annotation strategies. * Quality assessment: Evaluate your genome assemblies with confidence. Don’t miss out—secure your spot today! <https://genomics.ed.ac.uk/event/genome-assembly-and-annotation/> Genome Assembly and Annotation – Edinburgh Genomics<https://genomics.ed.ac.uk/event/genome-assembly-and-annotation/> genomics.ed.ac.uk<https://genomics.ed.ac.uk/event/genome-assembly-and-annotation/> [cropped-eg_favicon-180x180.png]<https://genomics.ed.ac.uk/event/genome-assembly-and-annotation/> We hope to see you at this unique and engaging course. Best regards, Dr Kathryn Campbell Genomics and Bioinformatics Training Coordinator - Edinburgh Genomics School of Biological Sciences University of Edinburgh Email: kcampb2(a)ed.ac.uk [C0537FE1-6FA3-49DE-BC61-6312CF32C502.png] ======================================================== Edinburgh Genomics' Privacy Notice can be viewed at: http://genomics.ed.ac.uk/about-us/privacy-notice This email and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. ======================================================== The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

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EVERSE Network launch event 18th February
by BeNeLux bioinformaticians forum 27 Jan '25

27 Jan '25

Dear Colleagues, We are delighted to announce the EVERSE Network for Research Software Quality Launch Event, which will take place online at 10h CET on Tuesday 18 February<https://indico.cern.ch/e/eversenetworklaunch>. The goal of this network is to improve policy and practice of research software in Europe and beyond. We welcome everyone who is interested in software quality to join us for the event. As well as presenting our ideas and plans, there will be ample opportunity for participants to give their own inputs into the goals and activities of the network. Please register for the event at https://indico.cern.ch/e/eversenetworklaunch and let’s build a build a strong and effective Network for Research Software Quality together. We look forward to seeing you there. Best wishes, Carlos [cid:image001.png@01DB70B3.A0C67860] Carlos Martinez-Ortiz Scientific community manager Netherlands eScience Center www.esciencecenter.nl<http://www.esciencecenter.nl/>

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[BC]2 Basel Computational Biology Conference
by BeNeLux bioinformaticians forum 21 Jan '25

21 Jan '25

Dear all, We were contacted by Elsa on behalf of the SIB Swiss Institute of Bioinformatics, which organises the [BC]<https://www.bc2.ch/>2<https://www.bc2.ch/> Basel Computational Biology Conference<https://www.bc2.ch/> (8-10 September 2025, Basel, Switzerland). This year's theme is “Bioinformatics meets AI: shaping the future of data-driven biology”. We wanted to inform you that the call for abstracts is now welcoming submissions until 27 February 2025. Keynote speakers: Serena Nik-Zainal (University of Cambridge) and Peer Bork (EMBL Heidelberg) We would be very grateful if you could help us disseminate this information by: * Forwarding this email to your colleagues and network, * Sharing our LinkedIn<https://www.linkedin.com/feed/update/urn:li:activity:7282341601920647170> and mastodon<https://mstdn.science/@SIB/113797870947913230> posts, * Including the news in your newsletter or website. ----------------------- By the way, our call for entries for the International Bioinformatics Awards 2025<https://www.sib.swiss/bioinformatics-awards> is still open, until 31 January ! The winners will be invited to present their work on Tuesday 9 September at the [BC]2 conference. ----------------------- Thank you very much for your support and let me know if you have any questions. Best regards, Elsa [Image removed by sender. SIB logo] Elsa Dubar Events & Communications Manager SIB | Swiss Institute of Bioinformatics Quartier Sorge, bâtiment Amphipôle - CH 1015 Lausanne - Switzerland t +41 21 692 40 47<tel:+41216924047> Elsa.Dubar(a)sib.swiss<mailto:Elsa.Dubar@sib.swiss> - www.sib.swiss<http://www.sib.swiss/> Contribute to the [BC]2 conference programme ! Submit your abstract for the [BC]<https://bc2.ch/tutorials-workshops-calls>2<https://bc2.ch/tutorials-workshops-calls> Basel Computational Biology Conference 2025<https://bc2.ch/tutorials-workshops-calls> by 27 February 2025. The information in this e-mail, and those ensuing, is confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, please destroy this message and notify the sender immediately.

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VIB - Reproducible Data Analysis: an Essential Capability in Modern Science
by BeNeLux bioinformaticians forum 17 Jan '25

17 Jan '25

Reproducible Data Analysis An Essential Capability in Modern Science The scientific method is historically linked to the possibility that other researchers can replicate and verify its results. As scientific analysis becomes more complex and interdisciplinary, ensuring reproducibility becomes more challenging specially in fields that combine different expertise. Learn about version control, containers, pipelines, and data analysis reproducibility. This will steer you towards the reproducibility of your research, as well as the impact and reliability of research findings and methods. Moreover, using the methods introduced here you can collaborate and experiment in ways that allow reproducibility and creativity to coexist and thrive. You have several opportunities to join us: Micro-credentials: a mini diploma to prove you can make reproducible data analysis Click for registration<https://studiekiezer.ugent.be/2024/micro-credential-reproducible-data-analy…>, Gent 28th February [UGent style guide][Logo's VIB] Or follow each module individually with certificate Reproducibility in practice Click for registration<https://training.vib.be/all-trainings/reproducibility-practice>, Gent 28th February Introduction to Git & GitHub Click for registration<https://training.vib.be/all-trainings/introduction-git-github-13>, Gent 10th March Docker and Apptainer for reproducible and automated data analysis Click for registration<https://training.vib.be/all-trainings/docker-and-apptainer-singularity-repr…>, Gent 31st March NextFlow for reproducible and automated data analysis Click for registration<https://training.vib.be/all-trainings/nextflow-reproducible-and-automated-d…>, Gent 28th April You will have the guidance of your VIB and ELIXIR trainers and plenty of opportunities to ask questions and discuss. [Logo's VIB] [cid:image006.png@01DB65AA.B4DD9DB0] * VIB Training & Conferences ELIXIR Belgium Technologiepark-Zwijnaarde 75, 9052 Ghent – Belgium https://technologytraining.sites.vib.be<https://technologytraining.sites.vib.be/> | https://www.elixir-belgium.org/training [Graphical user interface Description automatically generated]<https://vib.be/en/technology> [cid:image009.png@01DAEBD4.D382A6C0]<https://www.elixir-belgium.org/training>

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Internship on Graph Neural Networks for Protein Interaction Networks
by BeNeLux bioinformaticians forum 17 Jan '25

17 Jan '25

M2 Internship on Graph Neural Networks for Protein Interaction Networks Duration: 4-6 months Location: Computational Systems Biology Team, LPHI, University of Montpellier Many biological mechanisms rely on the synthesis, degradation, and activation of proteins. Among their numerous functions, proteins can act as signals, accelerating or reducing the production, degradation, or activation of other proteins, allowing the studied system to adapt to external stimuli. These interactions form complex networks known as Protein Interaction Networks (PIN), the study of which is essential for understanding cell function in health and disease. More formally, a PIN is a simple directed graph. However, the information it provides is static and insufficient to capture system dynamics. Consequently, Chemical Reaction Networks (CRNs) are often preferred. Unlike PINs, CRNs are bipartite directed graphs that represent both proteins and the chemical reactions they participate in. A key advantage of CRNs is that they can be translated into systems of ordinary differential equations, allowing for the modeling and simulation of a biological system’s temporal evolution. Since automating the transcription of a PIN into a CRN is not straightforward, the goal of this internship is to use a large collection of existing examples to train artificial intelligence algorithms for this task. Representing PINs as networks naturally suggests using graph neural networks , a rapidly advancing architecture that captures the permutation invariance inherent to graphs. Since the goal is to produce a CRN, which is also a network, the intern will study and apply available generative graph models (e.g., Variational Autoencoders, Attention Networks, Generative Adversarial Networks). The solution developed during this internship will have applications in systems biology for medical research. As a proof of concept, we will apply the method to generate executable models of cellular signaling in inflammation. This research is conducted in collaboration with King’s College London, Cardiff University, the Center for Integrative Biology in Toulouse, and NCBS in Bangalore. During the internship, the student may benefit from a short stay in UK, funded by the Sophie Germain program of the French Embassy in London. This internship can be extended into a Ph.D. project. Candidate profile: Theoretical and practical knowledge in machine learning and artificial intelligence is required, and an interest in biological applications would be appreciated. Application: Send a CV + cover letter + transcripts + names of references to [ mailto:ovidiu.radulescu@umontpellier.fr | ovidiu.radulescu(a)umontpellier.fr ]

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Internship opportunities for master students in bioinformatics @ IGMM (Montpellier, France)
by BeNeLux bioinformaticians forum 17 Jan '25

17 Jan '25

*Master students in Bioinformatics Internship Opportunities at IGMM, Montpellier* The Institut de Génétique Moléculaire de Montpellier (IGMM) is offering *three 6-months internships* for Master's students in *Bioinformatics, Computer Science, or Machine Learning*, with a reimbursement of approximately *600€/month*. Three projects available: 1. Interpretable Neural Network models for replication origins efficiency prediction in yeast. 2. Narrative-based Explainable AI for stratification of Multiple Myeloma patients and clinical decision-making. 3. Symbolic regression for the interpretable stratification of Multiple Myeloma patients. Type of Students: We are looking for Master's students with: * A background in *bioinformatics*, *computer science*, or *machine learning*. * Programming skills in python; Understanding of Machine Learning and of libraries like scikit-learn and and ideally also pytorch; * An interest in applying AI to biological or clinical data. * A strong motivation to work at the intersection of machine learning and genomics. Location: Montpellier, France. How to Apply: Send your *CV*, *academic transcripts*, and a brief *motivation letter* to *Daniele Raimondi* at *daniele.raimondi(a)igmm.cnrs.fr*. Applications will be considered on a rolling basis. -- 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

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