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

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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Postdoc in evolutionary genetics in childhood cancer - Utrecht, NL
by BeNeLux bioinformaticians forum 15 Jan '25

15 Jan '25

Dear all, I’m writing to advertise a postdoc position that we have just opened in my group at the Princess Máxima Center for Pediatric Oncology in Utrecht, the Netherlands. The project centers around better understanding the role of evolutionarily young proteins in human development and childhood brain cancers. The profile we are looking for is a computational postdoc with PhD experience in evolutionary genetics/genomics and an interest in figuring out how translation of RNAs has evolved. What we offer are a great team and working environment, a combined wet- and dry lab, a competitive salary & job benefits, and awesome science (if I can say so myself). The vacancy and application instructions can be found here: https://werkenbijprinsesmaximacentrum.nl/en/vacancy/postdoc-computational-e… You can also apply via LinkedIn: https://www.linkedin.com/jobs/view/4122630215 More information about our lab incl recent publications can be found here: https://research.prinsesmaximacentrum.nl/en/research-groups/van-heesch-group If you know someone who might be interested, it would be fantastic if you could forward the job ad or get them in touch with me. I’d be happy to provide more information about the project and lab. Thank you, Sebastiaan Sebastiaan van Heesch, PhD |Group Leader | Website<https://research.prinsesmaximacentrum.nl/en/research-groups/van-heesch-group> [signature_1961350581] [signature_2205367574] Princess Máxima Center for Pediatric Oncology Oncode Institute Heidelberglaan 25 | 3584 CS | Utrecht | The Netherlands Tel: +31 (0) 6 50 17 32 60 s.vanheesch(a)prinsesmaximacentrum.nl<mailto:s.vanheesch@prinsesmaximacentrum.nl>

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Learn Genome Assembly & Annotation @ Edinburgh Genomics
by BeNeLux bioinformaticians forum 13 Jan '25

13 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’re excited to announce our upcoming new Genome Assembly and Annotation Course, taking place online from 10-12 February 2025, 10am–3pm each day (with a 1-hour lunch break). This hands-on workshop is designed to explore the latest methods and tools for genome assembly and annotation, focusing on long-read sequencing technologies like PacBio and Oxford Nanopore. Whether you're working on de novo assembly or genome annotation for prokaryotes or eukaryotes, this course will provide you with the skills and knowledge to take your research further. Course Highlights * Explore the benefits and limitations of long-read sequencing technologies. * Hands-on practice with tools for de novo genome assembly and polishing. * Integration of Hi-C sequencing data for improved genome completeness. * Learn the differences between prokaryote and eukaryote genome annotation. * Assess the contiguity, completeness, and correctness of generated genomes. Spaces are limited, so register early to secure your spot! We look forward to welcoming you to this engaging and informative course. Many thanks, 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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Erasmus MC Rotterdam Bioinformatics PhD position on population genomics // Gene regulatory mechanisms underpinning cardiovascular diseases
by BeNeLux bioinformaticians forum 09 Jan '25

09 Jan '25

Dear all, A colleague of ours, Dr. Annique Claringbould, is offering a 3.5-year PhD at the department of internal medicine. If you or somebody you know are interested in analyzing cohort-based population data and working in a tightly-knit bioinfo community within the Erasmus MC, apply here: PhD candidate in gene regulatory mechanisms underpinning cardiovascular diseases | Werken bij Erasmus MC<https://www.werkenbijerasmusmc.nl/en/vacancy/1134229/phd-candidate-gene-reg…> Sincerely yours, V. (Vid) Prijatelj MPharm Bioinformatician PhD Candidate Genomics Core Facility / Department of Oral and Maxillofacial Surgery [cid:image001.png@01DB62B3.4351E470] 0107044577<tel:0107044577> [cid:image002.png@01DB62B3.4351E470] v.prijatelj(a)erasmusmc.nl [cid:image003.png@01DB62B3.4351E470] Dr. Molewaterplein 40, 3015 GD Rotterdam [cid:image004.png@01DB62B3.4351E470] P.O. Box 2040, 3000 CA Rotterdam [cid:image005.png@01DB62B3.4351E470] www.erasmusmc.nl<https://www.erasmusmc.nl> [cid:image006.png@01DB62B3.4351E470] [cid:image007.png@01DB62B3.4351E470]<https://www.facebook.com/erasmusmc> [cid:image008.png@01DB62B3.4351E470]<https://instagram.com/erasmusmc> [cid:image009.png@01DB62B3.4351E470]<https://www.youtube.com/user/erasmusmc> [cid:image010.png@01DB62B3.4351E470]<https://twitter.com/ErasmusMC> [cid:image011.png@01DB62B3.4351E470]<https://www.linkedin.com/company/erasmus-mc/> [cid:image012.png@01DB62B3.4351E470] [cid:image012.png@01DB62B3.4351E470] [cid:image012.png@01DB62B3.4351E470]

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Hands-On DNA Library Preparation for Short-Read Sequencing – Register Now!
by BeNeLux bioinformaticians forum 09 Jan '25

09 Jan '25

Dear all, We are excited to announce our upcoming DNA Library Preparation for Short-Read Sequencing Lab Course, offering you a comprehensive and hands-on experience in the art of preparing DNA libraries for short-read sequencing. Course Details: * Date: 6th February 2025 * Time: 9:00 AM – 5:00 PM * Venue: Edinburgh Genomics, Ashworth Laboratories, The King's Buildings Campus, University of Edinburgh, EH9 3FL, Scotland, UK * Registration Fee: £149 (University of Edinburgh), £159 (Other Universities), £169 (Industry) * Capacity: Limited to 12 participants * Register Now<https://genomics.ed.ac.uk/event/dna-library-preparation-for-short-read-sequ…> What You'll Learn: * Hands-on experience with the NEBNext UltraExpress™ FS DNA library preparation kit. * Preparing libraries from a validated control sample and an optional sample of your own. * Quality control (QC) and preparation of libraries for sequencing. * Theoretical background and practical tips from experts in sequencing. Who Should Attend? This course is perfect for anyone keen to learn DNA library preparation for short-read sequencing. Basic familiarity with molecular biology techniques is required, though additional support is available upon request. Workshop Highlights: * Full-day, in-person workshop with practical exercises. * Group discussions and Q&A with instructors from Edinburgh Genomics and NEB. * MiSeq loading demonstration and lab tour. Bring Your Own Sample (Optional): Participants may bring their own DNA samples to process. DNA must meet specific quality and concentration requirements (≥100ng at ≥7ng/µl). Secure your place today – spots are limited! Register Now<https://genomics.ed.ac.uk/event/dna-library-preparation-for-short-read-sequ…> Please feel free to get in touch with any questions. We look forward to seeing you on the 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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