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Vacancy PhD position in bioinformatics for computational mass spectrometry/food science
by BeNeLux bioinformaticians forum 20 Dec '23

20 Dec '23

We have an exciting new PhD position in bioinformatics for computational mass spectrometry/food science available at the University of Antwerp. The selected PhD student will develop novel bioinformatics tools to analyze the molecular composition of foods from untargeted metabolomics data. This project is at the forefront of computational biology and offers a unique opportunity to contribute to groundbreaking research in food science and nutrition. An exciting aspect of this position is our collaboration with multiple teams in South Africa, offering a global perspective and the chance to work with international partners. The application deadline for this position is January 14, 2024. For more detailed information and to apply, please visit our website at: https://www.uantwerpen.be/nl/jobs/vacatures/ap/?q=3225 Feel free to spread this opportunity within your network. Best, Wout Bittremieux Assistant Research Professor University of Antwerp

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Job Advertisement: Model system genome database manager (f/m/x)
by BeNeLux bioinformaticians forum 14 Dec '23

14 Dec '23

Dear Madams & Sirs, The Max Planck Institute for Multidisciplinary Sciences in Göttingen, Germany, is a leading international research institute of exceptional scientific breadth. With more than 40 research groups and some 1,000 employees from over 50 nations, it is the largest institute of the Max Planck Society. The department of Tissue Dynamics and Regeneration (Dr. Jochen Rink) invites applications for a position as Model system genome database manager (f/m/x) You will find the complete job description as attachment to this email with a request to publish it in your department/division. Should you have any questions or need further information, please do not hesitate to contact me. We thank you in advance for your support and wish you a happy holiday season. Best Regards Martina Lingl Assistant to Prof. Dr. Jochen Rink Department of Tissue Dynamics and Regeneration Dr. Sonja Lorenz Research Group Ubiquitin Signaling Specificity Max-Planck-Institute for Multidisciplinary Sciences Am Faßberg 11, 37077 Göttingen, Germany Phone: ++49 551 201 26100 Fax: ++49 551 201 2705 office.rink(a)mpinat.mpg.de<mailto:office.rink@mpinat.mpg.de> martina.lingl(a)mpinat.mpg.de<mailto:martina.lingl@mpinat.mpg.de>

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A Postdoc project in UHasselt
by BeNeLux bioinformaticians forum 07 Dec '23

07 Dec '23

Dear, Can you please forward and share the email below with your e-mail list ? It is about a new Postdoc project in DSI-UHasselt. Please CC me on the email. Thanks in advance and best regards, ziv shkedy *The data science institute in Hasselt University announces a position for a (m/f/x):* *Postdoc researcher in Bioinformatics/Biostatistics** (18-24 months): **High Dimensional Integrated Unsupervised and Supervised Analysis of Single Cell RNASeq Data* *General information about the project * The postdoc research project will be conducted in a close collaboration between the data science institute (DSI, https://www.uhasselt.be/en/instituten-en/dsi) in Hasselt University and a global pharmaceutical company. The main objective of the postdoc research project is to analyze single cell omics data for immune profiling purposes applied to vaccinology. The project is focused on algorithm/procedures/software testing and development using publicly and in house available dataset with application on real vaccine development . Both parts will be based on single cell omics data generated on *Chromium 10X Genomics platform*. Data analysis tools and software products that will be developed in this project would be available as R or Python packages with full documentation. *Project description* The research project consists of two main tasks: *Task 1 - Unsupervised analysis:* 1) To identify the best numerical embedding methods for TCR/BCR protein sequences in order to merge this feature with other OMICs layers. 2) To identify methods for single omics and multi-omics clustering (gene expression, individual TCR sequences, surface proteins) that can better approximate antigen-specificity. *Task 2 - Supervised analysis:* Based on the results obtained in part 1, we will define which of the identified features may be predictive of antigen specificity and cross-reactivity. *Data analysis methods*: cluster analysis for single cell RNAseq data (for both single and multi-omics setting) , biclustering, classification and prediction. *Profile and diploma* As a postdoc researcher you will join the dynamic functional genomics team in the data science institute (DSI) in UHasselt and will collaborate with scientists from both academia and industry. The research work related to both tasks will be conducted in a close collaboration between DSI and the pharmaceutical company and the postdoc researcher will work in both organizations. A successful candidate should have - PhD in bioinformatics/ statistical bioinformatics/biostatistics (with experience of high dimensional data). - A PhD whose research focuses on single cell analysis is an advantage but not a must. - A PhD whose research is on AI/ML methodologies for unsupervised and supervised HD data analysis is a plus. - You are acquainted with statistical methodologies and had exposure to computer programming in R/Python. - You published manuscripts in the area of bioinformatics/biostatistics. - You developed software package(s) as a part of your PhD research. - You are interested in developing new methodology from both theoretical and applied aspects. - You are interested in developing software to the pipeline for data analysis and implement this software within a company environment. - You are willing to closely collaborate with biologists/biostatistians/bioinformations from the pharmaceutical industry. - You have a strong interest in working on both vaccine and drug development problems. - You can work independently and within a team. - You have excellent communication skills. - You can lead a team of researchers within a project. - You enjoy working in a multidisciplinary and multicultural environment. - You speak and write English fluently. *Offer* The appointment takes effect from January 2024 and at the latest from March 2024 for a period of 18-24 months, depending on the candidate experience. *Further information* Prof. dr. Ziv Shkedy, +32 11-26 82 40, ziv.shkedy(a)uhasselt.be <christel.faes(a)uhasselt.be> *Application*Applicants must send their application to ziv.shkedy @uhasselt.be <christel.faes(a)uhasselt.be> *Please add a copy of your PhD diploma and CV (including publication list) to your application.* Deadline for the Application 15, January, 2024

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ABLS2024: Bioinformatics conference in Leuven 7-8 March 2024 - abstract deadline 9th of January
by BeNeLux bioinformaticians forum 07 Dec '23

07 Dec '23

Dear all, We are looking forward to inviting you to the 5th edition of our Applied Bioinformatics in Life Sciences conference ABLS24. 🤯 Topics will range from personalized medicine, structural bioinformatics and genome function. Join our invited scientists on stage for a selected talk, or present your research on a poster! More info here: https://www.vibconferences.be/events/applied-bioinformatics-in-life-science… 🗓 Abstract deadline: 9 January 2024 Best regards, Alex Alexander Botzki Team Lead Technology Training, ELIXIR Belgium Training Coordinator VIB Technology Training 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] [Hx1KyM2Q09lnAAAAAElFTkSuQmCC]

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FW: Community event: A.I. in Structural Biology Symposium, 19th Jan 2024, Brussels
by BeNeLux bioinformaticians forum 07 Dec '23

07 Dec '23

From: Carl Mensch <Carl.Mensch(a)uantwerpen.be> Date: Thursday, 7 December 2023 at 00:02 To: Ertaylan Gökhan <gokhan.ertaylan(a)vito.be> Subject: Community event: A.I. in Structural Biology Symposium, 19th Jan 2024, Brussels Dear All, As a reminder, we are pleased to invite you to our one-day symposium on AI's impact in structural biology, scheduled for 19th January 2024 at Hoek 38 (FWO, Brussels). This event, following the success of last year's symposium on AlphaFold, promises to offer insightful discussions and lectures on the evolving role of AI in the field. We are honored to have Arne Elofsson from Stockholm University as our keynote speaker. He will open the morning session of our symposium with his talk on the impact and advancements of AI in structural biology. Casper Goverde from EPFL will present on the application of deep learning-based tools in advancing our understanding and design of complex proteins. To conclude our morning lectures, Maxim Tsenkov from EMBL-EBI will delve into the AlphaFold database and Foldseek, offering valuable insights into these groundbreaking resources. Please fill out the registration form here<https://forms.gle/28eWrt3aXrTxuRpx5> to confirm your attendance and provide your lunch requirements (if you haven’t done so already). The symposium is held live at Hoek38, Brussels for our community. Additionally, the morning lectures will be live-streamed on our channels<https://www.vscentrum.be/events/alphafold-event-3> for those outside of the community, making them accessible to a wider audience. Best, Carl Mensch and Gökhan Ertaylan Dr. Carl Mensch | HPC Consultant | Computational chemist Faculty of Science | Department of Mathematics Campus Middelheim– M.G.309 Middelheimlaan 1 – 2020 Antwerp carl.mensch(a)uantwerpen.be<mailto:carl.mensch@uantwerpen.be> P +32 3 265 89 80<tel:+3232658980> [cidimage002.jpg(a)01D62873.83C42BF0]<https://twitter.com/VSC_HPC>[cidimage005.jpg(a)01D62873.83C42BF0]<https://www.linkedin.com/company/vschpc/mycompany/> [signature_2675831904]<https://www.vscentrum.be/>

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PhD Candidate in Computational and Developmental Biology
by BeNeLux bioinformaticians forum 05 Dec '23

05 Dec '23

Are you an aspiring researcher with an interest in embryonic development? And are you eager to understand how individual cells in the early mammalian embryo decide their future fate using computational approaches? Then join the Radboud Institute for Molecular Life Sciences as a PhD candidate! https://www.ru.nl/en/working-at/job-opportunities/phd-candidate-in-computat… The early mammalian embryo, or epiblast, is composed of pluripotent cells that can generate all specialised cell types of the body. The epiblast cell population is heterogeneous, showing stochastic differences in transcriptome and epigenome between cells that affect their differentiation potential. In this project, you will address how a system composed of intrinsically stochastic epiblast cells can show robust and deterministic fate decisions, utilising single-cell genomic/epigenomic datasets from in vitro developing mouse gastruloids that will be generated within the consortium. You will apply state-of-the-art genetic/epigenetic computational approaches, integrative -omics, cellular trajectory analysis, agent-based modelling and other types of predictive modelling, supported by our in-house computational biology unit. Dr. Marten Postma Assistant Professor Chair Examinations Board BSc BMW/MSc BMS Member SILS Educational Committee (SEC) Programme Developer MSc BioSB JD Track coordinator Systems Biology MSc BioSB JD Member Admission Committee MSc BioSB JD zoom : https://uva-live.zoom.us/j/2612815610 Room C2.102 (SILS) Swammerdam Institute for Life Sciences (SILS) University of Amsterdam (uVA) Science Park 904 1098 XH Amsterdam The Netherlands tel : +31 20 525 6225 e-mail : M.Postma(a)uva.nl<mailto:M.Postma@uva.nl> website : http://www.martenpostma.nl/science/

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Assistant/associate professor position in machine learning in bioinformatics
by BeNeLux bioinformaticians forum 04 Dec '23

04 Dec '23

Position: assistant/associate professor machine learning in bioinformatics The Wageningen Bioinformatics Group has a vacancy for an assistant / associate professor (depending on experience). In this role, you will contribute to the group’s research and teaching; set up and maintain a research line on machine learning/deep learning based method development in bioinformatics, with applications in the green life sciences; and help organize and deliver education in bioinformatics and data science. You will work on the Wageningen Campus in a group highly engaged in bioinformatics education and research, with an open, relaxed and collaborative atmosphere. For more information and an online application form (deadline January 8, 2024), please see https://www.wur.nl/en/vacancy/assistantassociate-professor-machine-learning… or contact Dick de Ridder (dick.deridder at wur.nl).

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Postdoc in bioinfomatics at University of Mons (Belgium)
by BeNeLux bioinformaticians forum 04 Dec '23

04 Dec '23

Dear all, The Metabolic and Molecular Biochemistry Department is recruiting a bioinformatician for a 2-year post-doctorate (with the possibility of a 3-year extension). You will be responsible for analyzing human genomic variants from open-access databases and DNA samples. The candidate must have : • either a Master’s degree in life sciences (biological or biomedical sciences) with a complementary Master’s and PhD in bioinformatics, • or a Master’s degree and PhD in bioinformatics. The skills required are as follows: • Knowledge of genetics and molecular biology. • Proficiency in the knowledge and IT tools required to analyze the human genome and its variants from complex data such as those generated by Next Generation Sequencing (NGS), both short-reads and long-reads. • Understand and use complex mathematical formulas to develop risk scores, among other things. • Work independently and as part of a team. • Create and manage projects. • Know how to use variant analysis software, or know how to design it. • Administration of scientific databases. Previous knowledge of the analysis of the human genome and its variations, as well as technical skills in sample preparation for NGS is an asset. https://web.umons.ac.be/fr/job/un-bioinformaticien-f-h-x-au-sein-du-service… Un bioinformaticien (f/h/x) au sein du Service de Biochimie Métabolique et Moléculaire - Université de Mons web.umons.ac.be Send us your curriculum vitae and a covering letter to the e-mail address frederique.coppee(a)umons.ac.be, quoting the job title in the subject line, before the 31th January 2024. Best wishes, Olivier Sand ELIXIR-FR Training Coordinator CNRS UAR3601 IFB-core/ UAR2014-US41 PLBS

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B-Cubed Hackathon/conference - project submission deadline 17th of December
by BeNeLux bioinformaticians forum 28 Nov '23

28 Nov '23

Dear all, // forwarding to BBC mailing list // My name is Laura, and I'm helping Quentin Groom with the organisation of the upcoming Hackathon on behalf of the B-Cubed project<https://b-cubed.eu/>. As the Hackathon is coming closer, I would like to extend a warm invitation to you and your colleagues to submit a project or participate. Event details: * Date: April 2nd to April 5th * Location: Herman Teirlinck, Brussels * Purpose: Collaborate and experiment with biodiversity data cubes The Hackathon provides a unique opportunity for individuals passionate about leveraging biodiversity data for impactful solutions. We are calling for project submissions! Why participate: * Engage with like-minded individuals. * Test the interoperability of data cubes with biodiversity and environmental data. * Enhance your data visualisation skills. To learn more about the Hackathon and submit your project, please visit our webpage<https://b-cubed.eu/b-cubed-hackathon>. Submission deadline: December 17th, 2023 Your valuable contribution can make a significant impact on the success of the Hackathon. We encourage you to share this email within your network. Feel free to reach out if you have any questions or need further information. Thank you for considering this invitation. We look forward to your participation. Kind regards, Laura Abraham laura.abraham(a)plantentuinmeise.be<mailto:laura.abraham@plantentuinmeise.be>

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EuBIC-MS Winter School 2024 - Last few days of early bird registration and abstract submission
by BeNeLux bioinformaticians forum 27 Nov '23

27 Nov '23

Dear all, We are reaching out to you regarding the upcoming EuBIC-MS Winter School 2024 in Winterberg, Germany. The EuBIC-MS Winter School, organized biennially by EuBIC-MS, focuses on user-oriented bioinformatics for mass spectrometry-based omics, bringing together experts and users (even less experienced ones) to share knowledge and insights in the ever-evolving field. The Winter School kicks off with an educational day featuring workshops and training sessions on established computational MS tools and workflows. Subsequent days showcase internationally renowned speakers delivering lectures and hands-on workshops, covering various aspects of identification, quantification, result interpretation, and the integration of MS data. The (preliminary) full program can be consulted via the following link <https://eubic-ms.org/events/2024-winter-school/eubic-ms-winter-school-2024- full-program/> : https://eubic-ms.org/events/2024-winter-school/eubic-ms-winter-school-2024-f ull-program/ The deadline for early bird registration and abstract submission is quickly approaching (this Friday). We highly recommend to submit your abstract ASAP and to take advantage of the reduced registration fee. Event Details Date: January 15-19, 2024 Location: Winterberg, Germany (with hopes for a snowy backdrop) How You Can Help We kindly request your support in spreading the word about the EuBIC Winter School 2024 with other members of your lab or institute. Contact and Registration For more information and registration details, please visit the official EuBIC Winter School website: https://eubic-ms.org/events/2024-winter-school/ Thank you for your support, and we look forward to the EuBIC Winter School 2024 being a collaborative and enriching experience for all participants. Best regards, Bart Van Puyvelde On behalf of the EuBIC-MS organization PS: EuBIC-MS is an open and inclusive community that unites researchers not only from across Europe but also from around the world. Anyone is welcome to join. If you are in the field of computational MS, you will have direct access to a vast community and to our most recent developments. If you are new to computational MS, joining our community is the perfect way to learn good practices for MS data analysis and ask questions to highly skilled researchers and developers. In both cases, it is a great way to contribute to the field in a community-driven fashion. If you are convinced, please go to our website or simply go to this link <https://eubic-ms.org/become-a-member/> : https://eubic-ms.org/become-a-member/

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