January 2024 - BBClist - maillist.psb.ugent.be

PhD position in Integrating of multiple -omics datasets
by Claesen Jürgen 04 Jun '24

04 Jun '24

Dear all, SCK CEN and UHasselt are looking for candidates for a PhD project with the title: "Integromics - Towards integration of big biomolecular data to enable systems biology" Description The last decades, development of high-throughput technologies such as next-generation sequencing, microarrays and mass spectrometry has led to a paradigm shift in biology and life sciences. Where previously one biomolecule (for example, a gene, or a protein) was studied as a single entity, these experimental techniques allow to study a set of biomolecules (for example, the genome or the proteome) in one go and in a limited amount of time. While, at first, experiments were analyzed independently from each other, combining information of several experimental techniques, and correlating them with environmental and/or clinical parameters, is, nowadays, of great interest. As a consequence, novel statistical and computational methodologies for the analysis of multi-omics datasets have to be developed, allowing a multi-dimensional view on complex biological processes. In this PhD project, we aim at the development of computational methods for the analysis of multi-omics datasets, that are commonly generated by the three biology units of SCK*CEN, which will improve the understanding and valorization of the data, and which will keep the biology units up to date with current developments in biology and bioinformatics. Profile and diploma As a doctorate researcher you will join the dynamic bioinformatics team at SCK CEN and CenStat (UHasselt). A successful candidate should have : * A master degree in biostatistics/applied statistics/bioinformatics/statistical bioinformatics. * You are acquainted with statistical methodologies and had exposure to computer programming in SAS/R/Winbugs/Python. * You can work independently and within a team. * You have excellent communication skills. * You are interested to develop new methodology from both theoretical and applied aspects. * You enjoy working in a multidisciplinary and multicultural environment. * You are willing to closely collaborate with biologists/biostatisticians. * You speak and write English fluently. * You have work experience with at least two different "omics" platforms. For more information contact: Dr. Claesen Jürgen (SCK-CEN), jclaesen(a)sckcen.be<https://academy.sckcen.be/en/Mailform?contactid=b22040b5-cf18-496f-a82a-3bc…> Prof. Shkedy Ziv (Hasselt University), ziv.shkedy(a)uhasselt.be<https://academy.sckcen.be/en/Mailform?contactid=51ae7733-8006-4347-b211-9a4…> Link to the project in SCK-CEN: https://academy.sckcen.be/en/Your_thesis_internship/AllTopics/Integromics--… Kind Regards, Jürgen

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10 PhD positions in single cell proteomics for thermophiles (PROHITS)
by BeNeLux bioinformaticians forum 31 Jan '24

31 Jan '24

Dear all, The PROHITS MSCA doctoral network has 10 open positions for PhD students to work on the development, both experimental and computational, of single-cell proteomics for thermophiles. In PROHITS we want to achieve a comprehensive understanding of the proteome of thermophilic prokaryotes at the single-cell level, spanning a range of temperatures, plus gain insights into the stability of proteins at these high temperatures and develop genome-scale metabolic models for such organisms. The overarching goal is to enhance our insights into thermophile biology and pave the way for the optimized design of cell factories - thermophilic cell factories are expected to play a key role in next-generation industrial biotechnology. We are inviting enthusiastic candidates to join this exciting interdisciplinary project as PhD researchers. More information on the positions and information on how to apply are available here, with a 15/3 deadline: https://prohits.eu/recruitment/ Hope to hear from you! Best, Wim --------------------------------------------------------------------------------------- Prof. Dr. Wim Vranken Tel: +32 (0)2 6291952<tel:+3226291952> (VUB) VUB - Building E, 5th Floor, E5.02, Pleinlaan 2 1050 Brussels, Belgium Structural Biology Brussels/Artificial Intelligence/General Chemistry/Biomedical sciences Associate professor - http://bio2byte.be/ ULB-VUB - Interuniversity Institute of Bioinformatics in Brussels (IB)2 Member and former director - http://ibsquare.be/ ELIXIR - Bringing together life science resources across Europe Co-lead of ELIXIR IDP community, member of ELIXIR-Belgium management board ---------------------------------------------------------------------------------------

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BSC: New vacancies - ELIXIR
by BeNeLux bioinformaticians forum 31 Jan '24

31 Jan '24

Hello, I hope this email finds you well. I am contacting you because we have opened two vacancies in the Life Sciences department, and we would be grateful if you could share them it with your contacts and post them in your website: * *Web Front-end Developer (RE2): *https://www.bsc.es/join-us/job-opportunities/17523lsinbre2* * * *Senior Research Engineer on Research Infrastructures for Precision Medicine projects (RE3): *https://www.bsc.es/join-us/job-opportunities/17323lsinbre3 If you need further information regarding any of our vacancies, or you need any additional steps from my side in order to disseminate it, please let me know. Thank you! Best regards, -- Laura Delshams(She/Her) /Human Resources - Talent & Development Officer/ *Barcelona Supercomputing Center – Centro Nacional de Supercomputación* <mailto:anais.delastre@bsc.es>Tel. +34- 93 413 40 72 <http://www.bsc.es/>laura.delshams(a)bsc.es www.bsc.es <http://www.bsc.es/>

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Invitation for AI4b.io symposium
by BeNeLux bioinformaticians forum 29 Jan '24

29 Jan '24

Dear all, On the 9th and 10th of April, the third AI4b.io symposium will take place in Delft. This 2-day symposium focuses on the interplay between AI and challenges in Biosciences, ranging from the small scale of genetic manipulation of microorganisms to the large scale of optimal scheduling of factory processes and everything in between. Keynote speakers that have confirmed so far include: * Tias Guns (KU Leuven, Belgium) * Jana Weber (Delft University of Technology, Netherlands) * Sanne Abeln (Utrecht University, Netherlands). Other than the topics that will be covered (see link below for more information), it is also a nice opportunity to meet people from different backgrounds (Industry and Academia). If you think this is interesting for you and would like to contribute to the Symposium with a poster or presentation, please subscribe to the event: https://www.ai4b.io/news-and-events/events/ai4b-io-annual-symposium-2024/ FYI: the deadline for sending an abstract will soon be extended by 2 weeks. Kind regards, Renger Jellema Senior Scientist M(0031) 6 1553 5460 Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands dsm-firmenich.com<https://www.dsm-firmenich.com/> [cid:image001.png@01DA52DD.72511F20]<https://www.dsm-firmenich.com/> [cid:image002.png@01DA52DD.72511F20] This email, including any attachments, may be confidential and legally privileged. If you are not the intended recipient, please accept our apologies, and please do not disclose, copy, or distribute information in this email nor take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Please inform us that this message has gone astray before deleting it. Thank you for your cooperation. ______________________________________________________________________ DISCLAIMER: This email and any files transmitted with it, including replies and forwarded copies subsequently transmitted from dsm-firmenich, are confidential and for the intended recipient only. If you have received this email by mistake then please notify the sender immediately and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited.

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Open Position @IDIBAPS: Head of Research Computing Platform
by BeNeLux bioinformaticians forum 29 Jan '24

29 Jan '24

Dear all, --- forward of opportunity --- At IDIBAPS, we are setting up a new platform on Research Computing and we are looking for highly skilled professionals, with empathy and creativity, to lead this new project. Please find the link to the open position: https://www.clinicbarcelona.org/uploads/media/default/0012/56/b9fc8e14b6946…. LinkedIn: https://www.linkedin.com/posts/michela-bertero-23a2584_httpsimtrcooloxyqprr…. The head of Research Computing will build and develop a new platform to support the IDIBAPS research community and its systems strategy. She/he will have a dedicated budget and be able to recruit a team, envisioned initially of 2 to 4 people. The mission of the new platform is to provide a central hub for the research community, transversal departments, and internal users to access expertise in computing, bioinformatics and research data management. The new platform will work in tight collaboration with the Information Systems department of the Barcelona Clínic Hospital and will play a central role for networking and exchange of best practice and standards in computing, facilitating interdisciplinary collaborations within the Campus Clínic. More info via: Michela Bertero, PhD Strategy Director August Pi i Sunyer Biomedical Research Institute (IDIBAPS) C/ Rosselló, 149-153 | 08036 – Barcelona 93 2271830 | 638 26 07 47| michela.bertero(a)idibaps.org<mailto:michela.bertero@idibaps.org> www.idibaps.org<https://eu-central-1.protection.sophos.com/?d=idibaps.org&u=aHR0cDovL3d3dy5…> | @idibaps --- Best regards, Alex

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April 29 – May 10, 2024: May Institute on computation and statistics for mass spectrometry and proteomics
by BeNeLux bioinformaticians forum 29 Jan '24

29 Jan '24

Dear colleagues, See below for a highly recommended course on computational mass spectrometry and proteomic. For more information, please contact Olga Vitek (o.vitek(a)northeastern.edu) Best, Wout ________________________________ Dear friends and colleagues: The May Institute on Computation and Statistics for Mass Spectrometry and Proteomics, taking place on April 29 – May 10, 2024 on the campus of Northeastern University in Boston MA, is now accepting applications. The application deadline is February 15, 2024. Instructors are leading experts, who contributed numerous experimental and computational methods and software. The target audiences are both beginners and experienced scientists, with both experimental and computational expertise. Participants can select a subset of the following programs: * April 29 - May 1, Quantitative proteomics with Skyline. Lead instructors: Tina Ludwig, Brendan MacLean and Lindsay Pino * May 1 – May 3, Beginners R and beginners statistics. Lead instructor: Ryan Benz * May 1 – May 3, Intermediate R, data visualization and statistics. Lead instructor: Kylie Bemis * May 6 – May 8, Statistics for quantitative mass spectrometry: methods and case studies with MSstats. Lead instructors: Olga Vitek and Devon Kohler * May 6, Analysis of mass spectrometry images with Cardinal. Lead instructor: Kylie Bemis * May 7, Modern software development practice with Python. Lead instructor: Charles Tapley Hoyt * May 8, Scientific writing. Lead instructor: Alicia Williams * May 8 – May 10, Interpretation of proteomic experiments in the context of biomolecular networks with INDRA. Lead instructor: Ben Gyori * May 10, Barnett Institute 50th Anniversary and Karger Medal Celebration. Featured speakers: Jenny Van Eyk and Nikolai Slavov A limited number of registration fee wavers will be available for students and postdocs affiliated with academic or nonprofit institutions in the US. Please share this widely. More information is at https://computationalproteomics.khoury.northeastern.edu/

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Learning to Code with Dodona: A Webinar for Educators - 13 March 2024, 11h-12h CET
by BeNeLux bioinformaticians forum 24 Jan '24

24 Jan '24

[cid:image010.png@01DA4EB4.82646BB0] Learning to Code with Dodona: A Webinar for Educators Discover how Dodona (https://dodona.be/en) can enhance your programming, statistics and data science education in this special webinar for educators. In 1 hour, you will learn about: 1. Dodona’s user-friendly interface, and how its automated feedback system smoothly integrates into your curriculum and significantly elevates the learning experience; 2. Dodona's extensive library of coding exercises, suitable for various languages and skill levels; 3. how to create personalized exercises to meet specific teaching goals. The session will be hands-on, so you’re sure to leave with actionable insights to effectively implement Dodona into your courses. Furthermore, Prof. Lieven Clement will share how he successfully created a basic R skills course with Dodona. That course was an independent learning module in his university class, illustrating the practical application of Dodona in a real-world academic setting. Join us for an engaging overview of how Dodona can be a vital tool in your educational arsenal! REGISTER HERE<https://us06web.zoom.us/meeting/register/tZ0uf-2gqj8tHNW0HJJdRfkeirXPgA0MbI…> [Bart Mesuere (@BartMesuere) / X] Bart Mesuere Prof. Big Data Science University of Ghent [Peter Dawyndt | ELIXIR Belgium] Peter Dawyndt Prof. Computational Biology University of Ghent [Prof. dr. Lieven Clement | UGAIN - UGent academie voor ingenieurs] Lieven Clement Ass. Prof. Statistical Genomics University of Ghent

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'RNA-seq Data Analysis' - BioSB course - 8-12 April
by BeNeLux bioinformaticians forum 23 Jan '24

23 Jan '24

Dear all, Check this out! ________________________________ RNA-sequencing Data Analysis<https://www.dtls.nl/courses/rna-seq-data-analysis-2024/> <https://www.dtls.nl/courses/rna-seq-data-analysis-2024/>BioSB course, Breda, 8 - 12 April 2024 (9th edition!) ________________________________ (Be quick, early bird discount ends on 11 February!) What is this course about? This course covers the basic concepts and methods required for RNA-seq analysis. Particular attention is given to the data analysis pipelines for differential transcript expression and variant calling. The course consists of a mixture of lectures and Galaxy, Linux and R practicals. Also the potential of long-read based RNA-seq and AI based analysis enrichments will be explored. Renowned teachers will be happy to teach you the latest insights and skills! More information and registration: click here<https://www.dtls.nl/courses/rna-seq-data-analysis-2024/> We look forward to welcoming you. Kind regards, Petra Aarnoutse Community manager BioSB [cid:part1.qY990pC0.sfRrox51@health-RI.nl]

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'RNA-seq Data Analysis' - BioSB course - 8-12 April
by BeNeLux bioinformaticians forum 23 Jan '24

23 Jan '24

Dear all, Check this out! ------------------------------------------------------------------------ *RNA-sequencing Data Analysis* <https://www.dtls.nl/courses/rna-seq-data-analysis-2024/> <https://www.dtls.nl/courses/rna-seq-data-analysis-2024/> *BioSB course, Breda, 8 - 12 April 2024 (9th edition!)*** ------------------------------------------------------------------------ *(Be quick, early bird discount ends on 11 February!) * * What is this course about?** *This course covers the basic concepts and methods required for RNA-seq analysis. Particular attention is given to the data analysis pipelines for differential transcript expression and variant calling. The course consists of a mixture of lectures and Galaxy, Linux and R practicals. Also the potential of long-read based RNA-seq and AI based analysis enrichments will be explored. Renowned teachers will be happy to teach you the latest insights and skills! *More information and registration: **click here* <https://www.dtls.nl/courses/rna-seq-data-analysis-2024/>* *We look forward to welcoming you.* ** *Kind regards, Petra Aarnoutse Community manager BioSB*** ***

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Disease Maps Community Meeting 2024: Abstract submission deadline extended
by BeNeLux bioinformaticians forum 22 Jan '24

22 Jan '24

[Apologies for multiple postings] Call for abstracts for the 8th Disease Maps Community Meeting extended! https://disease-maps.org/DMCM2024 Submit your abstracts via the EasyChair link<https://easychair.org/cfp/dmcm2024> by 31 January 2024. Register via this registration form<https://disease-maps.org/DMCM2024#:~:text=Please%20register%20by%2025th%20F…> by 24 February 2024. DMCM’24 a joint event of the Disease Maps Community<https://disease-maps.org/> and the ELIXIR Systems Biology Community<https://elixir-europe.org/communities/systems-biology>. See the agenda<https://disease-maps.org/DMCM2024/programme/> for more details. Keynote speakers * James Glazier, Professor of Intelligent Systems Engineering, Professor & Director of Biocomplexity Institute Biophysics, Indiana University, Bloomington, USA * Liesbet Geris, Collen-Francqui Research Professor in Biomechanics and Computational Tissue Engineering, University of Liège and KU Leuven, Belgium * Henning Hermjakob, Head of Molecular Systems Services, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK * Reinhard Schneider, Head of Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg Featured workshop imSAVAR Symposium: Disease maps and irAOPs in the immune system effects of immunomodulatory therapies. Scope We will focus on systems medicine topics, including tools, standards, and applications of bioinformatics, computational and systems biology to research on human diseases. Join us to discuss challenges of building reliable models of disease mechanisms from prior knowledge and data, and applying their predictions. The topics include, but are not limited to: * Curation of diagrammatic models of diseases using systems biology standards * Visual analytics of systems biology diagrams * Modelling of disease mechanisms: network-based, Boolean or continuous * Interpreting multi-omics data using systems biology diagrams * Using omics data for model building and parameterisation Abstract Submission Deadline: 31 January 2024 (the EasyChair link<https://easychair.org/cfp/dmcm2024>) Registration Deadline: 24 February 2024 (registration form<https://disease-maps.org/DMCM2024#:~:text=Please%20register%20by%2025th%20F…>) When: 25th-27th of March 2024 Where: University of Luxembourg, Campus Belval, Maison du Savoir 2, avenue de l’Université, L-4365 Esch-sur-Alzette, Luxembourg https://www.uni.lu/en/about/campuses/belval-campus For all details see https://disease-maps.org/DMCM2024<https://disease-maps.org/DMCM2024> With warm regards, on behalf of the organisers --- Marek Ostaszewski University of Luxembourg Luxembourg Centre for Systems Biomedicine (LCSB) Campus Belval | House of Biomedicine 6, avenue du Swing, L-4367 Belvaux, Luxembourg Tel: +352 46 66 44 5604<tel:+3524666445604> http://lcsb.uni.lu<http://lcsb.uni.lu/>

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