November 2023 - 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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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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3 open group leader positions at VIB.AI
by BeNeLux bioinformaticians forum 27 Nov '23

27 Nov '23

No images? Click here<https://highlightsciencewriting.cmail20.com/t/y-e-xyhhyid-dhfwdldd-d/> [http://i1.cmail20.com/ei/y/D2/DE6/F9B/004157/csfinal/VIB_AI-CenterforAIComp…] We're recruiting group leaders The brand new ‘VIB Center for AI & Computational Biology’, VIB.AI, in Flanders, Belgium, is looking for three new faculty members. If you use or develop artificial intelligence methods and mechanistic mathematical models to address fundamental questions in biology, we would love to hear from you. Vacancy ><https://highlightsciencewriting.cmail20.com/t/y-l-xyhhyid-dhfwdldd-r/> AI in biology We welcome applications across all domains of machine learning, artificial intelligence, and associated fields. Examples of research topics include but are not limited to: [icon VIB.AI] * development of new AI architectures for biology and hybrid models that combine deep learning with mechanistic models; * foundation models of genome regulation using single-cell and spatial multi-omics data; * AI-based modeling of protein structure and protein interaction networks; * AI-based modeling of cell morphology and tissue function using imaging and computer vision; * AI models of disease and digital twin applications. Biological applications are broad: microorganisms, plant biology, biodiversity and ecology, neuroscience, cancer, and immunology. We also welcome applicants with applied projects, including synthetic biology, AI-driven experiments (experiment-in-the-loop), and bio-engineering. [http://i3.cmail20.com/ei/y/D2/DE6/F9B/004157/csfinal/data-core-1394-c906fbd…] We offer The group leader positions at VIB are tied to a KU Leuven (tenure track) professor position and come with full salary and core funding (internationally competitive package) that is renewable for multiple additional 5-year periods, as well as access to state-of-the-art research and top-notch support core facilities, including support to attract talented PhD students and postdocs from across the world. Explore the vacancy<https://highlightsciencewriting.cmail20.com/t/y-l-xyhhyid-dhfwdldd-y/> [Lab space] A brand new collaborative center in Flanders, Belgium VIB.AI's core mission is to study fundamental problems in biology by combining machine learning with in-depth knowledge of biological processes. Additionally, we are committed to fostering computational and AI research excellence across all VIB Centers, amplifying collaboration and pushing the boundaries of innovation across the institute About VIB.AI<https://highlightsciencewriting.cmail20.com/t/y-l-xyhhyid-dhfwdldd-j/> [http://i5.cmail20.com/ei/y/D2/DE6/F9B/004157/csfinal/Stein-3bc395c491cc79fe…] "AI models trained on large biological datasets can greatly accelerate discovery in life sciences. Today, high-throughput technologies and data science are steering biomedical research, and VIB.AI aims to be at the forefront of this revolution." VIB.AI Director Stein Aerts Join our team More about VIB.AI ><https://highlightsciencewriting.cmail20.com/t/y-l-xyhhyid-dhfwdldd-t/> [http://i2.cmail20.com//static/eb/master/13-the-blueprint-3/images/tweet-whi…] Tweet <https://highlightsciencewriting.cmail20.com/t/y-tw-xyhhyid-dhfwdldd-h/> [http://i3.cmail20.com//static/eb/master/13-the-blueprint-3/images/linkedins…] Share <https://highlightsciencewriting.cmail20.com/t/y-li-xyhhyid-dhfwdldd-k/> [http://i4.cmail20.com//static/eb/master/13-the-blueprint-3/images/forwardto…] Forward <https://highlightsciencewriting.forwardtomyfriend.com/y-dhfwdldd-57FA63C8-x…> VIB.AI VIB vzw Rijvisschestraat 120 9052 Ghent vib.be/ai<https://highlightsciencewriting.cmail20.com/t/y-l-xyhhyid-dhfwdldd-i/> Preferences<https://highlightsciencewriting.updatemyprofile.com/y-xyhhyid-57FA63C8-dhfw…> | Unsubscribe<https://highlightsciencewriting.cmail20.com/t/y-u-xyhhyid-dhfwdldd-c/>

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PhD position to study diatoms available at Ghent University (Belgium)
by BeNeLux bioinformaticians forum 24 Nov '23

24 Nov '23

Job description: The Laboratory of Protistology and Aquatic Ecology (Ghent University) and Comparative Network Biology group (VIB) invite applications for a fully-funded PhD studentship for 4 years to study life cycle dynamics in coastal diatom populations. Diatoms are major primary producers in freshwater and marine ecosystems but little remains known about the role of endogenous and external factors triggering life cycle transitions, and in particular how global change affects the growth and life cycling of diatom populations. Recent pioneering work in our lab has revealed the genes involved in life cycle transitions (sexual reproduction, resting spore formation, dormancy,…), suggesting a high degree of conservation in several of them. This makes it possible to monitor the expression of these genes to track the growth and life cycle dynamics of multiple species simultaneously. This PhD will take a (meta)transcriptomics approach to track life cycle events of dominant diatoms species in benthic and planktonic coastal ecosystems along the East-Atlantic coasts and link these to the dynamics of population-level cell size structure and local environmental conditions. In parallel, laboratory bulk- and single cell RNA-seq experiments will be set-up to identify and validate environmental factors triggering life cycle events. The successful candidate will participate in field work, laboratory essays, the analysis of metatranscriptome data and the design and testing of molecular probes to track life cycle events in natural conditions. For more information, please visit: [ https://www.ugent.be/en/work/scientific/phd-student-38 | https://www.ugent.be/en/work/scientific/phd-student-38 ] Michiel Van Bel - Senior bioinformatician Applied Bioinformatics And Biostatistics VIB-UGent Center for Plant Systems Biology Ghent University Technologiepark-Zwijnaarde 71 - 9052 Ghent - Belgium Tel. +32(0)9 331 36 95 [ http://www.psb.ugent.be/ | www.psb.ugent.be ] Genome editing, cutting-edge technology for a sustainable agriculture

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Systems toxicology at Leiden University
by BeNeLux bioinformaticians forum 20 Nov '23

20 Nov '23

Dear BBC mailing list, could you advertise the following vacancies? The research group of Prof. Bob van de Water aims to unravel cell signaling programs that underlie adverse xenobiotic-induced adverse responses. In particular, high throughput toxicogenomics analysis is applied with innovative gene co-expression network models thus contributing to a system toxicology approach in qualifying and quantifying adverse responses. We are currently looking for 2 PhD candidates (or 1 PhD candidate and 1 PostDoc): * https://www.linkedin.com/jobs/view/3747285843/?refId=GOG0G6SMSPi0LdoHR%2FJD… * https://www.linkedin.com/jobs/view/3759844679/ Please forward these positions to anyone interested! Kind regards, Giulia [cid:49faf4e2-0be7-46ef-ab73-175d8c110d9a] Giulia Callegaro, PhD Assistant Professor of Drug Safety and Toxicogenomics Phone +31 71 527 6105 Web https://www.universiteitleiden.nl/en/science/drug-research/drug-discovery-a… Leiden University | Faculty of Mathematics and Natural Sciences - Div. of Drug Discovery and Safety, Leiden Academic Center for Drug Research (LACDR) | Gorlaeus Lab. Room GW2.07, Einsteinweg 55, 2333 CC Leiden NL Linkedin<https://www.linkedin.com/in/giulia-callegaro-0904b86a/> Github lab page<https://github.com/vdWater-Callegaro-lab> Orcid<https://orcid.org/0000-0002-7627-7271> Make flexibility work: If you get an email from me outside of normal working hours, it's because I'm sending it at a time convenient to me. There is no expectation on you to read or reply until your normal working hours.

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PhD positions in structural bioinformatics and in drug design
by BeNeLux bioinformaticians forum 20 Nov '23

20 Nov '23

*********************************************************************** We're hiring! 10 PhD positions available at 5 universities (Maastricht, Paris, Uppsala, Münster and Barcelona) as part of a MSCA Doctoral Network PRAETORIAN. *********************************************************************** The network will encompass multidisciplinary collaborations of PhD students and researchers as well as patient organisations and commercial parties who will collectively be focusing on the next generation of therapeutics and diagnostics in immunothrombosis and in particular on sepsis. Within the network there is explicit application of in silico methodology to interact with chemical, biomedical and medical colleagues, at the Maastricht and Paris universities. For those who wish to be active in a multidisciplinary international setting, please have a look on our website: https://www.praetorian-dn.eu/ for more information and possibility to send an application. [Image preview] *********************************************************************** [signature_2610298709] Gerry Nicolaes, PhD  Associate Professor Cardiovascular Research Institute Maastricht Biochemistry Department PRAETORIAN Horizon-MSCA-doctoral network coordinator https://www.praetorian-dn.eu/ Universiteitssingel 50, 6229 ER Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 3881688 F +31 43 3884159 g.nicolaes(a)maastrichtuniversity.nl<mailto:g.nicolaes@maastrichtuniversity.nl> www.maastrichtuniversity.nl <http://www.maastrichtuniversity.nl/> http://www.3dstructure-function.nl<http://www.3dstructure-function.nl/>  [signature_1401234634]Please consider your environmental responsibility before printing this e-mail. ***********************************************************************

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CFP OLA'2024 Optimization & Learning @Dubrovnik
by BeNeLux bioinformaticians forum 19 Nov '23

19 Nov '23

Apologies for cross-posting. Appreciate if you can distribute this CFP to your network. **************************************************************************************** OLA'2024 International Conference on Optimization and Learning 13-15 May 2024 Dubrovnik, Croatia http://ola2024.sciencesconf.org/ SCOPUS Springer Proceedings **************************************************************************************** OLA is a conference focusing on the future challenges of optimization and/or machine learning methods and their applications. The conference OLA'2024 will provide an opportunity to the international research community in optimization and learning to discuss recent research results and to develop new ideas and collaborations in a friendly and relaxed atmosphere. OLA'2024 welcomes presentations that cover any aspects of optimization and/or machine learning research such as big optimization and learning, optimization for learning, learning for optimization, optimization and learning under uncertainty, deep learning, new high-impact applications, parameter tuning, 4th industrial revolution, computer vision, hybridization issues, optimization-simulation, meta-modeling, high-performance computing, parallel and distributed optimization and learning, surrogate modeling, multi-objective optimization ... Submission papers: We will accept two different types of submissions: - S1: Extended abstracts of work-in-progress and position papers of a maximum of 3 pages - S2: Original research contributions of a maximum of 12 pages Important dates: =============== Paper submission deadline Dec 16, 2023 Notification of acceptance Feb 09, 2024 Proceedings: Accepted papers in categories S1 and S2 will be published in the proceedings. A SCOPUS and DBLP indexed Springer book will be published for accepted long papers. Proceedings will be available at the conference. -- *********************************************************************** OLA'2024 International Conference on Optimization and Learning (SCOPUS, Springer) Dubrovnik, Croatia, May 13-15, 2024 https://ola2024.sciencesconf.org/ *********************************************************************** Prof. El-ghazali TALBI Polytech'Lille, University Lille - INRIA CRISTAL - CNRS

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Bioinformatics Software Developer
by BeNeLux bioinformaticians forum 17 Nov '23

17 Nov '23

Dear BBC mailing list, We are looking to expand the team at Cyclomics in Utrecht, NL with a Software developer. For more information please see: https://www.linkedin.com/jobs/view/3767449541/ Please forward this position to people who might be interested in joining us in improving our sequencing technology! With kind regards, Dami Rebergen

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'Integrated Modeling and Optimization', BioSB course, 11-15 Dec, Wageningen.
by BeNeLux bioinformaticians forum 17 Nov '23

17 Nov '23

Dear colleagues, Grab your chance to join the upcoming BioSB course, there are still some spots available! Integrated Modeling and Optimization<https://www.dtls.nl/courses/integrated-modeling-and-optimization-fundamenta…> Wageningen, 11 - 15 December 2023 In validating models one always meet with the need to fit models to data. So, the parameters that are present in any realistic model have to be chosen based on comparison of model predictions with data. In this matching process optimization techniques are indispensable. That’s why a considerable part of this course is spent on getting you acquainted with the optimization techniques that are nowadays available and widely used. Numerical optimization also is the basis for so-called flux balance analysis (FBA), commonly used to study large metabolic networks. This type of models and their analysis and simulation is also introduced in the course. Target audience The course is aimed at PhD students with a background in bioinformatics, systems biology, computer science or a related field, and life sciences. Participants from the private sector are also welcome. A working knowledge of mathematics, especially differential equations, is recommendable, but we will distribute preparation material to be studied by students missing the required background. Furthermore, at the start we offer a math refresher to help those participants who are not (yet) involved in modelling on a daily basis. More information: click here<https://www.dtls.nl/courses/integrated-modeling-and-optimization-fundamenta…>. Registration <https://www.aanmelder.nl/integrated_modeling/subscribe> We look forward to welcoming you. Kind regards, Petra Aarnoutse Community manager BioSB [cid:part1.gtMf3b8Y.pGBav90s@health-RI.nl]

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