- BBClist - maillist.psb.ugent.be

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/>

1 0

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

1 0

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.

1 0

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. ***********************************************************************

1 0

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

1 0

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

1 0

'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]

1 0

6 assistant professor vacancies in CS, AI, Bioinformatics at VU Amsterdm
by BeNeLux bioinformaticians forum 16 Nov '23

16 Nov '23

Dear all, The department of Computer Science at Vrije Universiteit Amsterdam is looking for assistant professors in the areas of computer science, bioinformatics and/or AI Please forward to people you know who may be interested. For details and application procedure, please see https://werkenbij.vu.nl/ad/6-assistant-professor-positions/69grev Best Regards, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1111 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +312059 87783<tel:+31205987783> - skype: kafeenstra - room NU 12A31| | | Feenstra(a)few.vu.nl<mailto:Feenstra@few.vu.nl> - www.few.vu.nl/~feenstra/<http://www.few.vu.nl/~feenstra/> | | | "Boom Boom Boom Boom, I Want You in My Room" (Venga | | | Boys) | |_____________|_______________________________________________________|

1 0

Vacancies
by BeNeLux bioinformaticians forum 25 Oct '23

25 Oct '23

Hi all, We’re Hartwig Medical Foundation, a non-profit organization that wants to make sure every cancer patient gets the best treatment available. To reach this goal, we offer a ‘complete DNA-test’ to hospitals to treat the patients of today. To help the patient of tomorrow, we collect the genomic data of the patients and together with treatment outcomes, make the data available to researchers. To make our ambitions a reality in the next couple of years, we’re looking to hire: * Software Developer ACTIN<https://www.linkedin.com/feed/update/urn:li:activity:7122119163413712896/?a…> * Software Developer IT Infrastructure Team<https://www.linkedin.com/feed/update/urn:li:activity:7122820576531869696/?a…> * Data Steward<https://www.linkedin.com/feed/update/urn:li:activity:7119921473523195904/?a…> * Moleculair Analist / Lab Technician<https://www.linkedin.com/feed/update/urn:li:activity:7109867983312670720/?a…> You can also find all our open positions at https://www.hartwigmedicalfoundation.nl/vacancies/. With kind regards, Daphne van Beek Innovation Specialist Absent on Monday [Hartwig Medical Foundation]<https://www.hartwigmedicalfoundation.nl/en/> A Science Park 408, 1098 XH Amsterdam T +31 (0)20 226 9712 W hartwigmedicalfoundation.nl<https://www.hartwigmedicalfoundation.nl/en/> | oncoact.nl<https://oncoact.nl/?lang=en> N Subscribe to our newsletter<https://mailchi.mp/475bfde5c6f3/nieuwsbrieven-hartwig-medical-foundation> [Facebook]<https://www.facebook.com/HartwigMedicalFoundation> [LinkedIn] <https://www.linkedin.com/company/hartwig-medical-foundation> [Twitter] <https://twitter.com/hartwigmedical> [Instagram] <https://www.instagram.com/hartwigmedicalfoundation/?hl=en> [YouTube] <https://www.youtube.com/channel/UCK8juCiUGC1OsEXPtdEEwPA> It is our mission to realize that every cancer patient receives a personalized treatment using a complete DNA test<https://oncoact.nl/?lang=en>.

1 0

Request to post: Computational biologist / AI method development - job opening @ BASF Ghent
by BeNeLux bioinformaticians forum 25 Oct '23

25 Oct '23

Dear Sir / Miss, Can you consider posting the following job opening in computational protein engineering / AI methods development in the BBC mailing list? The job opening is in Ghent. Since I did not see it posted (see previous request below) ... I was wondering whether I missed the post, or missed your feedback? With best regards, Koen From: Koen Bruynseels Sent: Monday, October 9, 2023 5:12 PM To: bbclist(a)psb.vib-ugent.be; bbclist(a)psb.ugent.be Subject: Computational biologist / AI method development - job opening @ BASF Ghent Dear, Can you share the following job opening in my team in Ghent with the mailing list? Best regards, Koen Computational Protein Engineer (basf.jobs)<https://basf.jobs/dark_blue_EMEA/job/Gent-Computational-Protein-Engineer/99…> Computational Protein engineer We are seeking an entrepreneurial and highly skilled Computational Protein Engineer with Expertise in AI methods and Molecular Biology to join our innovative team. The ideal candidate will possess a profound understanding of machine learning models in the field of protein engineering, a deep interest in plant molecular biology, and solid communication skills. As a crucial member of our research and development team, you will identify opportunities to leverage advanced AI models for protein design and optimization, and you will apply them to enhance crop traits for increased resilience and yield. Task package: * You will develop and utilize AI-driven and modeling approaches to analyze and predict protein structures, interactions, and functions, with a focus on optimizing traits related to pest control, disease resistance and yield enhancement. * You collaborate closely with cross-functional teams, including molecular biologists, agronomists, and bioinformaticians to integrate advanced methodologies into broader crop improvement programs. * You will identify creative opportunities for developing desired agronomic traits, by leveraging on your expertise in molecular biology and machine learning methods. * Furthermore, you will contribute to the development and execution of research plans, experimental designs, and data analysis pipelines. * You will stay abreast of the latest advancements in protein engineering, AI methodologies, and plant molecular biology, and apply this knowledge to drive innovation within the company. Expertise: * You have a Ph.D. or equivalent in Protein Engineering, Bioinformatics, Molecular Biology, or a related field. * You are known for your entrepreneurial attitude, with the ability to identify innovation opportunities that leverage on knowledge in molecular biology and machine learning methods. * Additionally, you have excellent verbal and written communication skills, with experience in conveying complex scientific concepts to both technical and non-technical audiences. * You have proven expertise in the development and application of machine learning models, including large language models (e.g., AlphaFold, ESMfold), for protein engineering and structure prediction. * Proficiency in molecular biology, including a deep understanding of genomics, gene expression, signaling pathways, and metabolic processes is a must. * Programming skills (Python, R, etc.) for data analysis and computational modeling are a plus. * You have demonstrated ability to work collaboratively in a fast-paced, interdisciplinary research environment. Benefits: * Responsibility from day one in a challenging but dynamic work environment and "on-the-job" training as part of a committed team. * Competitive compensation including attracting benefits as well as excellent career opportunities in an international company. BASF is a multinational company dedicated to revolutionizing agricultural science. We are committed to developing innovative solutions that address global challenges in food security and sustainability. Our diverse team combines expertise in computational protein engineering, artificial intelligence, and plant molecular biology to create cutting-edge technologies that redefine the agricultural industry. Do you have any questions about the application process or the job? Please contact Nele (Talent acquisition) Phone: +49 30 2005-58363. Dr. Koen Bruynseels Phone: +32 474 296 225, Email: koen.bruynseels(a)basf.com<mailto:koen.bruynseels@basf.com> Postal Address: BASF Belgium Coordination Center CommV, Technologiepark 101, 9052 Gent Zwijnaarde, Belgium [cid:image001.png@01DA0732.D91A4E30] BASF Business Services NV, Registered Office: Scheldelaan 600, 2040 Antwerp 4, Belgium Companies' Register: Handelsregister Antwerpen, 0463.642.875 Companies' Register: Rechtspersonenregister Antwerpen, 0463.642.875 Managing Director: Stefan Beck Information on data protection can be found here: https://www.basf.com/global/en/legal/data-protection-at-basf.html

1 0