- BBClist - maillist.psb.ugent.be

postdoc position available
by BeNeLux bioinformaticians forum 17 Dec '24

17 Dec '24

Dear colleagues, I have a two-year postdoc opening to work on an exciting AI for drug discovery project based at Imperial College in collaboration with the University of Cambridge. Further information at https://imperial.ac.uk/jobs/search-jobs/description/index.php?jobId=21928<https://t.co/ALtuTz5j4T> The deadline is 19/12/2024, but I will consider candidates beyond this until the position is filled. Best regards Pedro Dr. Pedro J. Ballester | Royal Society Wolfson Fellow & Senior Lecturer Imperial College | Department of Bioengineering Group website | https://ballestergroup.github.io/<https://ballestergroup.github.io/> College website | https://www.imperial.ac.uk/people/p.ballester/research.html <https://www.imperial.ac.uk/people/p.ballester/research.html> Networking profiles | https://www.linkedin.com/in/pedroballester/ https://x.com/pjballester <https://x.com/pjballester> Address | Sir Michael Uren Hub, White City campus, 86 Wood Lane, London - W12 0BZ, UK

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PhD position in bio- and cheminformatics
by BeNeLux bioinformaticians forum 15 Dec '24

15 Dec '24

Dear all, Wageningen Bioinformatics is looking for a PhD student in machine learning for bio- and cheminformatics. Are you looking for a PhD position at the intersection of biology, chemistry, and computer science? Are you interested in developing new machine learning methodologies in proximity to and collaboration with experimentalists? If yes, this fully funded PhD position might be an excellent match for you. Please find more information and an application link (deadline 5th January, 2025) here: https://www.wur.nl/en/education-programmes/phd-programme/graduate-schools/w… Daniel Probst & Dick de Ridder Bioinformatics Group, Wageningen University [cid:6d6bb479-cc02-472c-a697-cfc4f9cf82c0]<https://outlook.office.com/bookwithme/user/e1bf24157a0b4dfba8c0e0e3c99fcab4…> Book time to meet with me<https://outlook.office.com/bookwithme/user/e1bf24157a0b4dfba8c0e0e3c99fcab4…>

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ESSAI 2025 CALL FOR COURSE PROPOSALS - extended deadline
by BeNeLux bioinformaticians forum 12 Dec '24

12 Dec '24

(apologies for multiple postings) ESSAI 2025 CALL FOR COURSE PROPOSALS - extended deadline The 3rd European Summer School on Artificial Intelligence - ESSAI 2025 June 30 to July 4, 2025 Bratislava, Slovakia https://essai2025.eu/ <https://essai2025.eu/> IMPORTANT DATES: January 8, 2025 (AoE): Full course proposal submission January 31, 2025: Notification of acceptance or rejection ESSAI SUMMER SCHOOLS ESSAI 2025 is the third edition of the annual summer school on AI held under the auspices of the European Association for Artificial Intelligence (EurAI). ESSAI 2025 will provide an interdisciplinary setting in which courses are offered in all areas of Artificial Intelligence and also from wider scientific, historical, and philosophical perspectives. ESSAI is a central meeting place for students and young researchers in Artificial Intelligence to discuss current research and share knowledge. The first edition of ESSAI was held in Ljubljana, Slovenia, and the second one in Athens, Greece. Both editions were very successful and received excellent feedback from the student and lecturer participants. We look forward to a third edition of ESSAI, which we believe will be very successful as well. TOPICS AND FORMAT OF COURSES ESSAI aims to cover subdisciplines of AI and the interactions between them. Proposals for courses at ESSAI 2024 are invited in all areas of Artificial Intelligence, including but not limited to the following: * Autonomous Agents and Multi-agent Systems (MAS) * Causality and Causal Learning (CL) * Ethical, Legal and Social Aspects of AI (ELS) * Foundation Models (FM) * Knowledge Representation and Reasoning (KR) * Learning Theory (LT) * Natural Language Processing (NLP) * Neuro-Symbolic Learning and Reasoning (NSLR) * Planning & Strategic Reasoning (PLAN) * Reinforcement Learning (RL) * Robotics (ROB) * Safe, Explainable and Trustworthy AI (SET) * Search & Optimization (SO) * Supervised and Unsupervised Learning (ML) * Vision (VIS) * Human-In-The-Loop AI (HLAI) * AI for Social Good (A4SG) * Quantum Machine Learning (QML) Each course will consist of five 90-minute lectures offered daily (Monday-Friday) in the week the school takes place. COURSE CATEGORIES Each proposal should fall under one of the following two categories. *Introductory Courses* Introductory courses are intended to introduce a research area of AI to students, young researchers, and other non-specialists and to foster a sound understanding of its basic methods and techniques. Such courses should enable researchers from related disciplines to develop some comfort and competence in the topic considered. Introductory courses in a cross-disciplinary area may presuppose general knowledge of the related disciplines. *Advanced Courses* Advanced courses are targeted primarily to graduate students who wish to acquire a level of comfort and understanding of current research in an area of AI. While introductory courses will typically focus on one subarea of AI only, advanced courses are encouraged to present a broader perspective on AI, and they should be of interest beyond a single specific area. COURSE PROPOSAL GUIDELINES To be considered, course proposals should closely adhere to the following guidelines. Courses must be presented by lecturers who submitted the proposal. For courses with more than two lecturers, the role of each lecturer should be clearly explained and justified in the proposal. Course proposals should explicitly state the intended course category. Proposals for introductory courses should indicate the intended level, for example, as it relates to standard textbooks and monographs in the area. Proposals for advanced courses should specify the prerequisites in detail. Submitted proposals should include all of the following: a. Contact information for each proposer: Name, affiliation, address, email, web page b. General proposal information: Title, category c. Information about the course content: * Abstract of up to 150 words * Motivation and description (up to two pages) * Tentative outline * Expected level and prerequisites * Appropriate references (e.g., textbooks, monographs, proceedings, surveys) * Whether the course will appeal to students outside of the main area of the course. d. Information about the proposer(s): * Short CVs of the proposer(s) * Evidence that the proposer(s) are excellent lecturers with relevant teaching experience, particularly in delivering intensive interdisciplinary courses. The course proposals will be reviewed by a Program Committee covering all the research areas presented above. PARTICIPATION To keep registration fees to a minimum, all ESSAI's instructional and organizational work is performed completely voluntarily. However, the registration fees of organizers and instructors will be waived. In addition and where appropriate and possible, ESSAI will seek to partially reimburse travel and accommodation expenses associated with delivering a course. If lecturers can cover their travel and accommodation expenses from other sources, this is greatly appreciated. SUBMISSION INFORMATION By January 8, 2025 (AoE): Proposer(s) should upload a PDF with the full course proposal as detailed above. By January 31, 2025, Proposer(s) will be notified whether their proposal has been accepted or not. SUBMISSION PORTAL Please submit your proposals as a single PDF file to https://cmt3.research.microsoft.com/User/Login?ReturnUrl=%2FESSAI2025 <https://cmt3.research.microsoft.com/User/Login?ReturnUrl=%2FESSAI2025> ESSAI 2025 ORGANIZERS General Chair Vida Groznik University of Ljubljana Program Chairs Manolis Koubarakis National and Kapodistrian University of Athens Fabrizio Silvestri Sapienza University of Rome Local Chair Peter Drotár Technical University of Kosice ESSAI Steering Committee Members Giuseppe De Giacomo (Chair, EurAI Board representative) University of Oxford Brian Logan University of Aberdeen & Utrecht University Magdalena Ortiz Technical University of Vienna

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PhD position in the ULB Machine Learning group
by BeNeLux bioinformaticians forum 08 Dec '24

08 Dec '24

Dear all We are looking for a new phd student. Can you please share this information in your professional and social networks? This is the vacancy call; https://euraxess.ec.europa.eu/jobs/297798 Thank you Bien cordialement | Vriendelijke groet | Kind regards Tom ________________________________________________________________________________ prof. Tom Lenaerts co-head of the Machine Learning Group <http://mlg.ulb.ac.be/> Affiliated researcher at the AI lab <http://ai.vub.ac.be/> of the Vrije Universiteit Brussel and the Center for Human-Compatible AI <https://humancompatible.ai/>, UC Berkeley Département d’Informatique Université Libre de Bruxelles (ULB) Boulevard du Triomphe CP212 1050 Brussels. Belgium. Phone: +32 2 650 60 04 Fax: +32 2 650 56 09 Email: Tom.Lenaerts(a)ulb.be <mailto:Tom.Lenaerts@ulb.be> Linkedin <https://www.linkedin.com/in/tom-lenaerts-5606061/>

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Postdoc position in molecular artificial intelligence @ University of Antwerp
by BeNeLux bioinformaticians forum 02 Dec '24

02 Dec '24

Dear colleagues, We have an exciting position for a postdoctoral researcher in molecular artificial intelligence available at the University of Antwerp. You will collaborate with world-leading pharmaceutical companies to develop artificial intelligence solutions to analyze billion-scale mass spectrometry-based metabolomics data. The application deadline for this position is December 18, 2024. We especially encourage candidates with a PhD in quantitative sciences and a strong interest in applying their data science skills to relevant life science challenges to apply. For more detailed information and to apply, please visit our website: https://www.uantwerpen.be/en/jobs/vacancies/academic-staff/?q=3715&descr=Po… We strongly encourage passionate individuals with a keen interest in artificial intelligence and bioinformatics to apply for these positions. The University of Antwerp offers a vibrant research environment, state-of-the-art facilities, and a supportive community of scholars dedicated to pushing the boundaries of knowledge. Please feel free to share this information with anyone who may be interested or qualified. We appreciate your assistance in helping us spread the word and attract exceptional candidates to join our team. Sincerely, Wout Bittremieux Assistant Professor University of Antwerp

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Take Your Research Further with Coding Courses in 2025
by BeNeLux bioinformaticians forum 02 Dec '24

02 Dec '24

Somehow it’s already December, and 2025 is just around the corner! If learning to code has been on your to-do list, why not make it your New Year’s resolution? We’ve made it easy with three introductory coding courses in January, designed specifically for biologists and genomic scientists. They’re the perfect way to kickstart your coding journey and enhance your research and analysis skills in the year ahead. 🔍 R for Biologists | 15-17 January * Learn R from the ground up: objects, variables, and data types. * Master data importing, cleaning, and manipulation. * Create beautiful visualizations with ggplot2 and interactive plots. * Bring your own data for personalized guidance in our data clinic! Register here<https://genomics.ed.ac.uk/event/r-for-biologists-2025/> 🐍 Introduction to Python | 20-24 January * Get started with Python and explore how it benefits bioinformatics research. * Learn to manipulate text, work with files, and automate tasks with loops and conditions. * Discover advanced topics like regular expressions, dictionaries, and filesystem operations. * Gain practical skills to create efficient bioinformatics pipelines. * IN PERSON course - the perfect excuse for a trip to beautiful Edinburgh to see off the January blues! Register here<https://genomics.ed.ac.uk/event/introduction-to-python-for-biologists-2/> 💻 Linux for Genomics | 29-30 January * Navigate the Linux command line with confidence. * Learn file management, permissions, and shell scripting. * Explore essential tools for genomic data analysis, including seqtk, samtools, and bedtools. * Boost your productivity by integrating Linux into your workflows. Register here<https://genomics.ed.ac.uk/event/introduction-to-linux-for-genomics-3/> 🚀 Why Learn Coding with Us? Our expert-led courses are tailored for researchers, offering practical, hands-on exercises and real-world applications in genomics and biology. Looking to Advance Later in the Year? Take your skills to the next level with our advanced coding courses: * Snakemake<https://genomics.ed.ac.uk/event/snakemake-2/> | 24-27 March * Advanced Python<https://genomics.ed.ac.uk/event/advanced-python-for-biologists-2/> | 8-12 September * Data Exploration with Python<https://genomics.ed.ac.uk/event/data-exploration-with-python-2/> | 1-5 December Spaces are filling fast—don’t miss out! Start your coding journey in 2025 with confidence! If you have any questions please don’t hesitate to reach out. Kind regards, Dr Kathryn Campbell Genomics and Bioinformatics Training Coordinator - Edinburgh Genomics School of Biological Sciences University of Edinburgh Email: kcampb2(a)ed.ac.uk<mailto:kcampb2@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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Vacancy in complex genetics
by BeNeLux bioinformaticians forum 26 Nov '24

26 Nov '24

Warning! This email originated from outside of PSB. Do not click links or open attachments unless you recognize the sender and know the content is safe. -------------------------------------- Do you want to do your PhD in complex genetics? Or do you already have a PhD in statistical genetics (or related) and are you looking for a Postdoc position on cardiovascular genetics in wonderful Utrecht (NL)? In these positions, you will work as part of the NextGen consortium. We aim to identify genes and biological pathways involved in cardiovascular disease, with a focus on GWAS, PGS, and pharmacogenomics. Interested? You will be working with Jessica van Setten https://research.umcutrecht.nl/technologies/complex-genetics/ PhD position: https://www.werkenbijumcutrecht.nl/vacatures/wetenschap-en-onderzoek/phd-ca…<https://lnkd.in/e8BSHpCU> Postdoc position: https://www.werkenbijumcutrecht.nl/vacatures/wetenschap-en-onderzoek/postdo…<https://lnkd.in/etWWvVi5> Kind regards, Hanneke van Deutekom, PhD [Universitair Medisch Centrum Utrecht] Head of Bioinformatics | Department of Genetics Universitair Medisch Centrum Utrecht | Roomnumber STR.0.308 T: +31 88 75 681 16<http://+31%2088%2075%20681%2016> | M: +31 6 3111 7926<tel:+31631117926> | www.umcutrecht.nl<http://www.umcutrecht.nl/> Working on: Monday, Thuesday, Thursday, Friday [Image] LinkedIn<https://www.linkedin.com/in/hwmvandeutekom/> ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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Machine Learning Scientist in Multimodal Data Integration
by BeNeLux bioinformaticians forum 25 Nov '24

25 Nov '24

Warning! This email originated from outside of PSB. Do not click links or open attachments unless you recognize the sender and know the content is safe. -------------------------------------- Warning! This email originated from outside of PSB. Do not click links or open attachments unless you recognize the sender and know the content is safe. -------------------------------------- If you'd like to do Machine Learning research for Multimodal Data Integration in collaboration with Queen Mary University of London <https://www.linkedin.com/company/queen-mary-university-of-london/> and AstraZeneca <https://www.linkedin.com/company/astrazeneca/> this is your opportunity. You will integrate transcriptomics, proteomics and cell painting to characterise cells affected by genetic or chemical perturbations, and you will work at the AstraZeneca's offices in Cambridge, UK. Apply by the 8th Dec 2024! https://qmul-jobs.tal.net/vx/mobile-0/appcentre-ext/brand-4/candidate/so/pm…

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We are hiring 2 Researchers & 3 PhD Students! - ALSER Lab
by BeNeLux bioinformaticians forum 23 Nov '24

23 Nov '24

Warning! This email originated from outside of PSB. Do not click links or open attachments unless you recognize the sender and know the content is safe. -------------------------------------- Warning! This email originated from outside of PSB. Do not click links or open attachments unless you recognize the sender and know the content is safe. -------------------------------------- ALSER Lab is seeking outstanding, highly-motivated 2 Researchers (preferably Postdocs) and 1-3 PhD students from all over the world to join the team at Georgia State University. ALSER Lab is a research lab led by Mohammed Alser <https://alserlab.github.io/people/index.html> and is located in the beautiful city of Atlanta, Georgia. ALSER Lab is part of the Department of Computer Science <https://csds.gsu.edu/>, College of Arts and Sciences, Georgia State University, USA. The university is ranked as the top public university <https://www.usnews.com/best-colleges/rankings/national-universities/undergr…> for undergraduate teaching and 3rd most innovative public university <https://www.usnews.com/best-colleges/rankings/national-universities/innovat…> in the USA in 2025. The successful candidates will engage in cutting-edge research on building and accelerating bioinformatics analyses for modern omics data (e.g., sequencing, metagenomics, genomics, and pangenomics data). A typical day at ALSER Lab involves building intelligent hardware architectures and developing optimized algorithms and efficient software tools. More details are on: alserlab.github.io/research <https://alserlab.github.io/research/index.html>. We offer a competitive salary based on the candidate’s background and experience. We offer opportunities for professional growth, international collaboration, and sponsored participation in conferences. The Researcher position is a joint position with a supercomputer center in Spain, with an initial appointment of 1 year. The successful Researcher candidate will spend some time in the USA and Spain, but ALSER Lab will be the main mentor. Requirements for Researcher application: - Solid expertise in hardware acceleration, efficient software implementation, or AI-driven bioinformatics is a must. - PhD or MSc in a related field is a plus (but not required). Requirements for PhD Student application: - Strong skills in C, C++, Rust, or Python are a plus. - Understanding biology, bioinformatics, or omics data is a plus (but not required). - Proficiency in CUDA programming, hardware description languages (Verilog, VHDL), or processing-in-memory is a plus. - Expertise in developing efficient data structures and combinatorial algorithms (dynamic programming, greedy algorithms, approximation algorithms, graph theory) is a plus. - Requirements for application to PhD at Georgia State University must be fulfilled: <https://cas.gsu.edu/program/computer-science-phd/> - A BSc or MSc degree in computer science or its equivalent. - Minimum GPA 3.0/4.0. Application Deadline: Open until filled. Review of applications will begin ASAP. Application Submission: Use this simple form <https://forms.gle/Uvc4BmrpZFLmeo5T6>.

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Microbiome Data Analysis Workshop in Hasselt, December 16 and 17
by BeNeLux bioinformaticians forum 19 Nov '24

19 Nov '24

Warning! This email originated from outside of PSB. Do not click links or open attachments unless you recognize the sender and know the content is safe. -------------------------------------- On *December 16 and 17*, Hasselt University will organise the second edition of the *Microbiome Data Analysis Workshop* (MDAW). We have a nice cast of lecturers/speakers (Ksenia Guseva, Laura Symul, Leo Lahti, Georg Zeller, Thies Gehrman, Stijn Wittouck, Ziv Shkedy and Olivier Thas). This workshop will be of interest to a broad range of profiles, ranging from PhD students, post-docs to experienced professionals who need to work with microbiome data. We target people with backgrounds in biology, biomedical sciences, engineering, environmental sciences, …, but also statisticians and data scientists with an interest in the challenges specific to the microbiome. The workshop is sponsored by the Doctoral School of Hasselt University (reduced registration fee for PhD students). On day 1 of the workshop you will learn about the basics: going from reads to OTU/ASV tables, exploring and visualizing microbiome data, and differential abundance analysis. These take the form of lectures, including hands-on sessions. The second day continues with more advanced and emerging topics, brought to you by top experts who will guide you through cutting-edge techniques to manage and interpret microbiome datasets. Whether you’re a beginner or looking to enhance your skills, this is your opportunity to learn from the best! More information can be found here: https://www.uhasselt.be/MDAW25

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