- BBClist - maillist.psb.ugent.be

PhD position in plant virus bioinformatics
by Kupczok, Anne 18 May '22

18 May '22

Dear colleagues, The Evolutionary (Meta-)genomics group in the Bioinformatics Group at Wageningen University invites applications for a bioinformatics PhD student in ‘Virus diversity and evolution in natural plant ecosystems’. You might share our view that wild plant communities might act as viral reservoirs that are also connected to agricultural plants. Since viruses can spill over from natural to agricultural systems, it is highly relevant to characterize virus diversity in wild plants. Plant virus genomes are highly diverse and evolve rapidly. To know which role plant viruses play in shaping natural plant communities, we must characterize their biodiversity and evolution. You might be familiar with the phenomenon that plant virus infections are often asymptomatic, i.e., they do not cause overt disease, and can even be beneficial for the host. Recently, plant virus research expanded from the study of individual virus-host systems into characterizing global diversity using metagenomics, i.e., sequencing the genetic content of environmental samples without the need for prior virus isolation. Metagenomics led to the surprising observation that virus infections are ubiquitous, that there is a high incidence of mixed infection, and that most plant viruses identified in crops also occur in wild plants. There is growing evidence that viruses can impact plant ecosystems, which calls for a reappraisal of the role of viruses in natural ecosystems and accentuates the need to understand virus genomes and their function and evolution. The aim of this project is to develop bioinformatics methods to analyze plant virus metagenome data that has been sampled from wild plants in the Netherlands. This (and potentially your) project will contribute to understanding plant virus diversity and evolution in natural Dutch ecosystems. You will contribute to developing bioinformatics methods to discover and reconstruct virus genomes from high-throughput plant virus sequencing data and to analyze ecological and evolutionary properties of these viruses. To this end, we aim to analyze the effect of host range and mixed infections on intra-host diversity and estimate how recombination and selection impact virus genome evolution. Beyond the scientific and potentially application merits, you will build a wide network for your future career both within and outside Wageningen University. The research is embedded within the chair group of Bioinformatics at Wageningen University which is led by Prof. Dick de Ridder (https://www.bioinformatics.nl/) You will be supervised by Dr. Anne Kupczok (https://annecmg.github.io/) The research will be carried out in close collaboration with Dr. Mark Zwart at the Netherlands Institute of Ecology (NIOO-KNAW) (https://nioo.knaw.nl/nl/employees/mark-zwart) The position is for four years and funded by the graduate school Experimental Plant Sciences (https://www.graduateschool-eps.info/) We ask • a successfully completed MSc degree in bioinformatics or a related field; • excellent background in high-throughput sequencing analysis and comparative genomics; • affinity with ecology, evolution, and population genomics; • interest in close collaborations with experimental biologists and ability to work effectively as a team member and to carry out individual research; • very good level of oral and written English. Please find all details and instructions how to apply here: https://www.wur.nl/en/vacancy/PhD-position-Virus-diversity-and-evolution-in… For enquiries regarding the position and research topic, please contact Anne Kupczok: anne.kupczok(a)wur.nl<mailto:anne.kupczok@wur.nl> -- Dr. Anne Kupczok Assistant Professor Bioinformatics, Department of Plant Sciences, Wageningen University

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REMINDER - Register now! - Invitation Big Data in Life Science Education Congress on 10 June
by ALST Events 17 May '22

17 May '22

[cid:image012.jpg@01D86A21.E36E6EC0]Full Program available and registration deadline extended! Join us at the “Big Data in Life Science Education” congress at Breda! Thanks to the development of modern technology, the field of life sciences is evolving into a data-intensive world! Big data and Artificial Intelligence is immersing into every aspects of life sciences. To revolutionize our education together with the work fields, Avans School of Life Science and Technologies and the lectorate ATLS strive to innovate using novel life science techniques. Together with the work fields, we co-create the next generation research technicians by equipping them with cutting-edge skills in big data and techniques. At this seminar, experts and students will share their experiences and views on why it is important to invest in the ‘dry-lab’ skills. Henceforward, we will make use of this information to tailor-make future proof researchers together with the work fields. [FULL PROGRAM] Time: 09:00-18:00; Date: 10th June, 2022; Location: Hogeschoollaan 1, Breda. [Theme 1 (09:30-10:45) : Data driven BioMedical research (chair Kees Rodenburg)] Keynote: HPLC/UPLC in ATLS (Jos Brouwers, Lector ATLS, Avans Hogeschool) Expert speech: Personalized drug discovery by using AI in protein modeling (Henk-Jan Joosten, Bio- Prodict BV) Student presentation: FairHeartGalaxy (Bsc student, Bob van Rijthoven, Utrecht UMC/Avans) [Theme 2 (11:15-12:30): Development of Data intensive Biotechnology (chair Miaomiao Zhou)] Keynote: Data science beyond algorithm development (YMke de Jong, Center of Excellence Data & AI, Philips BV) Expert speech: Big data, biology and food safety (Anand Gavai, Wageningen Food Safety Research) Student presentation: Semi-real time fermentation monitoring by RNA-seq (Bsc student, Edwin van de Kind, COEBBE/ATLS) [Theme 3 (13:30-14:45) : Big data in Microbiology (chair Eefje Schrauwen)] Keynote: Data analysis during the Sars-Cov-2 pandemic (Bas Oude Munnink, ErasmusMC) Expert speech: PlasmidSimilarity (Casper Jamin, Maastricht University medical center+) Student presentation: Microbiome detection in COPD patiënts (Bsc student, Tim Verschuren, Avans/ATLS) [15:15-16:45 Parallel sessions] Session 1: MinION hands-on trouble shooting with a life-demo (trouble shooting) (Eefje Schrauwen) Session 2: see it and teach it, Galaxy workshop (MiaoMiao Zhou) Session 3: Employers meet Educators: what it takes to produce aN e-LAB analyst (Kees Rodenburg) [16:45 -18:00 Poster presentation with a beer] Registration You can register for the Big Data in Life Science Education until the 7th of June via this link: [cid:image009.png@01D86A1F.726E6EC0]<https://forms.office.com/r/UJnCdFZVEE> Do you have questions or want more information? Please contact events.alst(a)avans.nl<mailto:events.alst@avans.nl> Please feel free to spread this invitation around. We look forward to meeting you at our Breda campus! [cid:image011.jpg@01D86A1F.726E6EC0]

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Edinburgh Genomics - PromethION 24 Launch Event, Tuesday 24th May
by TRAIN edgenomics-training 17 May '22

17 May '22

Dear All We would like to invite you to join us for our PromethION 24 Launch Event on Tuesday 24th May. This seminar will feature updates from Oxford Nanopore, Edinburgh Genomics and a number of local researchers using nanopore technology. This is a great opportunity for those of you using, or thinking about using, long-read sequencing to get an update on this exciting new ONT technology. We will be offering tech-clinic appointments between 13:30-16:30 PM (please contact Danielle.folkard(a)nanoporetech.com<mailto:Danielle.folkard@nanoporetech.com> to book a meeting). The full agenda can be found at the registration link below. Please note that this is a hybrid event that's free to attend, but registration is required. We hope to see some of you there! ------------------------------------------------------------------------- Edinburgh Genomics -PromethION 24 Launch Event –Hybrid TUESDAY 24TH MAY 09:30 AM – 16:30 PM Room 1.19, Murchison House, King’s Buildings Campus Registration Link: https://nanoporetech.com/edinburgh-genomics-seminar https://nanoporetech.zoom.us/j/83859846262?pwd=UnBUTTVZcWZiN09UWUNUK0RQb2cv…. -------------------------------------------------------------------------- Kind Regards Nathan Medd and the Edinburgh Genomics team. -- Training and Outreach Manager - Edinburgh Genomics ======================================================== 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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Vacature Training Project Manager @ DTL/ELIXIR-NL - help spread the word!
by Celia van Gelder 17 May '22

17 May '22

*Apologies, Dutch only* Heb je belangstelling voor en ervaring met het runnen van training en capacity building gerelateerde projecten, bij voorkeur in het life sciences domain? Kom dan het DTL/ELIXIR-NL team versterken als *Training Project Manager*! De vacature is hier https://www.linkedin.com/jobs/view/3050945929/ . Het is ook mogelijk om deze functie te combineren met een bestaande gedeeltelijke aanstelling bij een van de DTL partners. Wil je eerst meer weten stuur me dan even een berichtje! Groet Celia -- Dr. Celia W.G. van Gelder Training Programme Manager DTL/ELIXIR-NL/Health-RI tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl websites: https://www.dtls.nl/, https://www.health-ri.nl/, https://www.elixir-europe.org/platforms/training skype: celia.van.gelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht Postal address: Postbus 8500 | 3503 RM Utrecht While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours.

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Upcoming Elixir-BE/VIB Trainings
by Bruna Piereck Moura 17 May '22

17 May '22

[cid:image001.png@01D869E7.D9F036B0] [signature_2008044598] Stay tuned and don't miss the opportunity to improve your skills and discuss science! Dear, As soon as June you have the chance to join two different Face-to-Face training sessions! You can get started with GitHub<https://email.vibconferences.be/t/r-l-tythddtk-btktijrzd-r/> and its version control and collaborative advantages on the 17th June, and teste the reproducibility of some papers in the 2nd ReproHack<https://email.vibconferences.be/t/r-l-tythddtk-btktijrzd-y/> organized by Elixir BE and VIB in the 29th of June. Click in the links to have more information and join us for this two great sessions that will be happening right before summer. ________________________________ Introduction to Git & GitHub 17 June 2022 - Leuven This workshop will take you through the basic use of Git and GitHub. Git is a free and open source distributed version-control system designed to maintain code, track changes, recover old versions and collaborate with other developers. Subscription and info: https://training.vib.be/all-trainings/introduction-git-github-3 ________________________________ ReproHack - A hackaton on reproducible data analysis 29 June 2022 - Ghent At this hackaton we gather for the second ReproHack organized in Belgium. ReproHack is an acronym for Reproducibility Hackaton and encourages papers to be published with reproducible code and accessible data. Subscription and info: https://training.vib.be/all-trainings/reprohack-hackaton-reproducible-data-… Looking forward to see you there, VIB bioinformatics core and Elixir training coordinators. [cid:image001.png@01D869E7.D9F036B0][signature_2008044598]

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Invitation to the Flanders AI Forum 7 June Antwerp
by Alexander Botzki 17 May '22

17 May '22

Hi all, FYI – please not that this is a translation of the original invitation in Dutch. Getting started with Artificial Intelligence? INVITATION - Tuesday, June 7, 2022 Discover on Tuesday 7 June what Flanders has to offer in the field of data use and Artificial Intelligence. We not only introduce you to concrete cases, but also offer you the opportunity to ask specific questions about digitization and the applications of Artificial Intelligence and the use of data within your own organization. All the different stakeholders come together on the Flemish AI forum. They discuss with each other, share their experiences and propose new products and applications. The program looks like this: 09.15 – 10.00: Networking with exhibition visit and coffee 10.00 – 12.00: Deep Dive sessions (choose from 7 themes): - AI and ethics: not difficult - Impact of European regulations on AI in Belgium - Boost your business with AI. - Discover the possibilities when the business and research worlds join forces - About learning and motivating: AI for everyone (or not?) - State of the Art AI for Contextual anomaly detection - State-of-the-Art AI support in flexible production environments 12.00 – 14.00: Networking with trade fair visit and sandwich lunch 14.00 – 15.45: Plenary session 15.45 – 17.30: Networking with exhibition visit and reception PRACTICAL Location: BluePoint Antwerp - Filip Williotstraat 9, 2600 Antwerp Date: June 7, 2022 Timing: 09:15 – 17:30 Price: FREE Reserve your place now! Tickets and Info (http://www.flandersaiforum.be/) This is a joint initiative of Agoria, Voka, VLAIO, imec, the EWI Department and the Flemish AI research platform. Best regards, Alex Alexander Botzki – Head of VIB Bioinformatics Core, ELIXIR Belgium Training Coordinator VIB Bioinformatics Core Technologiepark-Zwijnaarde 75 9052 Zwijnaarde Belgium tel +32 9 224 9870 https://vib.be/labs/vib-bioinformatics-core/research | https://www.bits.vib.be | @vibbioinfocore [signature_1661023229]

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Positions ThieleLab
by Nap, Bram 16 May '22

16 May '22

Dear all, There are several open positions in the Molecular Systems Physiology Group – ThieleLab https://www.thielelab.eu/open-positions If there are any questions about the positions, don’t hesitate to contact us! Kind regards, Bram Nap, PhD student / Marie Skłodowska-Curie Early Stage Researcher APC Microbiome Ireland Ryan Institute National University of Ireland, Galway Molecular Systems Physiology Group School of Medicine Orbsen Building | Galway, Ireland thielelab.eu CONFIDENTIALITY. The content of this email (including any attachment(s)), is/are confidential and may be privileged and is intended for the addressee only. Any reader of this message who is not the intended recipient or the employee or agent responsible to deliver this email to the intended recipient, is notified that any dissemination, distribution or copying of this communication is prohibited. If you receive this communication in error, please notify us immediately and please also delete all copies from your computer system. Thank you for your co-operation.

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fully-funded PhD studentships at Imperial College London
by Pedro Ballester 14 May '22

14 May '22

Dear all, I am inviting applications for two fully-funded PhD studentships for my new group in the UK: https://www.findaphd.com/phds/project/phd-studentship-in-artificial-intellig ence-for-phenotypic-virtual-screening/?p144453 https://www.findaphd.com/phds/project/phd-studentship-in-artificial-intellig ence-for-precision-oncology/?p144455 Best, Pedro

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advanced bachelor programme bioinformatics in Bruges (Belgium) (60 ECTS)
by Demeyere Mieke 10 May '22

10 May '22

Please forward to anyone who might be interested in a specialization in bioinformatics Dear Madam/Sir HOWEST University of Applied Sciences starts again in September 2022 with a remote bioinformatics study programme! Advanced Bachelor of Bioinformatics ... a small summary. Why? Bioinformatics is an emerging field, mastering these skills is a clear added value in the work field. Aim? Teaching dry-lab skills to people with a molecular biological background in order to function as a fully trained bioinformatician. Content? · Working with databases (build them, retrieve, access, store and share data in it) · High throughput analysis (working on pipeline, data analysis in R) · Construction of a bioinformatics tool (using php for web application, writing python scripts) · Other: comparative genomics analysis, machine learning, structural bioinformatics ... For more detailed information please access: https://www.bio-informatica.be/programme.pdf For Who? Everyone who holds a degree of higher education with sufficient knowledge of molecular biology on (at least) a bachelor level (e.g. Bachelor biomedical laboratory science, bachelor biochemistry, bachelor biotechnology ...); also relevant Master and PhD degrees are eligible. Duration? One year in daytime education in Bruges, Belgium. Two years via distance learning (starts in September 2022). Want more information? Contact us: Bit(a)howest.be<mailto:Bit@howest.be>, visit our website<https://www.howest.be/en/programmes/advanced-bachelor/bioinformatics> or watch our video<https://www.youtube.com/watch?v=THTK1S-LH34> or presentation in attachment. With kind regards Mieke Demeyere Opleidingscoördinator Biomedische Laboratoriumtechnologie/Programme coordinator Advanced Bachelor of Bioinformatics [cid:image006.png@01D86132.469E53F0] Howest University of Applied Sciences Campus Brugge Station Rijselstraat 5 - 8200 Brugge Tel.: +32 50 38 12 77 Fax: +32 50 38 11 71 www.howest.be/blt<http://www.howest.be/blt> en https://www.howest.be/nl/opleidingen/banaba/bio-informatica Bekijk onze navormingen en opleidingen via deze link<https://www.howest.be/nl/opleidingen/navormingen/biomedische-laboratoriumte…>. Denk aan het milieu vooraleer je dit bericht of de bijlagen uitprint!

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FW: OPen position for bio informatician at the HIC Cure Research Center
by Tim De Meyer 10 May '22

10 May '22

We have a unique postdoc position for our RID-HIV research program (RID-HIV) The RID-HIV Collaboratory “Reversing Immune Dysfunction for HIV-1 Eradication” is part of the Martin Delaney Collaboratories for HIV Cure Research, the flagship NIH program on HIV cure research. The perspective postdoc fellow will work closely with other lab members and our collaborators to develop software tools and perform single-cell multiomics and transcriptomics analyses of to generate new insights on the HIV viral reservoir at the single-cell resolution. More information: http://hivontrafelen.be/wp-content/uploads/2022/04/Postdoctoral-Fellow-posi…<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fhivontrafe…> Postdoctoral fellow position at the HIV Cure Research Center (www.HCRC.be)<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fhivontrafe…> What can we offer you - 3 year contract (first term) - Participate in an exciting and rapidly evolving new research area within a multidisciplinary environment hivontrafelen.be  Apply online through the e-recruitment system before the application deadline https://career012.successfactors.eu/career?company=C0000956575P&career_job_…<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcareer012…> Many thanks in advance, Linos Met vriendelijke groeten / Best Regards, PROF. DR. LINOS VANDEKERCKHOVE Arts-specialist Department of Internal Medicine | HIV Cure Research Center | MRBII Building Universitair Ziekenhuis Gent | C. Heymanslaan 10 | 9000 Gent T +32 9 332 33 98 | T +32 9 332 94 25 (Secretariaat) linos.vandekerckhove(a)uzgent.be<mailto:linos.vandekerckhove@uzgent.be> Ingang 38 | uzgent.be<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.uzgent…>

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