May 2022 - 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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Job offer in Artificial Intelligence / Bioinformatics at Dummen Orange
by Antonio Garcia-Uceda Juarez 31 May '22

31 May '22

Dear all, The job offer is available on: https://emea.dummenorange.com/site/nl/vacatures/detail?job=research-assista… We are looking for a bioinformatician or computer engineer (with MSc level) to join our team on building image analysis technologies to support plant breeding. Best, Antonio

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Postdoc Metabolomics Data Mining
by Bas E. Dutilh 30 May '22

30 May '22

Dear all, We're looking forward to including a metabolomics expert into our team of microbiome/virome enthusiasts! Attached please find attached a call for a* Postdoctoral Fellow "Metabolomics Data Mining" *in the new Viral Ecology and Omics Group at the Microverse Cluster in Jena. Please forward to any suitable candidates and consider retweeting: https://twitter.com/BEDutilh/status/1528728844244590592 Best regards, Bas -- Prof. Dr. Bas E. Dutilh <http://tbb.bio.uu.nl/dutilh> Viral Ecology and Omics Group | Metagenomics Group Microverse Cluster <https://microverse-cluster.de/en/> | Theoretical Biology and Bioinformatics <https://tbb.bio.uu.nl/> European Virus Bioinformatics Centre <http://evbc.uni-jena.de/> | Utrecht Bioinformatics Center <https://ubc.uu.nl/> Friedrich Schiller University Jena <https://www.uni-jena.de/en/> | Utrecht University <https://www.uu.nl/>

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Job offer at the Interuniversity Institute of Bioinformatics in brussels
by Tom Lenaerts 21 May '22

21 May '22

The job offer is available on : job offer: https://www.euraxess.be/jobs/697360 <https://www.euraxess.be/jobs/697360> We are looking for a bioinformatician (postdoctoral level) to join our team on identifying the oligogenic nature of rare diseases. Please spread the word. Tom

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Two PostDoc and one PhD position in Luebeck (apply by June 1st)
by Kircher, Martin 21 May '22

21 May '22

Hi everyone, we (kircherlab.github.io) have two bioinformatics positions available (PostDocs and PhD; https://tinyurl.com/igvfHLpostDoc and https://tinyurl.com/igvfHLphd) linked to the NHGRI Impact of Genomic Variation on Function (IGVF) Consortium (https://igvf.org/) We have another bioinformatics PostDoc opening (https://tinyurl.com/HLpostDoc) for supporting various projects in the lab as well as training/teaching efforts. Application deadline for all positions is *June 1st* and all positions will be located at the University of Lübeck, Germany (less than hour away from Hamburg). Research in our lab covers functional genomics, variant effects, machine/deep learning, data analysis and sequence analysis in human genetic and translational applications. Please find more details with the provided links. I hope you can share these job posts in your networks. Thank you so much! Martin ___________________________ Prof. Dr. Martin Kircher Professor of Regulatory Genomics Institute of Human Genetics, Campus Lübeck University Hospital Schleswig-Holstein (UKSH) Group Leader Computational Genome Biology Berlin Institute of Health @ Charité

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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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