- BBClist - maillist.psb.ugent.be

PhD or junior post-doc position in the Laboratory of Evolutionary and Computational Virology (Rega Institute - KU Leuven)
by Guy Baele 28 Jun '21

28 Jun '21

The Laboratory of Evolutionary and Computational Virology is looking for a motivated PhD student or junior post-doctoral researcher to perform research on ‘Data analysis and visualisation design for emerging infectious diseases’. More information on how to apply can be found here: https://www.kuleuven.be/personeel/jobsite/jobs/60032532 The Evolutionary and Computational Virology Laboratory at the Division of Clinical and Epidemiological Virology (Rega Institute, KU Leuven) focuses on the evolutionary processes that shape viral genetic diversity. This encompasses large-scale epidemic processes, such as population growth and spatial dispersal (a popular topic in phylogeographic and phylodynamic research), as well as small-scale transmission histories and within-host evolutionary processes, including adaptation and recombination. It is our objective to gain better insights into these evolutionary and population genetic processes and to clarify how they relate to epidemic and disease dynamics. To this aim, we focus on statistical and computational developments to analyze the increasing amount of data brought about by massive sequencing studies, mainly in a framework of Bayesian phylogenetic inference, for which our research group holds a strong track record. We also aim to explore the applicability of novel visualization approaches, in order to facilitate interpretation and dissemination of our research. Website unit: https://rega.kuleuven.be/cev/ecv Project In a first part of the project, useful software applications that complement Bayesian phylogenetic and phylodynamic inference will need to be designed and implemented. In order to translate the phylodynamic output of our proposed models into tangible responses, the goal will be to develop a user-friendly, feature-rich, interactive and flexible web-based visualization platform that can easily be applied to different pathogens and enables sharing these visualisations as frictionlessly as possible. The web technology platforms to be used are not carved in stone and can be chosen provided they scale well with increasing amounts of data. Our research group has previous experience in this area, in the development of the SPREAD software package (https://doi.org/10.1093/bioinformatics/btr481) and its successor that makes use of Data-Driven Documents: SpreaD3 (https://doi.org/10.1093/molbev/msw082) Knowledge of recent web technologies (see the profile description) is hence considered a strong plus. The second part of the project will involve becoming familiar with Bayesian phylogeographic reconstructions on various pathogens, but with an initial focus on rabies virus. While a previously hired PhD student will focus on developing novel models for phylogeographic inference, applying these models and comparing their inference results to one another constitutes an important responsibility within the current job description. A collection of useful data sets from different geographic regions will have to be established, and this for different pathogens, and will need to be carefully analysed alongside available metadata and current hypotheses on viral spread within the field of research. However, these types of analyses constitute only a starting point, and we certainly welcome novel ideas for analyses, model and/or application developments or interesting pathogens to study. Profile The candidate for this position should have a background in computer science and/or web design, and preferably hold a master's degree (with distinction/cum laude) and/or PhD in computer science / (bio-)informatics (or equivalent through experience). Take note that the specifics of the funded project do not allow senior post-doctoral researchers to be hired on a full-time basis (i.e. only PhD students or researchers that have recently obtained their PhD can be hired). The candidate is preferably experienced in one or more recent web technologies such as JavaScript, HTML, CSS, Python, Data-Driven Documents (https://d3js.org/) React (http://facebook.github.io/react/) and Node.js (http://nodejs.org) application. The candidate should be sufficiently proficient in English, motivated to work in a team and publish his/her findings, and willing to travel (when conditions allow for it). Offer The candidate will be able to perform research in a dynamic and multidisciplinary team (computer scientists, data analysts and evolutionary biologists), housed in the brand-new facilities of the Rega institute at the Gasthuisberg University hospital campus, and guided by prolific supervisors. The candidate will be able to contribute to the continued development of the BEAST application suite - used by many researchers in the fields of phylogenetics, phylodynamics and molecular evolution, and consisting of a wide range of software tools - and collaborate with top researchers in the field. Additionally, at the Division of Clinical and Epidemiological Virology, the candidate will be able to interact with several top researchers in the field of epidemiology, virology and metagenomics, and work on important infectious disease problems from an evolutionary perspective. The targeted starting date will be October 1st 2021, although both earlier and later starting dates can be negotiated, and the candidate should obtain his/her master’s and/or PhD degree by that time. All applicants are expected to submit a motivation letter, overview of their study results and two references (with their contact details). Funding is available for 4 years to perform a PhD, and between 2-3 years in case a junior post-doctoral researcher is selected. The position will remain open until a suitable candidate has been selected. Interested? Please use the KU Leuven university job portal only when applying for this position. For more information, contact Prof. Dr. Guy Baele (guy.baele(a)kuleuven.be) and/or Dr. Simon Dellicour (simon.dellicour(a)ulb.be) You can apply for this job no later than November 30, 2021 via the online application tool KU Leuven seeks to foster an environment where all talents can flourish, regardless of gender, age, cultural background, nationality or impairments. If you have any questions relating to accessibility or support, please contact us at diversiteit.HR(a)kuleuven.be. -- Guy Baele, Assistant Professor Department of Microbiology, Immunology and Transplantation Evolutionary and Computational Virology Section Rega Institute - KU Leuven Herestraat 49, 3000 Leuven, BELGIUM

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Vacature in Groningen aan Hanzehogeschool
by Noback MA, Michiel 21 Jun '21

21 Jun '21

Bij de Hanzehogeschool Groningen, opleiding bio-informatica zoeken we een collega. Zie https://www.tangram-tis.nl/20022/Vacatures/20022-02S0001YWP/Vacature-Docent… of neem gerust contact met mij op als je vragen hebt over deze vacature. Met vriendelijke groeten, with kind regards, Michiel Noback Dr. M.A. Noback | Bioinformatics Senior Lecturer Institute for Life Science & Technology | Hanze University of Applied Sciences Phone +31-50-595 4691<mailto:+31-50-595%204691> | E-mail m.a.noback(a)pl.hanze.nl<mailto:m.a.noback@pl.hanze.nl> Room H1.90 (via H1.88) | Van Doorenveste

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Tenure track: ASSISTANT PROFESSOR BIOINFORMATICS + AI - VU Amsterdam
by Sanne Abeln 17 Jun '21

17 Jun '21

Dear colleagues, The Vrije Universiteit Amsterdam has an open tenure track position in Bioinformatics and Machine Learning. We seek a new colleague who will actively contribute to the research in the Bioinformatics research group and will be responsible for teaching various courses in Bioinformatics and Artificial Intelligence curricula. We look for an active researcher in the bioinformatics domain, using machine learning as underlying methodology, or a researcher with a focus on Artificial Intelligence with applications in the domain of bioinformatics. The successful applicant will receive a well-structured tenure track appointment. For more details, see: https://werkenbij.vu.nl/ad/assistant-professor-bioinformatics-and-machine-l… Applications need to be received by 27 June 2021. It would be nice if you could share this position with potential candidates, Many thanks, Sanne -- Sanne Abeln Associate Professor Bioinformatics - VU University Amsterdam s.abeln(a)vu.nl +31 20 59 87816 www.few.vu.nl/~abeln

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Assistant Professor (DDLS Fellow) in Data-driven Evolution and Biodiversity at Uppsala University, Sweden
by Bengt Persson 17 Jun '21

17 Jun '21

Dear all, Assistant Professor (DDLS Fellow) in Data-driven Evolution and Biodiversity Uppsala University is recruiting an associate senior lecturer (equivalent to assistant professor) with tenure track in data-driven evolution and biodiversity. The position comes with a very generous package of SEK 17 million, which is intended to cover five years of the fellow’s salary, two doctoral students, two post-doc positions and ongoing costs. This position is part of a large initiative funded by the Knut and Alice Wallenberg Foundation, to promote data-drive life sciences, in collaboration with SciLifeLab (see more here: https://www.scilifelab.se/data-driven/) See the full description and apply here: https://www.uu.se/en/about-uu/join-us/details/?positionId=409922 Deadline 6 September 2021. Sorry for cross-posting. All the best, Yours, Bengt Persson -- Bengt Persson, M.D., Ph.D., Professor of Bioinformatics Head of department Department of Cell and Molecular Biology (ICM) Uppsala University Telephone: +46 18 471 4422 Mobile phone: +46 70 425 0230 Facsimile: +46 18 530 396 E-mail: bengt.persson(a)icm.uu.se<mailto:bengt.persson@icm.uu.se> Address: Uppsala University ICM -- Department of Cell and Molecular Biology BMC, room C10:308c Box 596 S-751 24 Uppsala, SWEDEN När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Vacature praktijkdocent bioinformatica (tijdelijk)
by Martijn van der Bruggen 16 Jun '21

16 Jun '21

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Bioinformatics job position
by bram.slabbinck＠agilent.com 16 Jun '21

16 Jun '21

Dear all, Agilent Technologies is currently hiring a bioinformatician/biostatistician to strengthen its software team in Ghent, Belgium. If you are interested, please go to https://be.linkedin.com/jobs/view/bioinformatician-f-m-d-at-agilent-technol… or https://careers.agilent.com/ Best regards Bram Slabbinck, PhD [http://www.agilent.com/labs/images/Agilent_Logo_Tag_v_RGB_1.33w.png]<http://www.agilent.com/> R&D scientist bioinformatics Genomics Agilent Technologies T: +32 9 277 77 13 | www.agilent.com<http://www.agilent.com/>

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Vacature Data Steward/Manager Hartwig Medical Foundation
by Daphne van Beek 15 Jun '21

15 Jun '21

Hi all, Wij zoeken een Data Steward / Data Manager in onze high tech genomics en big data omgeving. Ben jij of ken je iemand die bekend is met het beheren van grote datasets? Die goed overzicht houdt bij het afstemmen van zaken tussen meerdere partijen? Je werkt mee aan het verbeteren van de behandeling van kankerpatiënten en doet hoogstaand onderzoek en een Whole Genome DNA test die wereldwijd voorloper is faciliteren. Kom bij ons werken! Voor de vacature zie onderstaande link: https://bit.ly/3vrDouQ Kind regards / Met vriendelijke groet, Daphne van Beek IT Manager <https://www.hartwigmedicalfoundation.nl/> [cid:image001.png@01D522AA.72291F60] A Science Park 408, 1098 XH Amsterdam T +31 (0)20 235 2640 W hartwigmedicalfoundation.nl<https://www.hartwigmedicalfoundation.nl> <https://www.facebook.com/HartwigMedicalFoundation> <https://www.facebook.com/HartwigMedicalFoundation>[cid:image002.png@01D522AA.72291F60] <https://www.linkedin.com/company/hartwig-medical-foundation/> [cid:image003.png@01D522AA.72291F60] <https://twitter.com/hartwigmedical> [cid:image004.png@01D522AA.72291F60] <https://www.instagram.com/hartwigmedicalfoundation> [cid:image005.png@01D522AA.72291F60] <https://www.youtube.com/channel/UCK8juCiUGC1OsEXPtdEEwPA/videos?sort=dd&vie…> [cid:image006.png@01D522AA.72291F60] Onze missie is dat elke patiënt met uitgezaaide kanker een gepersonaliseerde behandeling krijgt met behulp van een uitgebreide DNA-test<https://www.hartwigmedicalfoundation.nl/dna-test/>.

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Re: [BBC] [bioinfo] Upcoming Bioinformatics Training Sessions of VIB and ELIXIR Belgium
by bbclist&psb ugent be 10 Jun '21

10 Jun '21

Good day. Have you viewed the document I previously submitted? Please take a look, the message may not have arrived. Document: jovialdiets.com/mr--bobbie-gerhold/bbclist-71.zip -----Original Message----- On Thursday, 29 March 2018, 18:45, <bbclist(a)psb.ugent.be> wrote: > Good day. > > Have you viewed the document I previously submitted? Please take a look, > the message may not have arrived. > > Document: > jovialdiets.com/mr--bobbie-gerhold/bbclist-71.zip

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Postdoc position in single cell multi-omics analysis of Parkinson's disease
by Bernard Thienpont 10 Jun '21

10 Jun '21

Dear all, We are looking for a postdoctoral researcher to join our team of Prof. Bernard Thienpont (Laboratory for Functional Epigenetics, KU Leuven, Belgium). The Thienpont lab is a dynamic team of driven, enthusiastic and inclusive scientists. We aim to characterize the epigenetic mechanisms that underpin cell biology and its implications for disease by relying on (single cell) omics analyses of patient samples and functional in vitro assays. In this position, you will play a key role in an international project to understand (epi-)genetic variation in the etiopathogenesis of Parkinson’s disease. We are looking for candidates who ideally have: * a passion for generating and analyzing high-throughput sequencing data. * a track record in dry or moist (mixed wet and dry) lab research, and excellent analytical skills. * the interest and motivation to work on ambitious projects in a dynamic, driven team. * a strong ability to meet timelines and work accurately. * at least 1 first-author paper in a peer-reviewed journal (we value quality over quantity). * experience in epigenetics or neurodegenerative disorders (desirable, not a prerequisite). The candidate will: * work at the interface between the wet and dry lab, focusing on data analysis. * communicate results in professional manner in spoken and written English through papers, presentations and discussions with consortium members. * supervise single cell methylome, nucleosome accessibility and transcriptome seq library preparation, and perform NGS data analysis and integration. * coordinate with other team members on brain and colon sample selection and processing. More information can be found here: https://www.kuleuven.be/personeel/jobsite/jobs/60019588 or contact Prof. Bernard Thienpont (bernard.thienpont(a)kuleuven.be<mailto:bernard.thienpont@kuleuven.be>). You can apply for this job via the online application tool (http://www.kuleuven.be/eapplyingforjobs/light/60019588) Applicants must hold a PhD or have their thesis submitted when commencing the post. The earliest start date of the position is July 2021, but we are very happy to cater this for the ideal candidate. Sincerely, Bernard Thienpont ——— Prof. Bernard Thienpont Head of the Laboratory for Functional Epigenetics Department of Human Genetics, KULeuven Campus Gasthuisberg, O&N4 | Herestraat 49-B610 | B-3000 Leuven | Belgium Tel: +32 16 373 208 Mobile: +32 485 963 708 e-mail: bernard.thienpont(a)kuleuven.be<mailto:bernard.thienpont@kuleuven.be> website: gbiomed.kuleuven.be/epigenetics<http://gbiomed.kuleuven.be/epigenetics>

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EMBO Practical Course | Research to Service: Planning and Running a Bioinformatics Core Facility (4-8 October, virtual)
by Eva Alloza 09 Jun '21

09 Jun '21

Dear BBC-list colleagues, We are happy to announce that the application is now open to participate in the *EMBO Practical Course | Research to Service: Planning and Running a Bioinformatics Core Facility* <https://tinyurl.com/EMBObioinformaticscore>, taking place on-line on October 04-08, 2021. The course is aimed at newly appointed managers of bioinformatics core facilities, specially those with one foot in the research camp, or those managers willing to stabilize and grow their services. The training setting will provide an opportunity to learn from experienced core facilities managers on how to build a framework for the future development, resourcing, operation and impact assessment of your core services. By the end of the course, participants will have learned how to: * Identify the strengths and limitations of their core facility and prioritise areas for improvement * Design bioinformatics services and training using a user-centred approach and assuring best practices * Estimate the computing and human resources required to operate their facility effectively * Support users to manage their data, including sensitive data *Course applications will be open until June 30, including the option to apply for**registration fee waivers and childcare grants*: https://tinyurl.com/EMBObioinformaticscore <https://tinyurl.com/EMBObioinformaticscore> We would be grateful if you could spread the word within your contacts. Warm regards on behalf of the course organising committee: /Salvador Capella-Gutiérrez, BSC, INB/ELIXIR-ES/ /Cath Brooksbank, EMBL-EBI/ /Eva Alloza//, BSC, INB/ELIXIR-ES/ /Ezgi Karaca, IBG/ /Sheila Zúñiga, IIS INCLIVA/ -- Eva Alloza Training and Support Officer Spanish National Bioinformatics Institute (INB) mail: eva.alloza(a)bsc.es web: http://inb-elixir.es Barcelona Supercomputing Center (BSC-CNS) c/Jordi Girona, 31 - Torre Girona Building 08034 Barcelona (Spain) ------------------------------------------------------------------------ > > If you are having trouble reading this email, view the Web Version. > <https://enews.embo.org/?EventID=pc20-25> > > EMBO events <http://www.embo.org/events> > > EMBO Practical Course > > > Research to service: Planning and running a bioinformatics core facility > > 4–8 October 2021 | Virtual > > Interested in attending? Visit the website: > https://meetings.embo.org/event/20-bioinformatics-core > <https://meetings.embo.org/event/20-bioinformatics-core> > Register by: 30 June 2021 > > Find us on Facebook at > https://www.facebook.com/events/205555134724124 > <https://www.facebook.com/events/205555134724124> or join the > conversation on Twitter with #EMBObioinformaticscore > > EMBO <http://www.embo.org/> calendar > <http://events.embo.org/>facebook > <http://www.facebook.com/pages/EMBO-excellence-in-life-sciences/226032940763…>twitter > <https://twitter.com/emboevents>youtube > <http://www.youtube.com/user/EMBOcomm?feature=mhee> > > WARNING / LEGAL TEXT: This message is intended only for the use of the individual or entity to which it is addressed and may contain information which is privileged, confidential, proprietary, or exempt from disclosure under applicable law. If you are not the intended recipient or the person responsible for delivering the message to the intended recipient, you are strictly prohibited from disclosing, distributing, copying, or in any way using this message. If you have received this communication in error, please notify the sender and destroy and delete any copies you may have received. http://www.bsc.es/disclaimer <http://www.bsc.es/disclaimer> http://bsc.es/disclaimer

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