- BBClist - maillist.psb.ugent.be

Datamanager position (vacancy in dutch)
by Hanneke van Deutekom 14 Jul '22

14 Jul '22

Hi all, The UMCU has a datamanager position available! See link (vacancy in dutch) Hou jij van data en wil je graag de diagnostiek helpen verbeteren? https://werkenbijumcutrecht.nl/vacatures/it/datamanager-upod-2022-2297 kind regards Hanneke van Deutekom

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Vacancy PhD student bioinformatics (genomics/new technologies) @Sciensano
by Kevin Vanneste 13 Jul '22

13 Jul '22

Dear all, The Bioinformatics Platform at the Belgian Institute of Health (www.sciensano.be<http://www.sciensano.be>) currently has a vacancy for a PhD student bioinformatics to work in the field of genomics and new technologies. A profile description has been added in attachment. More info and applications are available on our job site: https://jobs.sciensano.be/content/jobpage.asp?a=DETAIL&jdkid=974&l=DUTCH Sincerely, K Kevin Vanneste, PhD Senior scientist - Responsible Bioinformatics Platform Transversal activities in Applied Genomics (TAG) T + 32 2 642 50 65 [cid:image001.jpg@01D4595B.6D6E05D0] Rue Juliette Wytsmanstraat 14 * 1050 Brussels www.sciensano.be<http://www.sciensano.be/> P Please consider the environment before printing this e-mail

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BioSB course & event update - July 2022
by Celia van Gelder 13 Jul '22

13 Jul '22

Still some seats available! View this email in your browser <https://mailchi.mp/dtls/course-update-july2022?e=6c7bbf5973> <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> Course: Machine Learning 26-30 September, Amsterdam Course overview In this one-week course, the foundations of machine learning will be laid out and commonly used methods for unsupervised (clustering, dimensionality reduction, visualization) and supervised (mainly classification) learning will be explained in detail. Methods will be illustrated using recent examples from the fields of systems biology and bioinformatics. Methods discussed in the morning lectures will be put into practice during the afternoon computer lab sessions. You can find more information here <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…>. 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 basic statistics and linear algebra is assumed. Preparation material on statistics and linear algebra will be distributed before the course, to be studied by students missing the required background. *We still have some seats available, register now!* Register now <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> Course: Single-cell Analysis 10-14 October 2022, Leiden Course overview The course features a mix of lectures and practicals, and you will have the opportunity to perform hands-on analysis of scRNA-seq data in R. Topics to be covered in the course include (but not limited to): an overview of different single cell platforms, experimental design, preprocessing of scRNA-seq data, normalization, dimensionality reduction, clustering, batch correction, differential expression, trajectory inference. The fifth day of the course will be a mini-symposium featuring guest lectures from scientists using various single-cell techniques in their research. You can find more information here <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> . Target audience This course is aimed at both wet-lab researchers interested in learning how to analyze their own single-cell data sets, as well as bioinformaticians who are new to single-cell sequencing analysis. Basic knowledge of the programming language R is a prerequisite for participation in the course. Registration A first selection will be made among the registrations by September 1st. We will inform you a.s.a.p. if you are selected for the course. If you are selected for the course, you will receive a link for final registration and payment for the course. Register now <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> Course: Algorithms for genomics 10-14 October 2022, Delft Course overview Comparative genomics aims to compare large sets of genomes in order to understand and explain differences in traits of an organism. Contemporary methods are powered by fundamental algorithms and data structures, which are efficient and scale to large data sets. A thorough understanding of these algorithms and data structures is necessary for advanced users and developers in this area. In addition, understanding how comparative genomics is developing is important to shape your own research. In this course, we will cover genome analysis, variant analysis, and pangenomics. Core concepts, applications, and future trends will be discussed, with a focus on the algorithms and data structures underlying state-of-the-art methods. The course offers an engaging mix of lectures, paper discussions, hands-on tutorials, and a do-it-yourself project. You can find more information here <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> . Target audience The course is aimed at PhD students with a background in bioinformatics, computer science or a related field. Participants are expected to have experience in command-line usage (Unix shell) and programming (Python), and have basic knowledge of genomics. Register now <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> More upcoming BioSB courses - Integrated modeling and optimization (Fundamental), December 2022 BioSB course portfolio The courses are part of the BioSB Education programme of the Netherlands Bioinformatics and Systems Biology research school, which offers training and education in bioinformatics and systems biology. Find our course portfolio here <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> . <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> [image: Twitter] <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> [image: Facebook] <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> [image: Website] <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> *Copyright © 2022 Citing us where appropriate.* update your preferences <https://dtls.us3.list-manage.com/profile?u=3cef2d6f6da8f8059e2288298&id=d62…> - unsubscribe from this list <https://dtls.us3.list-manage.com/unsubscribe?u=3cef2d6f6da8f8059e2288298&id…> - DTL privacy statement <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> -- 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 twitter: celia_vgelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL 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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2 open positions in colorectal cancer bioinformatics
by Sara Verbandt 12 Jul '22

12 Jul '22

Dear all, The group of Prof Sabine Tejpar (KULeuven) is looking for 2 expert bioinformaticians to strengthen their team. The group performs deep characterization of colorectal polyps, tumors and metastases to understand tumor development and immune evasion to find novel biomarkers and design better therapies. The team exploits state of the art single cell (transcriptomics, genomics, methylation) and spatial (multiplex immune fluorescence, spatial transcriptomics analyses) to deeply mine the immune environment. These data are mined to define genomic, transcriptomic changes during tumor evolution and how these define the regional tumor environment. Selected candidates will have early access to clinical data and will become part of a large international network of single cell and imaging analysts. https://www.kuleuven.be/personeel/jobsite/jobs/60137752 https://www.kuleuven.be/personeel/jobsite/jobs/60137756 We would be very happy to have highly enthusiastic people join our team Kind regards Sara ------------------------------------------ Sara Verbandt, PhD Postdoctoral researcher Molecular digestive oncology KU Leuven UZ Herestraat 49 - box 818 B-3000 Leuven Tel. +32 16 37 76 75<tel:+32%2016%2037%2076%2075>

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positions available at NBIS in Sweden
by Lieven Sterck 04 Jul '22

04 Jul '22

Dear all, NBIS (National Bioinformatics Infrastructure Sweden) now has three bioinformatician positions available, all with application deadline August 15 . All three positions are permanent, all placed at Uppsala University in Sweden. NBIS is built up of 120 highly talented bioinformaticians, system developers, and data stewards, all working to support Swedish researchers. We also have a strong international component with a lot of collaboration in European projects, not the least through ELIXIR where NBIS also constitutes the Swedish node (ELIXIR-SE) . We are now in an expansive phase and need to strengthen our support teams. NBIS is a great place to learn and grow as a bioinformatician, with hundreds of exciting projects every year and a lot of support available from highly talented colleagues, and we are now hoping to add even more talent to our teams! 1-2 positions focus on genome assembly, in Swedish projects or in international projects in the European Reference Genome Atlas (ERGA) consortium. 1 position focuses on evolutionary and comparative genomic analyses on large genomes. Please note that these are not post doc positions, they are permanent staff scientist positions with the main responsibility to support research or infrastructure projects. Please see below for more information and how to apply. Note that we do not accept applications via email, please use the links provided in the webpages linked below: 1-2 positions in genome assembly: [ https://www.uu.se/en/about-uu/join-us/details/?positionId=518948 | https://www.uu.se/en/about-uu/join-us/details/?positionId=518948 ] 1 position in evolutionary genomics: [ https://www.uu.se/en/about-uu/join-us/details/?positionId=518909 | https://www.uu.se/en/about-uu/join-us/details/?positionId=518909 ] Please see contact details in the advertisements if you have any questions about the positions. Kind regards, Henrik ———————— Henrik Lantz Support manager, NBIS Uppsala, Sweden Lieven Sterck - Senior Scientist Bioinformatics VIB-UGent Center for Plant Systems Biology Ghent University Technologiepark-Zwijnaarde 71 - 9052 Ghent - Belgium Tel. +32(0)9 331 38 21 [ http://bioinformatics.psb.ugent.be/ | http://bioinformatics.psb.ugent.be ] "Facts are meaningless. You could use facts to prove anything that's even remotely true" - H. Simpson

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Two positions in Bioinformatics in Sedlazeck Lab
by sina-gmail 01 Jul '22

01 Jul '22

Dear all, We would like to inform you about two positions that are available in the Sedlazeck Lab (https://fritzsedlazeck.github.io/ <https://fritzsedlazeck.github.io/>) based in Human Genome Sequencing Center, Baylor College of Medicine, US. Postdoctoral Associate- Bioinformatics https://jobs.bcm.edu/job/Houston-Postdoctoral-Associate-Texa/901990400 <https://jobs.bcm.edu/job/Houston-Postdoctoral-Associate-Texa/901990400> Staff Scientist - Bioinformatician https://jobs.bcm.edu/job/Houston-Staff-Scientist-Bioinformatician-Texa/9014… <https://jobs.bcm.edu/job/Houston-Staff-Scientist-Bioinformatician-Texa/9014…> Best regards, Sina Majidian.

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ELIXIR Train the Trainer course at EMBL Heidelberg - 19-22nd of July
by Alexander Botzki 30 Jun '22

30 Jun '22

Hi all, -- FYI - on behalve of the organizers -- The Bio-IT<https://bio-it.embl.de/> project at EMBL<https://www.embl.org/>, in collaboration with de.NBI<https://www.denbi.de/>, is going to host an ELIXIR Train the Trainer in July. 📅 Course dates: 19th - 22nd July 🕛 Time: from 13:30 to 17:00 CEST ❓ ELIXIR Train the Trainer<https://elixir-europe.org/platforms/training/train-the-trainer> 🎫 Registration and more info: bio-it.embl.de/events/elixir-train-the-trainer<https://bio-it.embl.de/events/elixir-train-the-trainer/> Feel free to forward this information to your networks via email or retweet our event announcement: twitter.com/EMBL_BioIT/status/1541747996404097025<https://twitter.com/EMBL_BioIT/status/1541747996404097025>. Thank you! Best, Lisanna -- ___________________________________________________ Lisanna Paladin, PhD - Bio-IT<https://bio-it.embl.de/> member Bioinformatics Community Project Manager, EMBL Heidelberg<https://www.embl.org/sites/heidelberg/> email: lisanna.paladin(a)gmail.com<mailto:lisannapaladin@gmail.com>, lisanna.paladin(a)embl.de<mailto:lisanna.paladin@embl.de> ___________________________________________________

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Diatom research PhD position available in Ghent University
by Michiel Van Bel 27 Jun '22

27 Jun '22

Dear all, we would like to advertise the following PhD position: [ https://www.ugent.be/en/work/scientific/phd-student-27 | https://www.ugent.be/en/work/scientific/phd-student-27 ] 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

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Wanted: Bioinformatics Lab Manager (MSc or PhD)
by Bas E. Dutilh 22 Jun '22

22 Jun '22

Dear colleagues, I recently moved to the Cluster of Excellence “Balance of the Microverse” at the Friedrich Schiller University in Jena where I founded the Viral Ecology and Omics group (VEO). We focus on metagenomics and microbiome modelling with a particular focus on the role of viruses and bacteriophages. *We are now looking for a Bioinformatics Lab Manager to support the dry lab activities of the VEO group.* For more details, please email me. Check the link for further details including an application link: https://jobs.uni-jena.de/jobposting/ad8e538b469960841c8634247e83601c9546766… Best regards, Bas Your responsibilities: Install, update, and maintain the group’s software, create patches, raise issues if needed. Maintain databases on our system, manage/update database download scripts (see for example https://github.com/MGXlab/cirtap) Advise and help group members, including those with little experience. Create and maintain pipelines for often-used computational tasks. Establish and maintain best practices and dry lab rules, provide documentation, instruct students who use our computers in these best practices. Contribute to course development (see for example https://github.com/MGXlab/Viromics-Workshop-MGX) Collaborate productively with experimental and computational researchers. Your profile: - A MSc or PhD degree in bioinformatics with a focus on (meta-) genomics. Experience with bacteriophages is beneficial. - Experience with Linux, Bash, Python, R, Git, Snakemake, Conda, Slurm. - Experience with database maintenance and/or data stewardship is beneficial. - Experience with hardware (computers, HPC) is beneficial. - Enthusiasm and talent for working on interdisciplinary projects. - Excellent communication skills, ability to work in a team and to interact with people from diverse nationalities and scientific backgrounds. - You have a sense of responsibility, organisational skills, and ability to contribute to a friendly and collaborative academic working environment. - Languages: English and German. We offer: - Embedding in the VEO/MGX groups, a highly collaborative and energetic team of international scientists in viral ecology and metagenomics. - A comprehensive continuing education programme for personal development, individual qualification and development measures. - Jena – City of Science is a lovely and lively town with a vibrant local cultural agenda. Jena is among the most liveable cities in Germany. Situated on the Saale River and surrounded by the famous Thuringian Forest, this city is ideal for lovers of nature and hiking. - A family-friendly working environment with a variety of offers for families: University Family Office ‘JUniFamilie’ and flexible childcare options (‘JUniKinder’ program). - FSU’s occupational health promotion scheme ( https://www.uni-jena.de/en/Gesundheit) and a wide range of university sports activities. - Attractive fringe benefits, e.g. capital formation benefits (VL), Job Ticket (benefits for public transport), and an occupational pension (VBL). - Remuneration based on the provisions of the Collective Agreement for the Public Sector of the Federal States (TV-L) up to salary scale E 13 (depending on the candidate’s personal qualifications) including a special annual payment in accordance with the collective agreement. -- 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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MSCA INSPIRE Fellowship
by Claesson, Marcus 18 Jun '22

18 Jun '22

Hi all, Are you interested in a prestigious INSPIRE <https://www.ucc.ie/en/inspire/apply/> Fellowship, which is a Horizon 2020 Marie Sklodowska-Curie cofunded postdoctoral fellowship programme? The first call will open on the 30th of June and the project will be based in APC Microbiome Ireland, Cork, one of the world's leading microbiome institutes. The successful applicant would carry out bioinformatics-based research on the role of the microbiome in paediatric Crohn's disease under my supervision and in collaboration with Queen Mary University London. Please contact me for details at your earliest convenience. Feel free to circulate this to anyone you might be interested. Regards, Marcus J. Claesson, PhD Associate Professor of Bioinformatics School of Microbiology & APC Microbiome Ireland University College Cork Western Road, Cork, Ireland Tel: +353-(0)21-4901390 Email: m.claesson(a)ucc.ie<mailto:m.claesson@ucc.ie> http://orcid.org/0000-0002-5712-0623

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