September 2021 - BBClist - maillist.psb.ugent.be

Posting
by Christian WALTER 20 Sep '21

20 Sep '21

Hi, Please support us with posting of the following role: The University of Luxembourg aspires to be one of Europe's most highly regarded universities with a distinctly international and interdisciplinary character. It fosters the cross-fertilisation of research and teaching, is relevant to its country, is known worldwide for its research and teaching in targeted areas, and is establishing itself as an innovative model for contemporary European Higher Education. The University`s core asset is its well-connected world-class academic staff which will attract the most motivated, talented and creative students and young researchers who will learn to enjoy taking up challenges and develop into visionary thinkers able to shape society. Within the University, the Luxembourg Centre for Systems Biomedicine (LCSB) is a highly interdisciplinary research centre (IC), integrating experimental biology and computational biology approaches in order to develop the foundation of a future predictive, preventive and personalized medicine. Your Role... As a pioneer in its field, the LCSB develops many research and research-supporting applications in-house. Among these applications are tools to support data exchange and protection, as well as exciting visual data exploration and data analysis platforms. We are looking for a talented and enthusiastic new colleague, with or without background in data science, who can help us to design, develop, and maintain our ever-growing research infra-structure. * You will be part of a team which focuses on the development of a new state-of-the-art patient data exploration and visualization platform. * You will have opportunities to work on interesting new features using modern technological frameworks and tools. * As part of our team of experts you commit to a high quality standard by applying multiple testing technologies and industry best practices. * You have experience with most aspects of delivering production-level software. This begins with the collection and formulation of requirements and ends with the distribution, documentation, deployment, and maintenance of the finished product. * You have a good understanding of API and networking, which will help you navigate and connect with other applications in our service offering. What we expect from you... Essential Qualifications * A Un computer science or related fields. * Proven experience with Java 8 or higher. * Proven experience in Object Oriented Programming (OOP). * Proven experience with ORM systems such as Hibernate, or similar frameworks. * Experience with relational database systems. * Experience with git, or similar code versioning systems. Desirable Qualifications * Experience with web UI frameworks such as Angular, React, or Vue. * Experience with Linux service administration. * Experience with Elasticsearch. * Experience with Postgres. * Experience with Docker. What we offer... * Modern and bright office rooms. No cubicles or open space offices. * An environment in which continuous learning is actively encouraged and funded. * Modern and performant work equipment. * A large, diverse, and open-minded team of experts to rely on. * A real opportunity to create a positive impact on medical research and human betterment within a working environment. * An inflation-adjusted competitive salary according to personal work experience. * 32 days of annual leave and 40 hours of leave for personal reasons. * Compulsory social health insurance and private options at preferential rates. * Meal vouchers for use in restaurants and supermarkets. In Short... * Contract Type: Fixed Term Contract 24 Month (extension possible) * Work Hours: Full Time 40.0 Hours per Week * Location: Belval * Internal Title: Research and development specialist * Job Reference: UOL04127 How to apply... Applications (in English) should contain the following documents: * A detailed curriculum vitae (CV) * A cover letter describing previous project experience (if any) and future interests * A description of name and addresses of three referees if available We ensure a full consideration for applications received by the 15th of October 2021, however early submission is encouraged. Applications sent by e-mail will not be considered; please apply ONLINE. The University of Luxembourg embraces inclusion and diversity as key values. We are fully committed to removing any discriminatory barrier related to gender, and not only, in recruitment and career progression of our staff. In return you will get... * Multilingual and international character. Modern institution with a personal atmosphere. Staff coming from 90 countries. Member of the "University of the Greater Region" (UniGR). * A modern and dynamic university. High-quality equipment. Close ties to the business world and to the Luxembourg labour market. A unique urban site with excellent infrastructure. * A partner for society and industry. Cooperation with European institutions, innovative companies, the Financial Centre and with numerous non-academic partners such as ministries, local governments, associations, NGOs ... * Find out more about the University<https://wwwen.uni.lu/university/about_the_university> * Addresses, maps & routes to the various sites of the University<https://wwwen.uni.lu/contact> Further information... For further information, please contact: Dr. Venkata Satagopam (venkata.satagopam(a)uni.lu<mailto:venkata.satagopam@uni.lu>), Research Scientist, Bioinformatics Core Facility and Technical Coordinator of the ELIXIR-Luxembourg Node Online applications should be addressed to: Prof. Dr. Reinhard Schneider, Head of the Bioinformatics Core Facility and Head of the ELIXIR-Luxembourg Node Mit freundlichen Grüßen | Best regards [Image] Christian WALTER HR, Talent Acquisition Team Leader University of Luxembourg, CAMPUS BELVAL Maison du Savoir (Administration Tower) 2 Avenue de l'Université, L-4365 Esch-sur-Alzette T. +352 46 66 44-9471 | M. +352 621 398012 christian.walter(a)uni.lu<mailto:christian.walter@uni.lu> www.uni.lu<http://www.uni.lu/> A vibrant academic hub at the heart of Europe The University of Luxembourg aspires to be one of Europe`s most highly regarded universities with a distinctly international and interdisciplinary character. We are a great Place to Work. Connect with the University on: LinkedIn<https://www.linkedin.com/school/university-of-luxembourg/>, Job-Portal<http://recruitment.uni.lu/>, Facebook<https://www.facebook.com/uni.lu/>

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Postdoc position in ML for single-cell network inference, Ghent University
by Yvan Saeys 20 Sep '21

20 Sep '21

A postdoctoral position on machine learning for single-cell regulatory network inference is available at the Yvan Saeys lab at VIB/Ghent University, Belgium Application can be done online at: https://jobso.id/e47k About the lab The Data Mining and Modeling for Biomedicine group (headed by Yvan Saeys) at the VIB Center for Inflammation Research and Ghent University is located in the historical city of Ghent, Belgium. The Saeys lab is at the forefront of computational method development in single-cell omics, and has a longstanding collaboration with many wet labs in immunology, oncology and plant biology. Recently, the lab has started a single-cell facility with advance access to the newest single-cell multi-omics technologies (scRNA-seq, scATAC-seq, CITE-seq, and spatial proteomics and transcriptomics). A major focus of the lab is to model the dynamics of biological systems, and characterize their underlying gene regulatory networks. To this end, the lab develops new computational machine learning methods to improve the current state-of-the-art. Description The VIB-UGent Center for Inflammation Research (IRC) aims at unravelling the mechanisms of immunity and inflammation for better prevention and therapy of human chronic disease. Several high-end core facilities support and improve our research activities: microscopy, flow cytometry, transgenesis, cell culture, recombinant protein technology, single cell. For more information, please visit: https://www.irc.ugent.be The University of Ghent is a sustainable, family-friendly organization, which invests in its employees’ growth. We encourage diversity and attach great importance to an inclusive working environment and equal opportunities, regardless of gender identity, disability, race, ethnicity, religion or belief, sexual orientation or age. We encourage people from diverse backgrounds and with diverse characteristics to apply. The successful candidate will be responsible for developing novel methods (including trajectory inference and gene regulatory network inference) on single-cell omics data. The current position is part of a collaboration with BASF, a leading company in the plant biotechnology field, and the lab of Bert De Rybel at the VIB Center of Plant Systems Biology. The applicant should be highly motivated and passionate about driving and performing research and associated tasks and be able to work independently. The person will collaborate with PhD students and technicians to increase the impact of the research efforts. The position can be started from October 1 onwards. Profile • You obtained a PhD in Bioinformatics, Computer Science, Physics, Engineering, Bio-engineering, or equivalent. • Excellent track record in machine learning applied to the field of Bioinformatics • Solid programming experience is required (Python, R). • Experience with machine-learning/statistical analysis is required • Experience with plant research and/or population genetics is a plus. • Ability to work independently and in a team. We offer • Access to state-of-the-art compute infrastructure • A stimulating international research environment • Competitive salary and benefits • Financial support for 2 years. Starting date: as soon as possible How to apply? https://jobso.id/e47k Please complete the online application procedure and include a detailed CV, two reference letters, and a motivation letter. For more information: yvan.saeys(a)ugent.be -- =============================================================================== Prof. dr. Yvan Saeys VIB Group Leader Data mining and modeling for biomedicine UGent Department of Applied Mathematics, Computer Science and Statistics Krijgslaan 281, S9, B-9000 Gent Inflammation Research Center, a VIB-UGent Department Technologiepark-Zwijnaarde 71 , B-9052 Zwijnaarde , Belgium Tel : +32(0)9 331 37 40 Fax : +32(0)9 221 76 73 Mailto: yvan.saeys(a)ugent.be http://www.dambi.ugent.be ===============================================================================

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Fwd: Job: Software developer
by Klaas Vandepoele 18 Sep '21

18 Sep '21

Full job advertisement + how to apply? See [ https://career5.successfactors.eu/sfcareer/jobreqcareer?jobId=20584&company… | https://career5.successfactors.eu/sfcareer/jobreqcareer?jobId=20584&company… ] Job description The PLAZA platform for comparative, evolutionary, and functional genomics is a data resource that integrates gene and genome information. It offers a wide variety of tools to end-users through a web interface, in order to help speed up both small-scale and large-scale data analyses. Multiple independent instances of the platform exist, where each instance either focuses on a different phylogenetic clade/group of species, or uses improved gene annotations and genome assemblies compared to previous instances. To scale up the building of these instances, we are looking for a software developer to help with moving the PLAZA platform to cloud-based systems : * you assist in the building of new PLAZA instances in the cloud using real-world scenario's (e.g. different collaborators and research communities) * you help implementing quality checks on user-provided data and unit-tests to check the status and validity of newly build PLAZA instances * you implement configuration and administration utilities for other end-users, in order to allow those end-users to build PLAZA instances themselves * You will be integrated in a dynamic research group (Comparative Network Biology lab - http://bioinformatics.psb.ugent.be/cnb/) under the supervision of the primary developers of the PLAZA platform. Furthermore, you will have regular contacts with academic and industrial collaborators to explore novel technologies and boost new developments. Your profile * You have a degree in computer science, bioinformatics, (bio)engineering or equivalent * You are fluent in English * You have proficiency in at least one programming language (e.g. Java, Python, …) and one scripting language (e.g. Python, Perl, …) * You have hands-on experience with Linux/Unix environments and BASH scripting * You have a good working knowledge of relational databases and SQL * Knowledge of web development technologies (PHP, HTML, JavaScript, CSS), experience in virtualization technologies (e.g. Docker, Singularity)and experience in workflow technologies (e.g. Nextflow) are highly recommended skills * Experience in working with life-science data, experience with automated deployment tools (e.g. Puppet, Ansible, etc.) and version control experience (e.g. GIT) are desirable skills but not required Admission requirements You hold a Master’s degree or equivalent degree and you submit a transcript of your degree. For diplomas awarded outside the European Union, a certificate of equivalence (NARIC) must be submitted You apply online through the application tool by the application deadline and you submit all the required documents by the application deadline The admission requirements need to be fulfilled by the application deadline. What we offer We offer a contract of indefinite duration in function class A with a salary in accordance with the UGent salary scales 7.1 to 9.2, determined by your relevant experience at the level of the position. Remuneration (100% occupancy rate): min. € 21.278,78 – max. € 40.955,09; indexed gross monthly salary (at 174,10 %): min. € 3.087,20 – max. € 5.941,90. All Ghent University staff members enjoy a number of benefits, such as a wide range of training and education opportunities, 35 days of paid leave, bicycle commuting reimbursement, ecocheques, etc. A complete overview of all our fringe benefits (in Dutch). Selection procedure Our selection procedure consists of a cv-screening, an assessment (at Master’s level) and a selection interview with a selection committee. We will keep you informed of your application status. As Ghent University maintains an equal opportunities and diversity policy, everyone is encouraged to apply for this position. If you have a functional impairment, please let us know (selecties(a)ugent.be) so we can make the necessary adjustments. For more information regarding the selection procedure, please contact the Recruitment Office by emailing selecties(a)ugent.be. Please do not send your application by email, use the online application tool. For more information regarding the job description, please contact professor Klaas Vandepoele at +32 9 331 38 22 or Klaas.Vandepoele(a)psb.vib-ugent.be. Klaas Vandepoele - Professor Comparative Network Biology VIB-UGent Center for Plant Systems Biology Ghent University Technologiepark-Zwijnaarde 71 - 9052 Ghent - Belgium Tel. +32(0)9 331 38 22 [ http://www.psb.ugent.be/ | www.psb.ugent.be ] Genome editing, cutting-edge technology for a sustainable agriculture

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Job openings for a postdoc and bioinformatician in childhood cancer genomics
by Kemmeren-2, P.P.C. 17 Sep '21

17 Sep '21

Dear all, Currently within my lab, I have two great job opportunities! The first is a position for a postdoc in bioinformatics who can help us drive forward the Máxima pediatric cancer genome project. The second position for a data scientist/bioinformatician who can help us build a federated pediatric oncology cloud. The Princess Maxima Center is the largest nation-wide dedicated childhood cancer center in Europe and provides an exciting workplace. Within my group, we exploit cancer genomics data through a combination of bioinformatics and systems biology approaches with the goal of improving our understanding of childhood cancer initation and progression as well as improve patient care for children with cancer. Want to be part of this, then please apply using one of the links below. https://werkenbijprinsesmaximacentrum.nl/en/vacancy/postdoc-bioinformatics-… https://werkenbijprinsesmaximacentrum.nl/en/vacancy/data-scientist-bioinfor… Regards, Patrick -- Patrick Kemmeren, PhD Principal Investigator & head Big Data Core T +31 (0)88 972 90 00 | M +31 (0)6 53 11 25 53 [signature_976286354] Princess Máxima Center for Pediatric Oncology Heidelberglaan 25 | 3584 CS Utrecht | T +31 (0)88 972 90 00 | > Website<https://research.prinsesmaximacentrum.nl/en/research-groups/kemmeren-group>

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Postdoc position in ML for single-cell network inference, Ghent University
by Yvan Saeys 16 Sep '21

16 Sep '21

A postdoctoral position on machine learning for single-cell regulatory network inference is available at the Yvan Saeys lab at VIB/Ghent University, Belgium Application can be done online at: https://jobso.id/e47k About the lab The Data Mining and Modeling for Biomedicine group (headed by Yvan Saeys) at the VIB Center for Inflammation Research and Ghent University is located in the historical city of Ghent, Belgium. The Saeys lab is at the forefront of computational method development in single-cell omics, and has a longstanding collaboration with many wet labs in immunology, oncology and plant biology. Recently, the lab has started a single-cell facility with advance access to the newest single-cell multi-omics technologies (scRNA-seq, scATAC-seq, CITE-seq, and spatial proteomics and transcriptomics). A major focus of the lab is to model the dynamics of biological systems, and characterize their underlying gene regulatory networks. To this end, the lab develops new computational machine learning methods to improve the current state-of-the-art. Description The VIB-UGent Center for Inflammation Research (IRC) aims at unravelling the mechanisms of immunity and inflammation for better prevention and therapy of human chronic disease. Several high-end core facilities support and improve our research activities: microscopy, flow cytometry, transgenesis, cell culture, recombinant protein technology, single cell. For more information, please visit: https://www.irc.ugent.be The University of Ghent is a sustainable, family-friendly organization, which invests in its employees’ growth. We encourage diversity and attach great importance to an inclusive working environment and equal opportunities, regardless of gender identity, disability, race, ethnicity, religion or belief, sexual orientation or age. We encourage people from diverse backgrounds and with diverse characteristics to apply. The successful candidate will be responsible for developing novel methods (including trajectory inference and gene regulatory network inference) on single-cell omics data. The current position is part of a collaboration with BASF, a leading company in the plant biotechnology field, and the lab of Bert De Rybel at the VIB Center of Plant Systems Biology. The applicant should be highly motivated and passionate about driving and performing research and associated tasks and be able to work independently. The person will collaborate with PhD students and technicians to increase the impact of the research efforts. The position can be started from October 1 onwards. Profile • You obtained a PhD in Bioinformatics, Computer Science, Physics, Engineering, Bio-engineering, or equivalent. • Excellent track record in machine learning applied to the field of Bioinformatics • Solid programming experience is required (Python, R). • Experience with machine-learning/statistical analysis is required • Experience with plant research and/or population genetics is a plus. • Ability to work independently and in a team. We offer • Access to state-of-the-art compute infrastructure • A stimulating international research environment • Competitive salary and benefits • Financial support for 2 years. Starting date: as soon as possible How to apply? https://jobso.id/e47k Please complete the online application procedure and include a detailed CV, two reference letters, and a motivation letter. For more information: yvan.saeys(a)ugent.be -- =============================================================================== Prof. dr. Yvan Saeys VIB Group Leader Data mining and modeling for biomedicine UGent Department of Applied Mathematics, Computer Science and Statistics Krijgslaan 281, S9, B-9000 Gent Inflammation Research Center, a VIB-UGent Department Technologiepark-Zwijnaarde 71 , B-9052 Zwijnaarde , Belgium Tel : +32(0)9 331 37 40 Fax : +32(0)9 221 76 73 Mailto: yvan.saeys(a)ugent.be http://www.dambi.ugent.be ===============================================================================

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jobs at the Viral Ecology and Omics group
by Bas E. Dutilh 14 Sep '21

14 Sep '21

Dear colleagues, I'm excited to be starting a new Viral Ecology and Omics group (combined wet/dry lab) to study the role of #phages and #viruses in shaping the Microverse! At this point I'm looking for a bioinformatician/data steward to support the development of (meta-) genomics workflows and maintain our databases, see this job ad: https://www4.uni-jena.de/Universit%C3%A4t/Stellenmarkt/Verwaltung+und+Techn… Other job ads are posted here: https://microverse-cluster.de/en/jobs.html Please consider helping me reach a wider audience by retweeting this tweet: https://twitter.com/BEDutilh/status/1437797296150822919 All the best, Bas -- Dr. Bas E. Dutilh <http://tbb.bio.uu.nl/dutilh> Metagenomics Group <https://wiki.ubc.uu.nl/mgx/> Utrecht Bioinformatics Center <https://ubc.uu.nl/user/dutilh/> Institute of Biodynamics and Biocomplexity <http://www.ibb-uu.nl/research-groups/bas-dutilh-metagenomics-genomics/> Theoretical Biology and Bioinformatics <http://tbb.bio.uu.nl/>, Utrecht University <http://www.uu.nl/medewerkers/BEDutilh> +31 (0)30 253 4212

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Vacancy for junior/senior researcher Leuven
by Vera van Noort 14 Sep '21

14 Sep '21

https://www.kuleuven.be/personeel/jobsite/jobs/60059521?hl=en&lang=en We are hiring a junior/senior researcher with a Master/PhD in ecology, biology, biochemistry, biotechnology, bio-engineering, genomics or bioinformatics to collect, annotate and integrate genomics data and ecological information on marine micro-organisms. The candidate will focus on integrating existing resources targeted towards marine and/or aquatic organisms and mining literature for additional information. The gathered information will be used by the team of systems biologists and AI engineers who are involved in the ENZYMARES project https://catalisti.be/project/enzymares/ . For more information contact prof. Filip Volckaert (filip.volckaert(a)kuleuven.be<mailto:filip.volckaert@kuleuven.be> ) or prof. Vera van Noort (vera.vannoort(a)kuleuven.be<mailto:vera.vannoort@kuleuven.be> ) Please spread in your network! Vera van Noort

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PhD position in biophysical protein evolution in Brussels
by Wim VRANKEN 10 Sep '21

10 Sep '21

Dear all, Please see attached PDF for the description of a PhD position at the Interuniversity Institute of Bioinformatics in Brussels, jointly between the Bio2Byte group at the VUB and the EEG (Ecological & Evolutionary Genomics) group of ULB. We’re very excited to start with the work as soon as possible; by developing methods that can gather information about the environmental requirements of proteins, we should be able to provide very complementary information to protein folds, as now very accessible through AlphaFold. Best, Wim --------------------------------------------------------------------------------------- Prof. Dr. Wim Vranken Tel: +32 (0)2 6291952 (VUB) VUB - Building E, 5th Floor, E5.02, Pleinlaan 2 1050 Brussels, Belgium Structural Biology Brussels/Artificial Intelligence/General Chemistry/Biomedical sciences Research professor - http://bio2byte.be/ ULB-VUB - Interuniversity Institute of Bioinformatics in Brussels (IB)2 Member and former director - http://ibsquare.be/ ---------------------------------------------------------------------------------------

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open position
by Age Smilde 10 Sep '21

10 Sep '21

Dear All, On behalf of Morten Danielsen I post this open position: https://www.linkedin.com/feed/update/urn:li:activity:6840985311636455424<https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.linke…> Regards, Age Age K. Smilde Science Park Room C2.269 Phone: +31 20 525 5062 Email: a.k.smilde(a)uva.nl<mailto:a.k.smilde@uva.nl> Website: www.bdagroup.nl

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open position
by Age Smilde 09 Sep '21

09 Sep '21

Dear All, On behalf of Evrim Acar I post this open position. https://www.simula.no/about/job/phd-position-temporal-multi-modal-data-mini… Regards, Age Age K. Smilde Science Park Room C2.269 Phone: +31 20 525 5062 Email: a.k.smilde(a)uva.nl<mailto:a.k.smilde@uva.nl> Website: www.bdagroup.nl

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