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Summer School Trends in multi-omics data analysis for Microbial Ecology and Biotechnology
by BeNeLux bioinformaticians forum 26 May '23

26 May '23

Summer School Trends in multi-omics data analysis for Microbial Ecology and Biotechnology In 2023, the summer school will take place from July 6 to July 27 at the Helmholtz Centre for Environmental Research (Permoserstraße 15, 04318 Leipzig). If you are interested to enroll in this course please email Dr. Ulisses Nunes da Rocha<https://www.ufz.de/index.php?de=43142> - ulisses.rocha(a)ufz.de The Microbial Data Science group at the UFZ designed this course focusing on students at different levels of their academic careers (B.Sc., M.Sc., and Ph.D.) and postdoctoral researchers. When we created this course, we had two groups in mind. On the one hand, experienced bioinformaticians would understand how their skills fit microbial ecology and biotechnology research; on the other, those working in microbial ecology and biotechnology would develop their multi-omics analysis skills. This course is taught in collaboration with the University of Leipzig under the supervision of Prof. Dr. Peter Stadler (Webpage<http://www.bioinf.uni-leipzig.de/~studla/>). Further, it participates in the efforts of the Helmholtz Interdisciplinary GRADuate School for Environmental Research (HIGRADE<https://www.ufz.de/higrade/>) and the German National research Data Infrastructure for Microbiota (NFDI4Microbiota<https://nfdi4microbiota.de/>). ________________________________ Teaching Phylosophy Our teaching philosophy is centered on the conviction that educators should empower students to take control of their learning, nurturing the qualities that we expect our students to exhibit: dedication, professionalism, and self-motivation. To foster an environment where students are stimulated to learn, it is crucial to create a classroom where independent thought is highly valued, and all students are encouraged to achieve their full potential. To this end, we nurture intellectual skills (e.g., thinking, reasoning, interpreting, analyzing, reflecting, and questioning. I also believe in continually relating lecture and laboratory subjects to real-life situations. In this context, our team tries to foster problem-oriented learning. We believe this approach will help to make classes more interesting for students. ________________________________ Teaching format * Lectures on 'Trends in multi-omics analysis' (3 ECTs) = 30 h in presence and 70 h self-study. * Lectures on 'Multi-omics analysis in microbial ecology and biotechnology' (3 ECTs) = 30 h in presence and 35 h self-study. * Practical course on 'From data to answers: making sense of multi-omics data sets' (4 ECTs) = 30 h in presence and 105 h of self-study. Workload 10 ECTs = 300 working hours Competence Goals After active participation in the module 'Trends in multi-omics data analysis for Microbial Ecology and Biotechnology', students will be able to: * Define basic concepts and differents between genomics; transcriptomics and proteomics and metabolomics in single species and complex communities * Determine how wet-lab and experimental design may influence data mining and analysis of multi-omics data sets * Define basic concepts of multi-omics analysis in ecological and biotechnological applications * Design multi-omics data analyis related to ecology and biotechnology and to apply them in real multi-omics data sets * Give a scientific presentation * Translate multi-Omics data analyses into scientific texts and presentations Summary of Module's content The contents that make up this module are: Functional potential analysis; Description of ecosystem processes; Omics history; Omics technologies; Biodiversity analysis of high-throughput sequencing data; Research data management in the omics era; Phylogenomic analysis; Genome reconstruction from metagenomes; Amplicon sequencing analysis; Virus ecology and biotechnology; Reconstruction of metabolism at the genome level; Transcriptomics; Use of machine learning for omics analysis. The computational laboratory project will include: Genome reconstruction from the metagenome, machine learning, analysis of omics data, or metabolic reconstruction at the genome level (students can decide which of the projects they would like to participate in).

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Vacancy Bioinformatician/Data Scientist at Maastricht UMC+
by BeNeLux bioinformaticians forum 25 May '23

25 May '23

Dear all, We have a vacancy for a Bioinformatician/Data Scientist at our Department of Medical Microbiology, Infectious Diseseases and Infection Prevention at Maastricht UMC+. Please check out the details here: https://www.academictransfer.com/nl/328272/bioinformatician-data-scientist/… best regards, John Penders, PhD Associate Professor Co-director Euregional Microbiome Center Department of Medical Microbiology, Infectious Diseases and Infection Prevention NUTRIM School of Nutrition and Translational Research in Metabolism & Care and Public Health Research Institute (Caphri) Maastricht University Medical Centre+ Email: j.penders(a)maastrichtuniversity.nl<mailto:G.Goossens@maastrichtuniversity.nl> www.microbiomecenter.eu<http://www.microbiomecenter.eu> www.penderslab.com<http://www.penderslab.com> P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands T +31 43 3875134 F +31 43 3884128

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Job Vacancy - Senior Research Engineer on Research Infrastructures for Precision Medicine projects (RE3)
by BeNeLux bioinformaticians forum 25 May '23

25 May '23

Hello, I hope this email finds you well. My name is Albert Peiró. I work in BSC, in HR and I am contacting you because we have opened a vacancy in the Life Sciences department, and we would be grateful if you could share it with your contacts to see if they're interested: - Senior Research Engineer on Research Infrastructures for Precision Medicine projects (RE3): https://www.bsc.es/join-us/job-opportunities/17323lsinbre3 Feel free to contact me for anything you may need Kind regards, -- Albert Peiró Manrique /Human Resources / Management *Barcelona Supercomputing Center – Centro Nacional de Supercomputación* albert.peiro(a)bsc.es www.bsc.es <http://www.bsc.es/>

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open PhD position in computational biology
by BeNeLux bioinformaticians forum 25 May '23

25 May '23

Dear colleagues within the context of a Stichting Tegen Kanker project we are looking for a talented and highly motivated PhD candidate on single cell multi-omics glioblastoma research to join our enthusiastic team. Specifically, you will implement and optimize methodologies (cutting-edge computational and experimental single cell multi-omics) and analyse and integrate high-dimensional data to unravel the regulatory heterogeneity in glioblastoma and identify key regulatory programs of plasticity. For more info on the job profile, the offer and how to apply: https://www.ugent.be/en/work/scientific/phd-student-41 The lab for Computational Biology, Integromics and Gene Regulation - CBIGR - of prof. Vanessa Vermeirssen focuses on acquiring a functional understanding of gene regulation and signalling towards personalized medicine, using statistics, bioinformatics and machine learning, as well as high-throughput biology in the framework of gene regulatory networks. Our final goal is to use this knowledge in the development of novel preventive or therapeutic strategies for successful personal healthcare. We are part of the Department of Biomedical Molecular Biology and the Department of Biomolecular Medicine, with recognised expertise in molecular biology, omics technologies, bioinformatics and cancer at Ghent University. We are also partner of the Cancer Research Institute Ghent (CRIG), https://www.crig.ugent.be/en/prof-vanessa-vermeirssen-phd. I would be happy if you could distribute this further to interested candidates. Kind regards Vanessa Vermeirssen Vanessa Vermeirssen, PhD ---------------------------------------------------------- Prof. Dr. ir. Vanessa Vermeirssen Lab for Computational Biology, Integromics and Gene Regulation (CBIGR) Ghent University (UGent) Department of Biomedical Molecular Biology Department of Biomolecular Medicine Cancer Research Institute Ghent (CRIG) Zwijnaarde-Technologiepark 71, 9052 Ghent C. Heymanslaan 10, 9000 Ghent Belgium Email: vanessa.vermeirssen(a)ugent.be Phone: +32 (0)9 3313721 CBIGR IRC web page<https://www.irc.ugent.be/index.php?id=vermeirssenhome> CBIGR CRIG web page<https://www.crig.ugent.be/nl/node/1486> [CBIGRlogo2]

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Postdoctoral position in pathway/protein design
by BeNeLux bioinformaticians forum 24 May '23

24 May '23

Dear all, We are looking for candidates for a new position where we combine pathway and protein design for synthetic biology, in a close joint computational/experimental setup. Applications very welcome – please see attached PDF for more information! Best regards, Wim --------------------------------------------------------------------------------------- Prof. Dr. Wim Vranken Tel: +32 (0)2 6291952<tel:+3226291952> (VUB) VUB - Building E, 5th Floor, E5.02, Pleinlaan 2 1050 Brussels, Belgium Structural Biology Brussels/Artificial Intelligence/General Chemistry/Biomedical sciences Associate professor - http://bio2byte.be/ ULB-VUB - Interuniversity Institute of Bioinformatics in Brussels (IB)2 Member and former director - http://ibsquare.be/ ELIXIR - Bringing together life science resources across Europe Co-lead of ELIXIR IDP community, member of ELIXIR-Belgium management board ---------------------------------------------------------------------------------------

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Vacancy: Assistant Professor in plant systems/computational/synthetic biology at Maastricht University
by BeNeLux bioinformaticians forum 20 May '23

20 May '23

Dear All, Maastricht University has an opening for an assistant professor in systems, computational or synthetic biology with a focus on plants. The position will help develop new activities in plant systems biology at the Greenport Campus Venlo in the Southern Netherlands. The campus has a focus on research (from fundamental to applied) in relation to human health, the environment and relevant stakeholders. While located at Campus Venlo, the position will also be formally affiliated with the Maastricht Centre for Systems Biology (MaCSBio), an interdisciplinary research centre aimed at integrating and modelling biological data from different empirical domains using data-driven as well as theory-driven analytical and modelling approaches. For more details, please see: https://www.academictransfer.com/en/327187/assistant-professor-plant-system… Applications are due by May 31 2023. Best wishes, Marian Marian Breuer, PhD Assistant Professor Maastricht Centre for Systems Biology (MaCSBio) Maastricht University Paul-Henri Spaaklaan 1 – North Tower, Room 3.005 P.O. Box 616, 6200 MD Maastricht, The Netherlands marian.breuer(a)maastrichtuniversity.nl<mailto:marian.breuer@maastrichtuniversity.nl>

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open positions at the VEO Group
by BeNeLux bioinformaticians forum 17 May '23

17 May '23

Dear colleagues, The Viral Ecology and Omics Group (VEO) at the Microverse Cluster in Jena is looking to fill the following positions: - A Postdoctoral fellowship in Viral Ecology: https://twitter.com/BEDutilh/status/1658810066336718850 - A PhD student to study Bacteriophage Diversity: https://twitter.com/BEDutilh/status/1658810508022018049 - A PhD student to study Microbiome Structure: https://twitter.com/BEDutilh/status/1658810854001745920 I would be much obliged if you could spread the word. If you are still using Twitter, please retweet via the links above. Please reach out in case you have any questions. All the best, Bas -- Prof. Dr. Bas E. Dutilh <http://tbb.bio.uu.nl/dutilh> Viral Ecology and Omics Group <https://www.veo.uni-jena.de/> | 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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Open PhD position in "Genetics of rare neurological diseases"
by BeNeLux bioinformaticians forum 16 May '23

16 May '23

Dear all, We have an open vacancy for a PhD student in the Synofzik research group at the Hertie-Institute for Clinical Brain Research (HIH) at the University of Tübingen, Germany. "PhD student, TVL E13, 65%, 3 years (extension possible) in genomics analyses of rare neurological diseases” https://www.hih-tuebingen.de/fileadmin/web/img/content/Karriere/Ausschreibu… Feel free to share with others! Kind regards, Danique __________________________________ Danique Beijer, PhD Postdoctoral Research Fellow Division Translational Genomics of Neurodegenerative Diseases (Prof. Synofzik) Hertie-Institute for Clinical Brain Research Otfried-Müller-Str. 27 | 72076 Tübingen | Germany Phone: +49 (0) 7071 29-85548 Email: danique.beijer(a)uni-tuebingen.de<mailto:danique.beijer@uni-tuebingen.de> https://www.hih-tuebingen.de/en/research/independent-research-groups/transl…

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Vacancies available at VIB Data Core
by BeNeLux bioinformaticians forum 11 May '23

11 May '23

Dear all, We have several vacancies available at VIB Data Core. Feel free to spread further (or to apply!). Software developer > link <https://datacore.sites.vib.be/en/jobs#/job-description/55685> DevOps Galaxy > link <https://datacore.sites.vib.be/en/jobs#/job-description/55683> Data Steward > link <https://datacore.sites.vib.be/en/jobs#/job-description/55682> Project manager Data Analysis > link <https://datacore.sites.vib.be/en/jobs#/job-description/55684> Kind regards, Kim Kim De Ruyck VIB Data Core ELIXIR Belgium Node Coordinator Technologiepark-Zwijnaarde 71 9052 Zwijnaarde, Belgium

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PhD position on machine learning-based prediction of protein-protein interactions
by BeNeLux bioinformaticians forum 10 May '23

10 May '23

Dear all, We have a vacancy available in the Wageningen Bioinformatis group for a PhD position on protein structure-based machine learning (to predict protein interactions): https://www.wur.nl/nl/vacature/phd-position-on-machine-learning-based-predi… best regards, Aalt-Jan van Dijk Associate prof. Bioinformatics, Wageningen

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