May 2023 - 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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Postdoc Position at Schneeberger Group LMU Munich
by BeNeLux bioinformaticians forum 30 May '23

30 May '23

Dear all, The "Genome Plasticity and Computational Genetics" group led by Korbinian Schneeberger is looking for a postdoc to strengthen the team at LMU Munich: - https://job-portal.lmu.de/jobposting/0acd50c2ee814e23e6bb349698187f271d820e… - https://www.nature.com/naturecareers/job/12799906/postdoctoral-position-in-… Feel free to spread the word among those in your network who may be interested! Kind regards, Raúl Wijfjes AG Schneeberger, LMU Munich

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Two PhD/Postdoc research positions at Delft University of Technology
by BeNeLux bioinformaticians forum 27 May '23

27 May '23

Dear all, I have two openings for the following research positions, both with application deadline of 18 June 2023 (ongoing selection): * PhD or Postdoc on multimodal machine learning for molecular maps of human tissue in health & disease. Some topics of interest include (spatial) (single-cell) multi-omics integration, multimodal signature learning, cross-modality prediction, interpretability and explainability of multimodal ML, and more. The position involves close collaboration with multiple pathology and experimental labs in the US, with extensive expertise on spatial omics technologies (e.g. imaging mass spectrometry, sequence-based spatial transcriptomics), providing you with insight into the latest technologies. The position further interfaces with the large-scale consortia, including the Human BioMolecular Atlas Program (https://hubmapconsortium.org/) Kidney Predicion Medicine Project (https://www.kpmp.org/) and a Brain/Aging consortium). Read more and apply at https://www.academictransfer.com/en/328385/phd-or-postdoc-multimodal-machin…. * PhD on computational methods to uncover genetic diversity in complex disease from data acquired for large-scale cell "villages" of human donors coupled with single-cell molecular profiling. The position fits within a larger consortium, the iCELL Convergence Flagship, which I am co-leading (https://convergence.nl/flagship-convergence-in-a-dish/) The research of this particular position requires close collaboration with experts in molecular biology, stem cell research, and genetics at the Erasmus Medical Center in Rotterdam, Netherlands. Read more and apply at https://www.academictransfer.com/en/328386/phd-position-on-icell-individual…. Both positions are full-time and based in the beautiful city of Delft, in the Netherlands. Check out our Computational Molecular Biomedicine lab (https://goncalveslab.tudelft.nl/people.html) at the Delft University of Technology. We are part of the Pattern Recognition and Bioinformatics section, offering an inspiring research environment in data science and machine learning. Do not hesitate to get in touch in case you would like more information! -- Joana Gonçalves Assistant Professor TU Delft | EEMCS Faculty | Computer Science INSY Department | Pattern Recognition & Bioinformatics Meet (Zoom): https://tudelft.zoom.us/my/joanagoncalves Web: https://goncalveslab.tudelft.nl

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Upcoming BioSB courses
by BeNeLux bioinformaticians forum 26 May '23

26 May '23

Dear colleagues, Please note these upcoming, very interesting BioSB courses. Register in time and be welcome! Algorithms for Biomolecular Networks 26 - 30 June, Wageningen In this course, we will first give a brief overview of molecular biology, the advent of high-throughput measurement techniques and large databases containing biological knowledge, and the importance of networks to model all this. Next, we will discuss variing network models Building on the network inference methods, a number of ways of integrating various data sources and databases to refine biological networks will be discussed. The course is aimed at PhD students with a background in bioinformatics, computer science or a related field; a working knowledge of basic statistics and linear algebra is assumed. **************************************************** More information about the course can be found here<https://www.dtls.nl/courses/algorithms-for-biomolecular-networks/> Registration can be done here<https://www.aanmelder.nl/algorithms-biomolecular-networks/subscribe> **************************************************** Algorithms for Genomics 9- 13 October, Wageningen NOTE: deadline early bird rate = 14 August 2023 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 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. **************************************************** More information about the course can be found here<https://www.dtls.nl/courses/algorithms-for-genomics/> Registration can be done here<https://www.aanmelder.nl/algorithms_for_genomics/subscribe> **************************************************** Integrated Modeling and optimization 11- 15 December, Wageningen NOTE: deadline early bird rate = 16 October 2023 Only measurements cannot provide the answer to unravelling biological complexity. This is because the dynamical behavior of complex systems cannot be reduced to the linear sum of the functions of their parts. Given the huge complexity of biological systems, it is necessary to carefully understand the specific modelling requirements they pose, in order to define what a good model should look like. In this course we offer the participants the possibility to learn and exercise the modeling process. 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 mathematics, especially differential equations, is recommendable, but we will distribute preparation material to be studied by students missing the required background. Furthermore, at the start we offer a math refresher to help those participants who are not (yet) involved in modelling on a daily basis. **************************************************** More information about the course can be found here<https://www.dtls.nl/courses/integrated-modeling-and-optimization-fundamenta…> Registration can be done here<https://www.aanmelder.nl/algorithms-biomolecular-networks/subscribe> **************************************************** We hope to welcome you to one of our courses! Kind regards, Petra Aarnoutse, Community manager BioSB research school [https://www.dtls.nl/wp-content/uploads/2021/08/BioSB_logo_full_250x226.png] Supported by [cid:part1.agd20taj.BNf9VxMv@health-RI.nl]

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Job Offer Dissemination
by BeNeLux bioinformaticians forum 26 May '23

26 May '23

Good morning, I share with you the link of our newest offer, hoping you can share it with your contact list. The offer is: Research Engineer - Computational Biology Group (RE2): https://www.bsc.es/join-us/job-opportunities/23923lscbre2 Feel free to contact us if you have any doubt about it Thank you very much, -- 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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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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