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PhD position in Bioinformatics: Investigating protein evolution using machine learning
by BeNeLux bioinformaticians forum 18 Aug '23

18 Aug '23

The Bioinformatics group at Wageningen University is seeking a PhD student - do you want to apply state-of-the-art machine learning methods on gene sequences and protein structures to analyze evolutionary patterns? Then this vacancy may be of interest to you! Orphan genes are genes that can only be found in one species. Even though more and more sequencing data is available, we cannot find homologs of these genes outside of that single species. The evolution of such genes is particularly intriguing, since they might arise from very fast divergence beyond recognition or entirely novel “from scratch” from a region that did not code for a protein before. Alternatively, some might simply be artefacts of the automatic annotation. Orphan genes have been mainly studied in eukaryotes, where they are associated with organismal novelties and species-specific traits, and are generally thought to be important for adaptation. Much less is known about prokaryotic orphans. However, prokaryotes evolve rapidly and are exposed to changing environments, in which orphan genes might provide novel adaptations. In this project, we will investigate orphans in human gut microbiome species. We will use state-of-the art machine learning approaches to study the properties of orphans and to learn about their evolutionary origin and potential function. In particular, we plan to use predicted protein structures to detect remote homology and to investigate the properties of proteins with potentially novel functions. This work will contribute to a fundamental understanding of how proteins evolve. The research is embedded within the Bioinformatics Group at Wageningen University, the Netherlands. Your daily supervisors will be dr. Anne Kupczok and dr. Aalt-Jan van Dijk, with complementary expertise: molecular evolution of microbes (Anne Kupczok) and machine learning and protein structures (Aalt-Jan van Dijk). Your qualities The ideal candidate must have the following qualities: * A successfully completed MSc degree in bioinformatics, biology, data science or a related discipline; * Proficiency in programming (e.g. in Python); * Experience in applying machine learning to biological data; * Strong affinity with molecular evolution and/or prokaryote genomics; * Good statistical and mathematical skills; * Perseverance in problem solving; * Excellent writing and oral communication skills in English. You can find more information and the application link here: https://www.wur.nl/en/vacancy/phd-researcher-in-bioinformatics-investigatin… -- Dr. Anne Kupczok Assistant Professor Bioinformatics, Department of Plant Sciences, Wageningen University http://www.wur.nl/en/Expertise-Services/Chair-groups/Plant-Sciences/Bioinfo…

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Two bioinformatics positions at the Erasmus MC
by BeNeLux bioinformaticians forum 17 Aug '23

17 Aug '23

Dear all, We have two bioinformatics positions available at the Department of Hematology, Erasmus MC. Both with an application deadline set at 30 August 2023 (ongoing selection): Bioinformatician Hematology: The department of Hematology seeks to recruit a highly motivated bioinformatician to join the multiple myeloma research group at the Erasmus MC. Multiple myeloma remains an incurable hematological cancer. At the department of hematology, scientists and clinicians collaborate to study myeloma development, progression and therapy response. Our research depends on molecular techniques, including single-cell RNA and ATAC sequencing, spatial transcriptomics and proteomics, and multi-parameter flow cytometry. You will join a research team operating at the interphase of wet-lab and in-silico analysis, and will work in close collaboration with PhD students and postdocs. Together with other bioinformaticians in the department, you will work on the development and implementation of novel and existing bioinformatical analysis pipelines. https://www.werkenbijerasmusmc.nl/en/vacancy/93828/bioinformatician-hematol… Senior Bioinformatician Hematology: We seek to recruit a highly motivated and skilled senior bioinformatician. With the advent of high-throughput methodologies and the increased sequencing pace, the need for proficient data analysis and interpretation is ever-growing. To cope with this increased demand of expert-level data analysis, we are now expanding our bioinformatics team. In this position, you will be involved in the support and development of new computational tools in concert with the research programs active within our department, are responsible for managing the bioinformatics team, keep the bioinformatics and research teams updated on the latest technological developments and independently initiate new collaborations to further our departmental research aims. Our current primary focus is on single-cell technologies, including single cell transcriptomics and spatial multiomics, and the development of new computational tools supporting our high-throughput-dependent research goals. You will be tasked with supporting and developing these technologies to make a lasting impact on our research. https://www.werkenbijerasmusmc.nl/en/vacancy/93827/senior-bioinformatician-… Do not hesitate to get in touch in case you would like to receive more information! ---- Mathijs Sanders Assistant Professor

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Phd in computational oncology at Institut Curie, Paris - machine learning for fighting cancer
by BeNeLux bioinformaticians forum 16 Aug '23

16 Aug '23

To anyone who may be interested: There is a position open for a talented PhD student in computational oncology. See details below: https://sysbio.curie.fr/texts/PhdComputationalOncologyInstitutCurieParis.pdf https://twitter.com/SysBioCurie/status/1678314494856970241?s=20 Best --- Marek Ostaszewski University of Luxembourg Luxembourg Centre for Systems Biomedicine (LCSB) Campus Belval | House of Biomedicine 6, avenue du Swing, L-4367 Belvaux, Luxembourg Tel: +352 46 66 44 5604 http://lcsb.uni.lu

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PhD position in integrative analysis of multi-omics spatial data
by BeNeLux bioinformaticians forum 08 Aug '23

08 Aug '23

Hi all, We have an opening for a PhD position in our group at the Leiden University Medical Center (Netherlands) to develop computational methods to analyze multi-omics spatial data to decipher biological processes involved in kidney development and regeneration. This is a collaboration with the lab of Prof. Ton Rabelink (Nephrology). Please don't hesitate to contact me for more details. *Deadline: 13 August 2023* Cheers, Ahmed *Ahmed Mahfouz, PhD **| Associate **Professor, Department of Human Genetics* Leiden University Medical Center | Dept. of Human Genetics | P.O. Box 9600, 2300 RC Leiden | Postal zone S4-P Room R-04-022 | Phone +31 71 52 69513 https://www.mahfouzlab.org/

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PhD student in computational analysis of health trajectories (R1)
by BeNeLux bioinformaticians forum 07 Aug '23

07 Aug '23

Hello, I hope this email finds you well. I am contacting you because we have opened a new PhD Student vacancy in the Life Sciences department, and we would be grateful if you could share them it with your contacts and post them in your website: * *PhD student in computational analysis of health trajectories (R1): *https://www.bsc.es/join-us/fellowships/38623lscbr1 o Deadline 16th of Septemnber If you need further information regarding any of our vacancies, or you need any additional steps from my side in order to disseminate it, please let me know. Thank you! Best regards, -- Laura Delshams /Human Resources - Talent & Development Officer/ *Barcelona Supercomputing Center – Centro Nacional de Supercomputación* <mailto:anais.delastre@bsc.es>Tel. +34- 93 413 40 72 <http://www.bsc.es/>laura.delshams(a)bsc.es www.bsc.es <http://www.bsc.es/>

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Open slots for BePA!VIB International Summer School from 28/08
by BeNeLux bioinformaticians forum 04 Aug '23

04 Aug '23

Dear all, Due to several cancellation, I'd like to warmly invite you to fill the open slots for the up-coming BePA@VIB International Proteomics Summer School. Don't hesitate to register at https://training.vib.be/all-trainings/bepavib-international-proteomics-summ… Best regards, Alex Alexander Botzki VIB Technology Training, ELIXIR Belgium Training Coordinator Technologiepark-Zwijnaarde 75 9052 Zwijnaarde Belgium tel +32 9 224 9870 https://technologytraining.sites.vib.be | https://elixir-belgium.org/training [signature_490181756]

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3 PhD positions in Crete with competitive Salaries
by BeNeLux bioinformaticians forum 02 Aug '23

02 Aug '23

Dear Community, There are three PhD positions with competitive salaries available in my new, second research group (https://www.biocomp.gr/) that I am currently setting up in Crete under the auspices of the EU ERA chair program. We are looking for computer scientists, Bioinformaticians or "programming Biologists". If you want to do research where other people spend their vacations the Biodiversity Computing Group is the place to be. To apply please follow the link below: https://euraxess.ec.europa.eu/jobs/131920 Please feel free to get in touch with me for an informal exchange on the setup, the projects, and the perspectives at stamatak(a)ics.forth.gr Alexis -- Alexandros (Alexis) Stamatakis ERA Chair, Institute of Computer Science, Foundation for Research and Technology - Hellas Research Group Leader, Heidelberg Institute for Theoretical Studies Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology www.biocomp.gr (Crete lab) www.exelixis-lab.org (Heidelberg lab)

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Offer Dissemination
by BeNeLux bioinformaticians forum 02 Aug '23

02 Aug '23

Hi, I'm writing from Barcelona Supercomputing Center this mail to see if you could disseminate the following offer with your contact list. The offer is: Technical Research Manager (RE2): https://www.bsc.es/join-us/job-opportunities/37723lsinbre2 Thank you, -- 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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postdoc in AI for structure-based virtual screening
by BeNeLux bioinformaticians forum 01 Aug '23

01 Aug '23

Dear all, I have a postdoc position available at my group. I would be grateful if you could pass this opportunity on to relevant PhD graduates. The successful candidate will gain skills in the design and development of AI models that can discover drug leads for specific targets. An important part of the project will be rigorous virtual screening benchmarking. We will also carry out prospective studies guided by the developed models with collaborators at the University of Cambridge. An initial contract of 18 months will be offered, with the possibility of extending for a further 18 months. The deadline for applications is 8 September, and the ideal start date is 1 November or earlier. Further information and how to apply can be found https://www.imperial.ac.uk/jobs/description/ENG02670/research-associate Best regards, Pedro Dr. Pedro J. Ballester | Royal Society Wolfson Fellow & Senior Lecturer Imperial College | Department of Bioengineering Group website | https://ballestergroup.github.io/ College website | https://www.imperial.ac.uk/people/p.ballester/research.html <https://www.imperial.ac.uk/people/p.ballester/research.html> Networking profiles | https://www.linkedin.com/in/pedroballester/ https://twitter.com/pjballester <https://twitter.com/pjballester> Address | Sir Michael Uren Hub, White City campus, 86 Wood Lane, London - W12 0BZ, UK

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Two Exciting PhD Positions in Pharmacogenomics and Cancer Screening at our Group
by BeNeLux bioinformaticians forum 31 Jul '23

31 Jul '23

Dear colleagues, We are delighted to announce two new PhD positions available within our group, which will be held in partnership with VITO, the University of Hasselt, Jessa Hospital (Hasselt), and the University of Antwerp. We seek talented and motivated individuals with an interest in Pharmacogenomics and Cancer Screening to join us in these groundbreaking research projects. *PhD Position in Next-Generation Pharmacogenomics*This project focuses on facilitating genomics medicine and including the PGx information layer in the clinical decision process. The candidate will engage in developing a toolkit for implementing PGx workflows, and assessing and applying WGS PGx profiles in clinical practice, using data generated at the Jessa Hospital. We welcome applications from candidates with a background in genomics/bioinformatics, demonstrating strong analytical problem-solving skills, programming experience, and a strong interest in genomics and pharmacogenomics applications. This project is a strategical collaboration with VITO, Jessa Hospital (Hasselt) & University of Hasselt, and the candidate will be a member of all institutions. The full job description and requirements can be found here <https://jobs.vito.be/o/phd-position-nextgeneration-pharmacogenomics>. *PhD Position in Pioneering Evidence-Based Policy Advice for Colorectal Cancer Screening and Public Health Impact*This position focuses on the transformation of scientific discoveries into actionable policy recommendations in the fields of cancer screening and environmental health. The candidate will work with biomedical screening data, morbidity and mortality data on CRC, and geospatial data on environmental pollutants, socio-economic status, and lifestyle to provide policy makers with targeted, science-based advice. We are looking for a candidate with a background in biostatistics/bioinformatics, prior experience in (bio)statistical data analysis, familiarity with GIS, and a keen interest in translating scientific findings into policy advice. This is a joint project between VITO and the University of Antwerp, and the candidate will be a member of both institutions. For more information on the position and how to apply, please click here <https://jobs.vito.be/o/phd-position-pioneering-evidencebased-policy-advice-…> . Both positions offer a fully-funded 4-year research project, a competitive remuneration package, a hybrid working schema, participation in exciting projects, and career development opportunities in a dynamic, multi-disciplinary research team. Applications will be processed on a first-come-first-served basis, so we encourage you to apply early. If you have any questions or require further information, please feel free to contact us. Please share this opportunity within your networks and with any colleagues who might be interested. Best Regards, -- Gökhan Ertaylan, PhD VITO Research Lead Precision Health

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