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open positions AZ Delta Roeselare bioinformatics - Molecular Diagnostics CGP WGS Microbial sequencing
by BeNeLux bioinformaticians forum 20 Mar '23

20 Mar '23

Beste, In AZ Delta ziekenhuis, Roeselare, hebben we open posities voor biomedical data crunchers – bioinformatici, zowel op pre-doc als post-doc niveau. Je ontwikkelt, binnen de Dienst Laboratoriumgeneeskunde, pipelines voor genomische analyse van solide tumoren, NIPT en microbiële sequencing. Daarnaast werk je deeltijds op big data modeling binnen het innovatiecentrum RADar van AZ Delta. De resultaten van je werk hebben directe impact op patiëntenzorg, en je krijgt de kans om de lead te nemen in diverse translationele onderzoeksprojecten. Rock and roll en innovatie-gerichte werkomgeving! Dear, At AZ Delta hospital, Roeselare, we are looking for data crunchers/bio-informatics fluent in common languages such as Python/Bash. You will work on genomic data of patients (oncology, microbiology) and develop advanced pipelines for clinical use. You will also work part time on translational research projects and big data modeling in the AZ Delta innovation center, RADar (Google Cloud Customer Award 2022). Dutch language skills required. The lab has extensive sequencing capabilities (MiSeq, NextSeq, NovSeq, ONT) for targeted/CGP and whole genome sequencing. Your job will have a real impact on cutting-edge patient care. - Bio-informaticus (pre-doc): https://bit.ly/3Lmt6rx - Bio-informaticus (post-doc): https://bit.ly/3Fn8eN0 “ Prof. Dr. Geert Martens Met vriendelijke groeten [cid:image71706c.PNG@53e3da57.4b83e58f] Prof. Dr. Geert Martens Laboratoriumgeneeskunde Moleculaire diagnostiek t e geert.martens(a)azdelta.be<mailto:geert.martens@azdelta.be> ◦ w www.azdelta.be<http://www.azdelta.be> Brugsesteenweg 90 ◦ 8800 Roeselare AZ Delta: Campus Rumbeke, campus Brugsesteenweg Roeselare, campus Menen en campus Torhout. Deze e-mail en alle bijlagen bevatten vertrouwelijke informatie die wordt beschermd door het beroepsgeheim en de discretieplicht. Deze informatie is strikt persoonlijk en moet confidentieel behandeld worden. Als deze e-mail niet voor u bedoeld is, mag u de inhoud van deze e-mail niet lezen, kopiëren of doorgeven aan anderen.

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PhD candidate vacancy data science
by BeNeLux bioinformaticians forum 15 Mar '23

15 Mar '23

Dear maillist, At RIVM are recruiting a PhD candidate with a background in data science and interest to work in the domain of healthy and sustainable foods. The project is call See 'werkenvoornederland.nl': https://www.werkenvoornederland.nl/vacatures/phd-student-data-science-artif… Or academictransfer.nl PhD student data science/artificial intelligence for protein transition | RIVM - AcademicTransfer<https://www.academictransfer.com/en/324529/phd-student-data-scienceartifici…> Would it be possible to promote the vacancy through your network? KR Marga Ocke ----------------------------------------------------------------- Marga C Ocké, PhD Centre for Nutrition, Prevention and Health Services National Institute for Public Health and the Environment (RIVM) Postal address: PO Box 1, 3720 BA Bilthoven, the Netherlands Visiting address: Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands T: +31 88 6893814; M: +31 6 52096988 ----------------------------------------------------------------- See http://www.wateetnederland.nl for information on the Dutch food consumption surveys Dit bericht kan informatie bevatten die niet voor u is bestemd. Indien u niet de geadresseerde bent of dit bericht abusievelijk aan u is verzonden, wordt u verzocht dat aan de afzender te melden en het bericht te verwijderen. Het RIVM aanvaardt geen aansprakelijkheid voor schade, van welke aard ook, die verband houdt met risico's verbonden aan het elektronisch verzenden van berichten. www.rivm.nl<http://www.rivm.nl/> De zorg voor morgen begint vandaag This message may contain information that is not intended for you. If you are not the addressee or if this message was sent to you by mistake, you are requested to inform the sender and delete the message. RIVM accepts no liability for damage of any kind resulting from the risks inherent in the electronic transmission of messages. www.rivm.nl/en<http://www.rivm.nl/en> Committed to health and sustainability

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Postdoc position computational epigenomics available within Epi-Guide-Edit NWO Key Technology consortium
by BeNeLux bioinformaticians forum 15 Mar '23

15 Mar '23

Dear all, The NWO Key Technology funded Epi-Guide-Edit consortium is dedicated to developing tools for durable epigenetic editing across different applications including health and agriculture. Within the consortium we have a postdoc position (1 fte for 3 years or 0.8 fte for 4 years) available focused on single-cell resolution pooled epigenetic CRISPR/dCas screens to study epigenetic reprogramming in (breast cancer) cell lines. The position offers ample possibilities for the development and application of state-of-the art bioinformatics methods. The position is embedded in the group of the program coordinator, Prof. dr. Pernette Verschure, Swammerdam Institute for Life Sciences and the Dept. of Medical Biochemistry, Amsterdam University Medical Centers (AUMC), University of Amsterdam (UvA), NL. For computational analyses you will work closely together with Dr. Perry Moerland, Bioinformatics Lab, Dept. of Epidemiology and Data Science, AUMC, UvA, NL and Dr. Remco Loos, Informatics & Predictive Sciences, Bristol Myers Squibb, Spain. Further details on the position can be found in the attachment. Feel free to contact me (p.d.moerland at amsterdamumc.nl) if you have any questions. Best wishes, Perry --- Dr. ir. P.D. Moerland Bioinformatics Laboratory | Epidemiology and Data Science (EDS) Amsterdam UMC | Location AMC | J1B-225 | Meibergdreef 9 | 1105 AZ AMSTERDAM E: p.d.moerland(a)amsterdamumc.nl<mailto:p.d.moerland@amsterdamumc.nl> W: https://bioinformaticslaboratory.eu/ ______________________________________________________ AmsterdamUMC disclaimer : www.amsterdamumc.org/disclaimers

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Open position in the CBIO lab: single-cell proteomics
by BeNeLux bioinformaticians forum 14 Mar '23

14 Mar '23

A fully-funded position for a PhD student (4 years) or a post-doctoral researcher (2 - 3 years, depending on experience) is open in the Computational Biology and Bioinformatics lab (CBIO) at the de Duve Institute, UCLouvain in Brussels, Belgium. The CBIO lab (https://lgatto.github.io/cbio-lab) has developed a leading expertise in mass spectrometry-based single-cell proteomics data processing, analysis and interpretation (https://paperpile.com/shared/paTK2y) and is looking for a researcher to contribute to this research theme. The position will focus on computational and statistical approaches, including research software development, integration with other omics modalities, and could, depending on the candidate interests and experience, also include a small wet lab component. The successful candidate will have a degree in bioinformatics, statistics, computer sciences, biomedical sciences, bio-engineering, or equivalent and be able to demonstrate experience and/or keen interest in one or several of the following: - experience in one or multiple omics experimental technologies, data processing, analysis and/or interpretation - experience in mass spectrometry and proteomics is an advantage; - a keen interest in understanding and tackling biomedically relevant questions; - interest in robust method development; - background/expertise in statistics, machine learning and/or artificial intelligence; - open and reproducible research (e.g. Rmarkdown, Jupyter notebooks, Github, version control, ...); - research software development (e.g. unit testing, version control, continuous integration, ...); - experience in R/Bioconductor data structures, in particular those used for omics data analysis (e.g. SummarizedExperiment, SingleCellExeriment, QFeatures, ...); - contribution to an open and inclusive research environment; - good written and oral communication skills. The project is funded by the Fonds National de la Recherche Scientifique (FNRS). The position is open immediately until filled. To apply for the position, please send the following documents to Laurent Gatto: - A cover letter describing why you would like to join the lab and how you match the requirement; - A detailed CV including, depending on seniority, some or all of the following: a list of publications, pre-prints, posters and/or software contributions; a link to publicly available code/data analysis you have contributed to; education and professional experience; current and past positions; awards; obtained funding; teaching experience; any additional information you deem relevant. - If no code is publicly available, please include code chunks that illustrate best your programming experience and interests. - Among your publications/software/projects, select up to 3 and provide a short narrative describing why these are important in your career, your specific contributions and/or the unique skills you have gained through these. - A list of at least 2 (for a PhD application) or 3 (for a post-doctoral researcher application) academic references. Expectations are different for PhD or PDRA application and will be assessed accordingly. More information is available here: https://lgatto.github.io/scp-job-2023/

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VACANCY: PhD position in computational cancer biology (@NKI and VU Amsterdam)
by BeNeLux bioinformaticians forum 10 Mar '23

10 Mar '23

Dear all, For an exciting project using state-of-the-art single cell measurements to elucidate the mechanisms behind multi-drug combinations we are looking for an enthusiastic PhD candidate with a strong quantitative background. The position is shared between the groups of Lodewyk Wessels (NKI) and Evert Bosdriesz (VU). More information in the link. <https://www.nki.nl/careers-study/vacancies/phd-position-in-computational-si…> PhD position in computational single-cell cancer biology | Netherlands Cancer Institute<https://www.nki.nl/careers-study/vacancies/phd-position-in-computational-si…> nki.nl<https://www.nki.nl/careers-study/vacancies/phd-position-in-computational-si…> [apple-touch-icon-180x180.png]<https://www.nki.nl/careers-study/vacancies/phd-position-in-computational-si…> Kind regards, Evert Bosdriesz ---- Assistant Professor Bioinformatics - VU Amsterdam www.evertbosdriesz.org | e.bosdriesz(a)vu.nl

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ACADEMIC POSITIONS - Pontificia Universidad Católica de Chile
by BeNeLux bioinformaticians forum 10 Mar '23

10 Mar '23

________________________________________ De : Luis Larrondo <llarrondo(a)bio.puc.cl> Envoyé : jeudi 9 mars 2023 21:33 À : GONZE Didier Objet : BIOMAT BIOCOMP INGLES.pdf Dear Didier I hope you are doping fine Do you think you could distribute this among potential candidates? Thanks so much L Luis F. Larrondo Ph.D. Howard Hughes Medical Institute International Research Scholar Director Millennium Institute for Integrative Biology (iBio) Full Professor Departamento de Genética Molecular y Microbiología Facultad de Ciencias Biológicas Pontificia Universidad Católica de Chile Alameda 340, Casilla 8331150 (ZIP code), Santiago, Chile Office: 56-2-23541916 Cell-phone: 56-9-82275080 Lab : 56-2-26862348 E-mails: llarrond(a)bio.puc.cl<mailto:llarrond@bio.puc.cl> lflarron(a)puc.cl<mailto:lflarron@puc.cl> http://larrondolab.bio.puc.cl<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flarrondola…>

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Special issue of TCS/C on Foundations of SysBio
by BeNeLux bioinformaticians forum 07 Mar '23

07 Mar '23

Special issue of Theoretical Computer Science (track C) on Foundational Methods in Systems Biology Submission: continuous, cut-off date May 15, 2023 ================================================================= Dear Colleague, With this email we would like to invite you to submit a paper to the special issue of the Theoretical Computer Science journal (series C: Natural Computing) on “Foundations of Systems Biology”. This special issue is aligned with the conference series on “Computational Methods in Systems Biology (CMSB)” and shares its topics of interests. We look for original research articles on foundational aspects of systems biology and their applications. Topics of interest include, but are not limited to: • formalisms for modelling biological processes; • methods and tools for biological system analysis, modelling and simulation; • frameworks for model verification, validation, analysis, and simulation of biological systems; • high-performance methods for computational systems biology; • identification of biological systems; • network modelling, analysis, inference; • automated parameter and model synthesis; • multi-scale modelling and analysis methods; • design, analysis, and verification methods for synthetic biology; • methods for biomolecular computing and engineered molecular devices; • data-based approaches for systems and synthetic biology; • optimality and control of biological systems; • machine learning for systems biology. Submitted papers should not be under consideration for publication elsewhere. Extended versions of manuscripts that have been published in conference proceedings (CMSB or other conferences) can be submitted to this special issue if they have been extended by at least 30% and the differences between the two versions are explained in the introduction. The manuscripts should include all content in the article, rather than in appendices or in supplementary information. Please prepare your article in LaTeX in the Elsevier journal paper format (https://www.elsevier.com/authors/author-schemas/latex-instructions) and submit it using the editorial manager (https://www.editorialmanager.com/TCS/default.aspx) The tile of the special issue is “Foundations of Systems Biology” (short title VSI: FoundSysBio). In order to properly assign your submission to the special issue we are preparing, it is crucial to select VSI: FoundSysBio twice, as Article Type (starting the submission procedure) and Requested Editor (in Review Preferences). All papers for the special issue will be reviewed following the standard refereeing procedure for Theoretical Computer Science. Submissions will be reviewed on a continuous basis, with a cut-off date set for May 15, 2023. We suggest an upper limit of 40 pages on the length of the paper in the LaTeX style of the journal; please contact us if you need more pages for your manuscript. To keep track of the papers, please inform us of after the submission with an email to ion.petre(a)utu.fi and apaun(a)fmi.unibuc.ro. With best wishes, Ion Petre and Andrei Paun Guest editors of the special issue of TCS/C on Foundations of Systems Biology

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Two days left to submit your abstract for the BioSB 2023 conference!
by BeNeLux bioinformaticians forum 06 Mar '23

06 Mar '23

Extended BioSB 2023<http://www.aanmelder.nl/biosb2023> abstract submission deadline for oral presentations Due to holidays in the Netherlands we decided to extend the abstract submission<https://www.aanmelder.nl/biosb2023/abstract-submission> deadline for oral presentations by a few more days. New deadline: Wednesday 8 March 2023, 23h59 Submission topics You can submit an abstract for one of the following topics. Find a more detailed description of the topics on the submission topics webpage:<https://www.aanmelder.nl/biosb2023/submissiontopics> * Cancer research * Other health research * Plant and animal research * Microbes and microbial communities * Viruses and phages * Synthetic biology * Multi-scale modeling of patterning * Mechanistic modeling * Big data and omics * Structural biology/bioinformatics * Artificial intelligence * Phenotyping * Single-cell techniques * Evolutionary Systems Biology and Bioinformatics * ELIXIR * Miscellaneous Submission deadlines * Oral presentations: Extended to 8 March 2023, 23h59 * Notification oral presentations: 24 March 2023 * Demo presentations: 14 April 2023 * Poster presentations: 14 April 2023 Read more here<https://www.aanmelder.nl/biosb2023/abstract-submission> [signature_4119193094]<https://www.dtls.nl/biosb/>

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Call for nominations BioSB Young Investigator Award 2023
by BeNeLux bioinformaticians forum 06 Mar '23

06 Mar '23

Call for nominations for the BioSB Young Investigator Award 2023 You can now nominate a young researcher for the BioSB Young Investigator Award 2023<https://www.aanmelder.nl/biosb2023/yia> (14th edition). This award will be given to a promising young researcher in the bioinformatics or systems biology field. The winner will receive a voucher of 500 Euros sponsored by the BioSB research school (to be spend on a conference or course participation of choice) and will be invited to present an honorary lecture in the plenary programme of the BioSB 2023 conference<http://www.aanmelder.nl/biosb2023>. Who is eligible? The candidate must have conducted his/her bioinformatics or systems biology research primarily in a Dutch institute. The primary result on which the award will be based is the PhD thesis written by the candidate (The thesis needs to have been submitted to the PhD reading committee at a Dutch university before 28 March 2023). >> Nomination deadline: 24 March 2023! << Find the criteria and how to apply for the award here!<https://www.aanmelder.nl/biosb2023/yia> [signature_3447934674]<https://www.dtls.nl/biosb/>

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Postdoc positions in University College Dublin
by BeNeLux bioinformaticians forum 03 Mar '23

03 Mar '23

Dear BeNeLux bioinformaticians, My lab are currently looking to recruit computational biology postdocs. We are a collaborative interdisciplinary research group based in the Conway Institute in University College Dublin. We are broadly interested in understanding how mutations in cancer alter molecular interaction networks and in identifying ways to target these alterations therapeutically. We have a particular interest in identifying and understanding synthetic lethal interactions in cancer. You can read more about areas of specific research interest here: https://cancerdata.ucd.ie/research/ The ideal candidate for these roles will have good programming and analytics skills and prior experience in the use of data-integration approaches to understand biology. Prior experience of cancer biology or genetic interactions is a plus, but certainly not a prerequisite for the roles. Further details on the positions are available here: https://cancerdata.ucd.ie/vacancies/ Feel free to contact me (colm.ryan(a)ucd.ie) if you have any questions Kind regards Colm

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