March 2023 - BBClist - maillist.psb.ugent.be

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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Virtuome 2023 Undergraduate Summer Research
by BeNeLux bioinformaticians forum 02 Mar '23

02 Mar '23

Dear all, The Molecular Systems Physiology group at the University of Galway will be running the now 4th consecutive edition of Virtuome, our all-Ireland fully digital undergraduate research experience in digital health, also open to international participants. We therefore invite talented STEAM undergraduate students (1st - final years) to apply for this summer's Virtuome 2023<https://www.thielelab.eu/virtuome2023> from 22nd May – 14th July. If acceptable, would you be able to share the invitation with your undergraduate STEM student groups, please? The relevant flyer is attached, in addition to the direct link here: https://www.thielelab.eu/virtuome2023 Best wishes, Cyrille Cyrille Thinnes, MBA, DPhil Engagement Manager for the Virtual Metabolic Human<https://vmh.life/> Research Fellow Molecular Systems Physiology Group University of Galway | Ryan Institute | APC Microbiome Ireland School of Medicine Orbsen Building | Galway, Ireland https://www.thielelab.eu

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Call for nominations: BioSB Young Investigator Award 2023
by BeNeLux bioinformaticians forum 02 Mar '23

02 Mar '23

Call for nominations: 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<http://www.dtls.nl/biosb> (to be spent on 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). Find more criteria here: https://www.aanmelder.nl/biosb2023/yia >> Nomination deadline: 24 March 2023! << [signature_3923017907]<https://www.dtls.nl/biosb/>

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Open PhD position in microbial genome evolution
by BeNeLux bioinformaticians forum 02 Mar '23

02 Mar '23

Dear colleagues, I am pleased to announce an open PhD position at the newly founded Archaeal and Bacterial Evolution team at Utrecht University. The team is embedded within the Theoretical Biology and Bioinformatics group chaired by Berend Snel and Rob de Boer. The successful candidate will investigate bacterial and archaeal genome organisation, focusing on the evolutionary mechanisms behind, and the biological impacts of, current genome architectures. Strong interests in evolution, genome biology or microbiology, as well as experience in bioinformatics, are highly valued. Find the full call here: https://www.uu.nl/en/organisation/working-at-utrecht-university/jobs/phd-po… For enquiries, don't hesitate to contact me: d.tamaritchulia(a)uu.nl Best regards, Daniel Tamarit Assistant Professor Theoretical Biology and Bioinformatics Utrecht University

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Open position in the CBIO lab: spatial proteomics and PTMs
by BeNeLux bioinformaticians forum 01 Mar '23

01 Mar '23

On-line: https://lgatto.github.io/spatprot-job-2023/ PDF: see attachment Please do share this position with your students and colleagues. A position for a PhD student (4 years) or a research assistant (1 year contracts, renewable) is open in the CBIO lab focusing on protein sub-cellular localisation (spatial) proteomics, post-translational modification and machine learning. The goal of the project is to apply and extend existing spatial proteomics methods and software infrastructure (such as the pRoloc package) to focus more specifically on the detection and the effect of post-translational modifications in protein and proteoform sub-cellular localisation. This position is part of the FWO-funded Protein Contours project, in collaboration with Win Vranken from the VUB and Lennart Martens from the VIB and Ghent University. The successful candidate will have a degree in bioinformatics, statistics, computer sciences, biomedical sciences, or equivalent and be able to demonstrate experience and/or keen interest in at least 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, …); - 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. About the CBIO lab The Computational Biology and Bioinformatics lab is headed by Prof Laurent Gatto and is composed of students and researchers with expertise in biomedical sciences, statistics, omics data analysis and bioinformatics. Details about our work and the members can be found at https://lgatto.github.io/cbio-lab/. The lab supports a friendly and supportive work environment through flexible working hours and the possibility to work remotely. The lab meetings are typically scheduled in-person (or mixed remote/in-person) to favour interactions among lab members. While joining the lab and contribution to our research, you will also have the opportunity to get involved in the international Bioconductor community. The lab members have opportunities to join courses and conferences in Belgium and abroad to present their work. Academic environment The de Duve Institute is a multidisciplinary biomedical research institute (250-300 scientists) hosting several laboratories the UCLouvain, as well as the Brussels branch of the Ludwig Institute for Cancer Research. The focus is on basic research in the fields of tumour immunology and signal transduction in cancer, genetics and development, including human genetics, stem cells and organ development, infection and inflammation and metabolism and hormones. The de Duve Institute also features several core facilities, including imaging, transgenesis, mass spectrometry, flow cytometry and cell sorting, as well as genomics. The de Duve Institute provides access to a high-performance computing cluster and storage, managed by a dedicated IT team. Application 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 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; awards; 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 projects, select 1 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 academic references. References [1] Gatto et al. Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata. Bioinformatics 2014. DOI:10.1093/bioinformatics/btu013. [2] Crook et al. A Bayesian mixture modelling approach for spatial proteomics. PLOS Computational Biology 2018. DOI:10.1371/journal.pcbi.1006516. [3] Crook et al. Inferring differential subcellular localisation in comparative spatial proteomics using BANDLE. Nature Communication 2022. DOI: 10.1038/s41467-022-33570-9. --- Prof Laurent Gatto Computational Biology Unit (CBIO) de Duve Institute - UCLouvain Avenue Hippocrate, 75 - bte B1.74.10 1200 Brussels, Belgium Tel: +32 (0)2 764 74 15 http://lgatto.github.io/about

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