February 2024 - BBClist - maillist.psb.ugent.be

Learn more about Version control and Reproducibility
by BeNeLux bioinformaticians forum 09 Jul '24

09 Jul '24

Dear colleague, I bet you can relate with this image! [Image preview]Improve your versioning and research reproducibility! You have two opportunities to join uss! Check what fits you best! Click here to register: 29/Feb and 01/March - registration to: Introduction to Git & GitHub<https://training.vib.be/all-trainings/introduction-git-github-10> 16/May and 17/May - registration to: Introduction to Git & GitHub <https://training.vib.be/all-trainings/introduction-git-github-9> Come learn with us, at VIB<https://www.linkedin.com/company/vib/>, how to use Git and GitHub to a better version-control, code maintenance and to collaborate with your colleagues all together! Bruna Piereck Bioinformatics Training Expert VIB Technology Training ELIXIR Belgium Technologiepark-Zwijnaarde 75, 9052 Ghent - Belgium https://technologytraining.sites.vib.be<https://technologytraining.sites.vib.be/> | https://www.elixir-belgium.org/training [Graphical user interface Description automatically generated] [cid:image005.png@01DA5823.9AD438B0]

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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 researcher in Bioinformatics/Biostatistics (18-24 months): High Dimensional Integrated Unsupervised and Supervised Analysis of Single Cell RNASeq Data
by BeNeLux bioinformaticians forum 26 Feb '24

26 Feb '24

Dear, Can you please forward and share the email below with your e-mail list ? It is about a new Postdoc project in DSI-UHasselt. Please CC me on the email. Thanks in advance and best regards, ziv shkedy *The data science institute in Hasselt University announces a position for a (m/f/x):* *Postdoc researcher in Bioinformatics/Biostatistics** (18-24 months): **High Dimensional Integrated Unsupervised and Supervised Analysis of Single Cell RNASeq Data* *General information about the project * The postdoc research project will be conducted in a close collaboration between the data science institute (DSI, https://www.uhasselt.be/en/instituten-en/dsi) in Hasselt University and a global pharmaceutical company. The main objective of the postdoc research project is to analyze single cell omics data for immune profiling purposes applied to vaccinology. The project is focused on algorithm/procedures/software testing and development using publicly and in house available dataset with application on real vaccine development . Both parts will be based on single cell omics data generated on *Chromium 10X Genomics platform*. Data analysis tools and software products that will be developed in this project would be available as R or Python packages with full documentation. *Project description* The research project consists of two main tasks: *Task 1 - Unsupervised analysis:* 1) To identify the best numerical embedding methods for TCR/BCR protein sequences in order to merge this feature with other OMICs layers. 2) To identify methods for single omics and multi-omics clustering (gene expression, individual TCR sequences, surface proteins) that can better approximate antigen-specificity. *Task 2 - Supervised analysis:* Based on the results obtained in part 1, we will define which of the identified features may be predictive of antigen specificity and cross-reactivity. *Data analysis methods*: cluster analysis for single cell RNAseq data (for both single and multi-omics setting) , biclustering, classification and prediction. *Profile and diploma* As a postdoc researcher you will join the dynamic functional genomics team in the data science institute (DSI) in UHasselt and will collaborate with scientists from both academia and industry. The research work related to both tasks will be conducted in a close collaboration between DSI and the pharmaceutical company and the postdoc researcher will work in both organizations. A successful candidate should have - PhD in bioinformatics/ statistical bioinformatics/biostatistics (with experience of high dimensional data). - A PhD whose research focuses on single cell analysis is an advantage but not a must. - A PhD whose research is on AI/ML methodologies for unsupervised and supervised HD data analysis is a plus. - You are acquainted with statistical methodologies and had exposure to computer programming in R/Python. - You published manuscripts in the area of bioinformatics/biostatistics. - You developed software package(s) as a part of your PhD research. - You are interested in developing new methodology from both theoretical and applied aspects. - You are interested in developing software to the pipeline for data analysis and implement this software within a company environment. - You are willing to closely collaborate with biologists/biostatistians/bioinformations from the pharmaceutical industry. - You have a strong interest in working on both vaccine and drug development problems. - You can work independently and within a team. - You have excellent communication skills. - You can lead a team of researchers within a project. - You enjoy working in a multidisciplinary and multicultural environment. - You speak and write English fluently. *Offer* The appointment takes effect from January 2024 and at the latest from March/April 2024 for a period of 18-24 months, depending on the candidate experience. *Further information* Prof. dr. Ziv Shkedy, +32 11-26 82 40, ziv.shkedy(a)uhasselt.be <christel.faes(a)uhasselt.be> *Application*Applicants must send their application to ziv.shkedy @uhasselt.be <christel.faes(a)uhasselt.be> *Please add a copy of your PhD diploma and CV (including publication list) to your application.* Deadline for the Application 30, March, 2024

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Postdoc opportunity for Bioinformatician and Computational Biologist
by BeNeLux bioinformaticians forum 22 Feb '24

22 Feb '24

Are you a Computational Biologist or Bioinformatician with a Ph.D. degree who is eager to unravel the onset and development of Multiple Sclerosis, please apply to this great opportunity: https://www.werkenbijerasmusmc.nl/en/vacancy/96762/computational-biologist-… All the best, Harmen van de Werken _______________________________________________________________ More info: EMC homepage<https://www.erasmusmc.nl/en/research/researchers/werken-harmen-van-de> and/or EMC Immunology<https://www.immunology.nl/research/harmen-van-de-werken/> and @vandeWerkenLab<https://twitter.com/vandeWerkenLab>

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Disease Maps Community Meeting 2024: Registration deadline extended
by BeNeLux bioinformaticians forum 22 Feb '24

22 Feb '24

[Apologies for multiple postings] Registration for the 8th Disease Maps Community Meeting extended! https://disease-maps.org/DMCM2024 Register via this registration form<https://disease-maps.org/DMCM2024#:~:text=Please%20register%20by%2025th%20F…> by 2nd of March 2024. When: 25th-27th of March 2024 Where: University of Luxembourg, Esch-sur-Alzette, Luxembourg [link<https://www.uni.lu/en/about/campuses/belval-campus>] DMCM’24 a joint event of the Disease Maps Community<https://disease-maps.org/> and the ELIXIR Systems Biology Community<https://elixir-europe.org/communities/systems-biology>. See the agenda<https://disease-maps.org/DMCM2024/programme/> for more details about our keynote speakers, talks and posters. Featured workshop imSAVAR Symposium: Disease maps and irAOPs in the immune system effects of immunomodulatory therapies. https://imsavar.eu<https://imsavar.eu/> Scope We will focus on systems medicine topics, including tools, standards, and applications of bioinformatics, computational and systems biology to research on human diseases. Join us to discuss challenges of building reliable models of disease mechanisms from prior knowledge and data and applying their predictions. The topics include, but are not limited to: * Curation of diagrammatic models of diseases using systems biology standards * Visual analytics of systems biology diagrams * Modelling of disease mechanisms: network-based, Boolean or continuous * Interpreting multi-omics data using systems biology diagrams * Applications of omics data for model building and parameterisation With warm regards, on behalf of the organisers --- 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<http://lcsb.uni.lu/> --- 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<http://lcsb.uni.lu/>

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(Generative) AI in Biology - BioSB HotTopics Seminar
by BeNeLux bioinformaticians forum 21 Feb '24

21 Feb '24

BioSB is happy to invite you to the next BioSB HotTopics meeting: (GENERATIVE) AI in BIOLOGY 27 March, from 13:00 on, O2 building, VU Amsterdam BioSB HotTopic Symposia are organized with the goal of bringing together researchers (novice and experienced) around a topic to learn from each other in an informal setting. These symposia are usually very enthusiastically received, so be sure to attend! Information and Registration: Check our website<https://www.dtls.nl/events/biosb-hottopics-symposium-generative-ai-in-biolo…> and see poster below. Be aware: Registration deadline = 11 March! [cid:part1.0vZB3cl0.ffmV0RFF@health-RI.nl] Best wishes, Petra Aarnoutse Community manager BioSB [cid:part2.dbNkk8e9.wKT62UXk@health-RI.nl]

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BioSB2024 - YOUNG SCIENTIST AWARD!
by BeNeLux bioinformaticians forum 21 Feb '24

21 Feb '24

Dear colleagues, As announced, researchers from TU Delft and the BioSB research school are well on their way organizing the tenth edition of: BioSB2024<https://www.aanmelder.nl/biosb2024> 18 - 19 June 2024, Egmond aan Zee, The Netherlands (Click here<https://www.aanmelder.nl/biosb2024> for more information). Are you a PhD candidate of bioinformatics or systems biology and finished your PhD recently (or very soon) than check out the: BioSB Young Investigator Award 2024! (info on how to apply, check the website<https://www.aanmelder.nl/biosb2024/yia2024>) During BioSB 2024, we will present the 15th edition of the BioSB Young Investigator Award. The winner will receive a voucher of 500 Euros sponsored by the BioSB research school and will be invited to present an honorary lecture in the plenary programme. The submission deadline is set to April 12, 2024. Stay tuned as information on the 4 confirmed keynotes will follow the coming weeks, thanks to the Co-chairs of the conference: Jana Marie Weber and Jasmijn Baaijens and the rest of this engaged committee: Sandra Smit, Michiel Adriaens, Anton Feenstra, Ahmed Mahfouz, Julia Kamenz, Ali May, Renee Menezes, Andrew Stubbs, Celia van Gelder and Vartika Bisht. We hope to see you soon @BioSB2024! Best wishes, Petra Aarnoutse Community manager BioSB ----------------------------------------------------------------- See also our former message: CALL FOR ABSTRACTS ALERT ALERT ALERT - Coming up - ALERT ALERT ALERT BioSB2024<https://www.aanmelder.nl/biosb2024> 18 - 19 June 2024, Egmond aan Zee, The Netherlands (Click here<https://www.aanmelder.nl/biosb2024> for more information and registration). This tenth edition of the successful BioSB conference series is co-organised by the TU Delft and the BioSB Research school. Are you a bioinformatician, and/or working in the field of systems and computational biology or interrelated disciplines (eg life sciences & health, agriculture, food & nutrition research)? Take advantage of this opportunity to showcase your research at @BioSB2024! Be quick, the submission deadline is closing soon. Submit your abstract before 8 March! <https://easychair.org/conferences/?conf=biosb2024> Check the website<https://www.aanmelder.nl/biosb2024/abstract-submission> for further details. We hope to see you soon @BioSB2024! Best wishes, Petra Aarnoutse Community manager BioSB [cid:part1.7UVFcwCZ.hyZTHslW@health-RI.nl]

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BioSB2024 - CALL FOR ABSTRACTS - Deadline 8 March
by BeNeLux bioinformaticians forum 21 Feb '24

21 Feb '24

ALERT ALERT ALERT - Coming up - ALERT ALERT ALERT BioSB2024<https://www.aanmelder.nl/biosb2024> 18 - 19 June 2024, Egmond aan Zee, The Netherlands (Click here<https://www.aanmelder.nl/biosb2024> for more information and registration). This tenth edition of the successful BioSB conference series is co-organised by the TU Delft and the BioSB Research school. Are you a bioinformatician, and/or working in the field of systems and computational biology or interrelated disciplines (eg life sciences & health, agriculture, food & nutrition research)? Take advantage of this opportunity to showcase your research at @BioSB2024! Be quick, the submission deadline is closing soon. Submit your abstract before 8 March! <https://easychair.org/conferences/?conf=biosb2024> Check the website<https://www.aanmelder.nl/biosb2024/abstract-submission> for further details. We hope to see you soon @BioSB2024! Best wishes, Petra Aarnoutse Community manager BioSB [cid:part1.Vkwvp6sH.WetEqhhw@health-RI.nl]

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ABLS2024: only 3 days left until the final registration deadline
by BeNeLux bioinformaticians forum 19 Feb '24

19 Feb '24

Dear colleague, There are only 3 days left until the Final Registration deadline, of 22 February, so this is a last chance to join your colleagues at the 5th edition of Applied Bioinformatics in Life Sciences. This VIB Conference will take place on 7-8 March 2024 in the beautiful city of Leuven, Belgium. Find out what 18 key academia researchers have to say about the latest developments in: Personalized medicine and clinical bioinformatics >From genome to function >From single cell to organism Synthetic biology and structural bioinformatics Make sure not to miss this opportunity and register now for ABLS24. Register here: https://www.vibconferences.be/events/applied-bioinformatics-in-life-science… Best regards, Alex Alexander Botzki Team Lead Technology Training, ELIXIR Belgium Training Coordinator VIB Technology Training ELIXIR Belgium Technologiepark-Zwijnaarde 75, 9052 Ghent – Belgium https://technologytraining.sites.vib.be<https://technologytraining.sites.vib.be/> | https://www.elixir-belgium.org/training [Graphical user interface Description automatically generated] [Hx1KyM2Q09lnAAAAAElFTkSuQmCC]

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two postdoc positions in bioinformatics of Cyanobacteria - Liège
by BeNeLux bioinformaticians forum 13 Feb '24

13 Feb '24

Dear all, We have two >2-year positions in ULiège (Belgium) to work on the genomics of Cyanobacteria (and fungi). One is for a computational biologist and the other for a bioinformatician experienced in FAIR science. Please have a look here (Faculty of Sciences) for more information: https://www.uliege.be/cms/c_9131376/en/scientific-positions. Inquiries to me (denis.baurain(a)uliege.be<mailto:denis.baurain@uliege.be>) or Luc Cornet (luc.cornet(a)uliege.be<mailto:luc.cornet@uliege.be>). Best regards, Denis Baurain -- Prof. Denis BAURAIN Président du Collège de Doctorat BBMC-BIM University of Liège InBioS - PhytoSYSTEMS, Eukaryotic Phylogenomics Sart Tilman, Quartier Vallée 1 Chemin de la Vallée 4, Bât. B22 4000 Liège Belgium "If I Had More Time, I Would Have Written a Shorter Letter." Blaise Pascal, 1657

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