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Job Offer - Research Engineer - Use of acoustic information in chatbots (RE1)
by BeNeLux bioinformaticians forum 12 Mar '24

12 Mar '24

Hello, I hope this email finds you well. I am contacting you because we have opened a new Reasearch Data Engineer data vacancy for two candidates 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: * *Research Data Engineers (RE1-RE2) - Biomedical data integration and FAIR data management**:*https://www.bsc.es/join-us/job-opportunities/6624lsltre1 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, Aldara Cárdenas Pereira /Human Resources - Junior HR Talent Acquisition Officer/ *Barcelona Supercomputing Center - Centro Nacional de Supercomputación* aldara.cardenas(a)bsc.es www.bsc.es <http://www.bsc.es/>

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5th Workshop in single cell data analyses 2024 (Roscoff, France)
by BeNeLux bioinformaticians forum 12 Mar '24

12 Mar '24

Dear all, Please find below the announcement for the 5th Workshop in single cell data analyses 2024 Best, Morgane ------------------------------------ Training : Single-Cell : Transcriptomics, Spatial and Long reads (sincellTE) Date : 20th October 2024 – 25th October 2024 Place : Roscoff, France Deadline pre-registration: 7th May 2024 This one-week class focuses on the large-scale study of heterogeneity across individual cells from a genomics and transcriptomics points of view. Recent technological developments enable the characterization of molecular information at a single cell resolution for large numbers of cells. The high dimensional omics data that these technologies produce comes with novel methodological challenges for the analysis. In this regard, specific bioinformatics and statistical methods have been developed in order to extract robust information. This course is directed towards engineers and researchers who regularly need to undertake single-cell data analysis as well as PhD students and postdoctoral fellows in computational biology or bioinformatics that are interested in the development of methods and pipelines for highly dimensional single-cell data analysis. A wide range of single cell topics will be covered in lectures, demonstrations and practical classes. Among others, the areas and issues to be addressed will include the choice of the most appropriate single-cell sequencing technology, the experimental design and the bioinformatics and statistical methods and pipelines. For this edition, new courses/practicals will focus on spatial transcriptomics, long reads, artificial intelligence and FAIR access to the data/code. Requirements : Participants must have prior experience on NGS data analysis with everyday use of R and/or Python and good knowledge of Unix command line. Before the training, participants are advised to familiarize themselves with the processing and primary analyses steps of scRNA-seq datasets. It is not necessary to have personal single-cell data to analyse. All information and pre-registration: https://moodle.france-bioinformatique.fr/course/view.php?id=27

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Quest for Orthologs meeting in Montreal
by BeNeLux bioinformaticians forum 09 Mar '24

09 Mar '24

Dear all, We would like to warmly invite you to the 2024 edition of the Quest for Orthologs meeting (QFO8), to be held on July 17-18, 2024 (right after the ISMB) at the University of Quebec in Montreal, Canada. You can now submit your abstract on the event’s website https://event.fourwaves.com/qfo8 . The abstract submission is open until 26 April 2024. Confirmed speakers so far include Dr. Elena Kuzmin, Dr. Markus Hecker, Dr. Fiona Brinkman, and Dr. Christine Orengo. Best regards, QFO8 organizing committee

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ISMB 2024 CompMS – Save the date & call for proposals
by BeNeLux bioinformaticians forum 09 Mar '24

09 Mar '24

— ISMB 2024 CompMS – Save the date & call for proposals — [https://lh7-us.googleusercontent.com/O9LcuwC_7daAW4J8dfF4Slz7UeSm9KM6DyxOVu…] Dear colleagues, Please join us during the ISMB 2024 conference in Montreal, Canada for the Computational Mass Spectrometry (CompMS) COSI session on July 12–16, 2024. The Intelligent Systems for Molecular Biology (ISMB) is the world’s largest bioinformatics/computational biology conference. Every year it brings together scientists from computer science, molecular biology, mathematics, statistics, and related fields and provides an intense multidisciplinary forum for disseminating the latest developments in bioinformatics/computational biology. The conference fosters fresh dialogues, collaboration and learning opportunities, and is a gathering which shapes the future of the field. At the heart of the scientific program are ISCB’s Communities of Special Interest (COSIs), enabling community involvement and bolstering ISMB’s reputation as the leading conference in the field. The CompMS COSI promotes the efficient, high-quality analysis of mass spectrometry data through dissemination and training in existing approaches and discussion of new, innovative approaches. The CompMS initiative aims to exploit synergies between different mass spectrometry-based application domains, in particular proteomics, metabolomics, and lipidomics. A strong scientific and technical program showcases the best international developments in bioinformatics and computational biology, making ISMB 2024 a must attend event. Virtual participation options are also available. New this year! Join us for the CompMS social event at 3 Brasseurs (1255A Crescent St, Montreal, Quebec H3G 2B1, Canada) on Monday July 13, 2024 for a fun get-together with your fellow computational mass spectrometry enthusiasts! Register for the social event during your ISMB conference registration. New this year! We are delighted to offer travel fellowships for early-career researchers (ECRs)! Fill out this form<https://forms.gle/HVYXSjQkMLvG87Zq5> to apply for one of the C$400 travel fellowships. Eligibility criteria include being an early career researcher (undergraduate student, graduate student, postdoctoral researcher, or equivalent) and having submitted an abstract to the CompMS track. Date: * ISMB: July 12–16, 2024 * CompMS COSI: July 13, 2024 * CompMS social event @ 3 Brasseurs: July 15, 2024 Venue: Palais de Congrés de Montréal, Montreal, Canada / virtual Website: https://www.iscb.org/ismb2024 Key dates April 19, 2024: Abstract & travel fellowship submission deadline May 13, 2024: Talk/poster acceptance notifications May 20, 2024: Late poster submission deadline May 28, 2024: Late poster acceptance notifications July 12–16, 2024: ISMB conference Call for proposals Abstract submission for ISMB 2024 is now open! Submit your abstract to ISMB to present your work at the leading bioinformatics/computational biology conference. Attend the CompMS session to learn about the latest algorithmic advances in computational mass spectrometry. Please remember to select the CompMS COSI as your session of interest upon submitting your abstract. Call for abstracts: https://www.iscb.org/ismb2024/submissions/abstracts ECR travel fellowship application: https://forms.gle/HVYXSjQkMLvG87Zq5 We look forward to seeing you at ISMB! The CompMS organizing committee. Wout Bittremieux Isabell Bludau Marie Brunet Lindsay Pino Timo Sachsenberg We are grateful to acknowledge sponsoring by MSAID. [https://lh7-us.googleusercontent.com/4O-y2Fd55JO2rRlkuBxCnth-qHvAM42eqObx3G…]

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Job opening: Head Data System Architect
by BeNeLux bioinformaticians forum 07 Mar '24

07 Mar '24

Dear BBC list reader, We have an job opening for a head data system architect at TUDelft for the CROP-XR ‘Nationaal Groeifonds’ program. You can find the job posting below and in the following url: https://www.tudelft.nl/over-tu-delft/werken-bij-tu-delft/vacatures/details?… Best regards, Marcel Reinders, TUDelft. ---------------------------------------------------------------------------- Head Data System Architect Designing the nation-wide data infrastructure with which the Netherlands will create eXtra Resilient (XR), sustainable, and climate-adaptive crops by adopting a smart data approach. Job description We are searching for the head data system architect with a vision to design a scalable infrastructure combining cloud systems, high performance computing, storage and distribution of complex data streams, systems to learn machine and mechanistic models, and who has an affinity with plant biology. As such you should be comfortable with designing a data lake and/or data warehouse optimized for agricultural data. You should be at ease with various data storage models including relational databases, object storage, and other storage modalities. Importantly, you base decisions on acquired technical expertise to model complex relationships tailored to agricultural informatics needs.The nation-wide infrastructure will be built as part of the National Growth fund CropXR program in which more then 50 business partners and four universities take part. To setup this DataXR infrastructure a significant team will be appointed that will implement your vision on sharing and analysing data (a budget of ~10ME is reserved for that). Your job will include integrating the needs of many partners, building the expert team, as well as collaborating with multidisciplinary implementation teams and data providers. Requirements Master degree in computer science or related field. Proven technical expertise on design and implementation of data infrastructures. For example, experience with setting up data warehouses or data lakes. Experience and certification with (a) major cloud provider(s) is considered a plus. Experience with hybrid architectures is a plus. Affinity with designing and implementing data models that meet both technical and business needs. Proven ability to work effectively within multidisciplinary teams. Fluent in written and spoken English. Strong desire to contribute shaping the data infrastructure of the future for academic and industrial plant biology. Conditions of employment Appointment will be a the Delft University of Technology, within the Faculty of Electrical Engineering, Mathematics and Computer Science (EEMCS), ensuring a strong engineering embedding. Intense collaborations with other partners is required. * A salary based on scale 10 or 11 (depending on the working experiencce and education level of the candidate) of the CAO for Dutch Universities with a minimum of € 3.226 - € 5.090, (scale 10) € 4.332 - € 5.929 (schale 11) gross per month based on a fulltime contract (38 hours), plus 8% holiday allowance and an end-of-year bonus of 8.3%. * An excellent pension scheme via the ABP. * The possibility to compile an individual employment package every year. * Discount with health insurers. * Flexible working week. * Every year, 232 leave hours (at 38 hours). You can also sell or buy additional leave hours via the individual choice budget. * Plenty of opportunities for education, training and courses. * Partially paid parental leave * Attention for working healthy and energetically with the vitality program. TU Delft (Delft University of Technology) Delft University of Technology is built on strong foundations. As creators of the world-famous Dutch waterworks and pioneers in biotech, TU Delft is a top international university combining science, engineering and design. It delivers world class results in education, research and innovation to address challenges in the areas of energy, climate, mobility, health and digital society. For generations, our engineers have proven to be entrepreneurial problem-solvers, both in business and in a social context. At TU Delft we embrace diversity as one of our core values<https://www.tudelft.nl/en/about-tu-delft/strategy/integrity-policy/tu-delft…> and we actively engage<https://www.tudelft.nl/en/about-tu-delft/strategy/diversity-inclusion> to be a university where you feel at home and can flourish. We value different perspectives and qualities. We believe this makes our work more innovative, the TU Delft community more vibrant and the world more just. Together, we imagine, invent and create solutions using technology to have a positive impact on a global scale. That is why we invite you to apply. Your application will receive fair consideration. Challenge. Change. Impact! Faculty Electrical Engineering, Mathematics and Computer Science The Faculty of Electrical Engineering, Mathematics and Computer Science (EEMCS) brings together three scientific disciplines, with two Computer Science departments: Software technology and Intelligent Systems <https://www.tudelft.n/ewi/over-de-faculteit/afdelingen/intelligent-systems> (both affiliated with this position). EEMCS drives the TU Delft AI Initiative that unites and strengthens the AI, data and digitalisation<https://www.tudelft.nl/ai> developments at TU Delft. The Computer Science departments recently initiated a dedicated Research Engineering task force that supports all researchers with complex computer science implementations. Expertise that you can exploit. Click here<https://www.tudelft.nl/ewi/> to go to the website of the Faculty of Electrical Engineering, Mathematics and Computer Science. CropXR CropXR<https://cropxr.org/> was launched in 2023 to help make agricultural production less vulnerable to climate change and less dependent on artificial fertilizers and chemical pesticides. The institute is a joint venture of the universities of Amsterdam, Delft, Wageningen and Utrecht in partnership with Plantum, the Dutch plant breeding sector association. CropXR brings together efforts from different academic disciplines (such as plant sciences, computational and data sciences, and social sciences) and private industry to help bring about sustainable change. It receives support from NWO, the Dutch National Growth Fund, and the Foundation for Food & Agricultural Research. Learn more about CropXR at cropx.org Additional information If you have any questions, please contact prof. Marcel Reinders (m.j.t.reinders(a)tudelft.nl<mailto:m.j.t.reinders@tudelft.nl>). Application procedure Are you interested in this vacancy? Please apply before April 15, 2024 via the application button and upload your motivation and CV. * A pre-employment screening can be part of the selection procedure. * You can apply online. We will not process applications sent by email and/or post. * Please do not contact us for unsolicited services.

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Postdoctoral research position at the Barts Cancer Institute - Queen Mary University London
by BeNeLux bioinformaticians forum 06 Mar '24

06 Mar '24

Hi all, Are you an enthusiastic PhD interested in developing bioinformatics approaches to understand the role of transposable elements in cancer? Ozgen Deniz <https://www.bartscancer.london/staff/dr-ozgen-deniz/>'s team at the Barts Cancer Institute <https://www.bartscancer.london/> (Queen Mary University of London) has a postdoctoral opening. Check it out and apply! https://www.jobs.ac.uk/job/DFN649/postdoctoral-research-assistant Application deadline *20th March* Thanks, Sergio --------------------------- We are looking for a computational postdoctoral research assistant to join our group at the Barts Cancer Institute, London. The appointed PDRA will be integrated into a multidisciplinary team and will collaborate with bioinformaticians, experimentalists and clinicians and develop/apply transposable elements-centered bioinformatic pipelines for transcriptomic and epigenomic data sets. The post is funded by the Cancer Research UK, full time (35 hours per week) and fixed term appointment for 30 months with potential extension. The application deadline is 20th March. For more information and questions, see the job advertisement attached and contact us (o.deniz(a)qmul.ac.uk)

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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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