- BBClist - maillist.psb.ugent.be

Two postdoc positions in machine learning for single-cell genomics
by Laura CANTINI 30 Nov '22

30 Nov '22

Dear colleague, I have an opening for *two postdoc positions in machine learning for single-cell genomics* in my team, currently at École Normale Supérieure (ENS https://www.ens.psl.eu/en) and soon (Jan 2023) joining Institut Pasteur (https://www.pasteur.fr/fr) The team is also part of the PaRis Artificial Intelligence Research InstitutE (PRAIRIE https://prairie-institute.fr/) The extended text of the call is attached. I would be grateful if you could forward the enclosed description to potentially interested candidates or colleagues. Best, Laura Cantini

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PhD Positions in Computational Research, Data Science and AI at the German Cancer Research Center (DKFZ)
by DKFZ PhD Program 28 Nov '22

28 Nov '22

Dear Colleague, I would like to draw your attention to our International PhD Program at the German Cancer Research Center (DKFZ) in Heidelberg, Germany, which might be of interest to your students who are seeking further research in the area of Computational Research, Data Science and Artificial Intelligence. The application deadline is 15. December 2022 and more information about the program and how to apply online can be found here<https://www.dkfz.de/en/phd-program/index.html?campaign=phd/compmsc>. I would be very grateful if you could forward this information and the infosheet attached to potential candidates at your institution. If you prefer not to receive similar e-mails in the future, please do not hesitate to contact me. Many thanks and best wishes, Michaela Steiner PhD Program Office DKFZ International PhD Program (M070) German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 280 69120 Heidelberg Germany phone: +49 6221 42-3426 www.dkfz.de<http://www.dkfz.de/>/phd [cid:image003.jpg@01D37287.86ACA850] Management Board: Prof. Dr. med. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537

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Last CFP OLA'2023 @Malaga (Spain)
by El-Ghazali Talbi 24 Nov '22

24 Nov '22

Apologies for cross-posting. Appreciate if you can distribute this CFP to your network. **************************************************************************************** OLA'2023 International Conference on Optimization and Learning 3-5 May 2023 Malaga, Spain http://ola2023.sciencesconf.org/ SCOPUS Springer Proceedings **************************************************************************************** OLA is a conference focusing on the future challenges of optimization and/or machine learning methods and their applications. The conference OLA'2023 will provide an opportunity to the international research community in optimization and learning to discuss recent research results and to develop new ideas and collaborations in a friendly and relaxed atmosphere. OLA'2023 welcomes presentations that cover any aspects of optimization and/or machine learning research such as big optimization and learning, optimization for learning, learning for optimization, optimization and learning under uncertainty, deep learning, new high-impact applications, parameter tuning, 4th industrial revolution, computer vision, hybridization issues, optimization-simulation, meta-modeling, high-performance computing, parallel and distributed optimization and learning, surrogate modeling, multi-objective optimization ... Submission papers: We will accept two different types of submissions: - S1: Extended abstracts of work-in-progress and position papers of a maximum of 3 pages - S2: Original research contributions of a maximum of 10 pages Important dates: =============== Paper submission extended deadline Dec 16, 2022 Notification of acceptance Feb 17, 2023 Proceedings: Accepted papers in categories S1 and S2 will be published in the proceedings. A SCOPUS and DBLP indexed Springer book will be published for accepted long papers. Proceedings will be available at the conference. Prof. El-ghazali TALBI University of Lille - CRISTAL UMR CNRS INRIA Lille Nord Europe ************************************************** OLA'2023 Int. Conf on Optimization and Learning May 3-5, 2023, Malaga, Spain http://ola2023.sciencesconf.org **************************************************

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Postdoc position rose pangenomics
by Smit, Sandra 23 Nov '22

23 Nov '22

The Genome Biology Unit of Wageningen University is looking for a postdoc to explore diversity in a rose pangenome. The vacancy will be open until Dec 1st and the description can be found here: https://www.wur.nl/en/vacancy/postdoc-position-exploring-diversity-in-a-ros… Are you interested in genetic diversity in one of the world’s most well-known plant species and are you ready to contribute to this state-of-the-art genomics project with your extensive bioinformatics experience? We look forward to your application. Kind regards, Sandra --- Sandra Smit Assistant professor Bioinformatics Group Wageningen University The Netherlands Sandra.Smit(a)wur.nl ---

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Bioinformatician position at the Spanish National Cancer Research Center (CNIO)
by Eva Alloza 23 Nov '22

23 Nov '22

Dear all, The Bioinformatics Unit <https://www.cnio.es/en/research-innovation/scientific-programmes/structural…> at the Spanish National Cancer Research Center (CNIO) in Madrid, Spain, and part of INB/ELIXIR-ES, has an *open position for a bioinformatician*. The selected candidate will work in the collection, analysis, and interpretation of biological/clinical data, with a focus on high-throughput sequencing data. He/She will design data analysis strategies and develop and use computational tools for the exploration of large cancer data sets. The vacancy will be open until December 5th and the description can be found here: https://www.cnio.es/en/empleo/advanced-degree-for-the-bioinformatics-unit-t… Best regards, -- -- Eva Alloza Training coordinator and support officer Spanish National Bioinformatics Institute (INB/ELIXIR-ES) coordination node mail:eva.alloza@bsc.es web:http://inb-elixir.es Barcelona Supercomputing Center (BSC-CNS) Pl. Eusebi Güell, 1-3. E-08034 Barcelona, Spain

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PhD project in UHasselt and SCK-CEN
by Ziv SHKEDY 22 Nov '22

22 Nov '22

Dear, Can you please forward and share this email with your e-mail list ? It is about a new PhD project in DSI-UHasselt. Please CC Prof. Jurgen Claesen ( jurgen.claesen(a)uhasselt.be) on the email. Thanks in advance, ziv shkedy & Jurgen Claesen . *A 4 years full time PhD project in DSI, UHasselt & SCK-CEN.* *Title: Integromics - Towards integration of big biomolecular data to enable systems biology* 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 analysed 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. The PhD project is a joint project between CenStat, DSI and SCK•CEN ( https://www.sckcen.be/en) The thesis project is focused on methodologies for the analysis of multi-omics datasets allowing a multi-dimensional view on complex biological processes. In the current thesis project, we focus on methods for the analysis of multi-omics datasets (gene expression, proteomics etc), that are commonly generated by the three biology units of SCK•CEN (https://www.sckcen.be/en) which will improve the understanding of the biological data of interest. The datasets for the project are already available and will be provided (with R program to read the data) at the beginning of the project. Starting date: during the second part of 2023. Project duration: 4 years. Student's profile: MSc in biostatistics/statistics/bioinformatics or equivalent. Supervision UHasselt: Prof. Ziv Shkedy (ziv.shkedy(a)uhasselt.be) and Prof. Jurgen claesen (jurgen.claesen(a)uhasselt.be) Supervision SCK-CEN Dr. Surya Gupta (surya.gupta(a)sckcen.be)

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Vacancy for a PhD student in microbial genomics, bioinformatics, and systems biology
by Stefan WECKX 22 Nov '22

22 Nov '22

Dear all, The Research Group of Industrial Microbiology and Food Biotechnology (IMDO) of the Vrije Universiteit Brussel (https://imdo.vub.ac.be) Belgium, is looking for a highly motivated PhD student to perform PhD research in the framework of the HealthFerm project (Horizon Europe; https://www.healthferm.eu/) The overall aim of this project is to unravel the interactions between the microbiota of cereal-based fermented foods, in particular sourdough and borş, and the human gut microbiome and health. More in detail, the PhD student will perform genotypic characterization of a selection of microorganisms obtained by the project consortium by means of advanced genome sequencing (second and/or third generation sequencing methodologies), gene prediction, and functional annotation. Genome-wide metabolic models will be made for a selection of promising microorganisms to better understand and predict their metabolism and physiology. The candidate needs to have a university degree at Master level (Bioengineering Sciences or an equivalent degree), with in-depth knowledge of and interest in (food) microbiology, biochemistry, bioinformatics, including hands-on experience with Linux and scripting (Python, R), fermentation technology, and/or food science and technology. Important additional qualifications are sense of initiative and responsibility, group spirit, motivation and dynamism, a hardworking attitude, persistence, and good communication and reporting skills. Good knowledge of the English language (spoken and written) is required. The candidate will be embedded in a young, creative, dynamic, pluralistic, diverse, and international working environment. Salary according to the applicable scales for PhD students. Benefits according to the university's general benefits scheme (https://jobs.vub.be/content/Benefits/) If interested, please contact and send your application letter with curriculum vitae and Transcript of Records to Prof. Dr. Stefan Weckx, stefan.weckx(a)vub.be<mailto:stefan.weckx@vub.be>. Thank you for spreading this vacancy announcement within your network. Best regards, Stefan Weckx [Logo VUB]<http://www.vub.ac.be/> Prof. Dr. Stefan WECKX Research Group of Industrial Microbiology and Food Biotechnology Department of Bioengineering Sciences Faculty of Sciences and Bioengineering Sciences Vrije Universiteit Brussel VUB - IMDO - Pleinlaan 2 - 1050 Brussels - Belgium T +32 (0)2 629 38 63 (direct) T +32 (0)2 629 32 45 (secretary) F +32 (0)2 629 27 20 E stefan.weckx(a)vub.be<mailto:stefan.weckx@vub.be> www.vub.be<http://www.vub.be/> - imdo.vub.ac.be<http://imdo.vub.ac.be/> - disclaimer<http://huisstijl.vub.ac.be/styleguide/disclaimer> [http://www.vub.ac.be/sites/vub/files/Handtekening/triangle.png]

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R&D Data Sciences & AI Graduate Programme - AstraZeneca UK
by Sergio Martinez Cuesta 22 Nov '22

22 Nov '22

If you have a quantitative science focussed bachelor’s or master’s degree and a desire to explore and develop your skills in data science and artificial intelligence within a global biopharmaceutical organisation, our R&D Data Science & AI Graduate Programme could be the perfect start to your career. You’ll gain invaluable insight, exposure and opportunities across our diverse, Research and Development organisation. We’ll accelerate your learning and help you achieve your potential. To find out more, please check: https://careers.astrazeneca.com/job/cambridge/r-and-d-data-sciences-and-ai-… Thanks, Sergio

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Two calls for Tutorials - ISMB/ECCB and [BC]2
by Celia van Gelder 18 Nov '22

18 Nov '22

*FYI* Dear colleagues, Please note that there are two open calls for tutorials: 1. Tutorials for ISMB/ECCB 2023 <https://www.iscb.org/ismbeccb2023-submissions/tutorials> – deadline for submissions *19 December 2022*. 1. Tutorials and Workshops for [BC]2 2023 <https://www.bc2.ch/tutorials-workshops-calls> – deadline for submissions *8 January 2023*. You are most welcome to submit your proposals and forward this message to anyone. Many thanks and all the best, Patricia -- *Patricia Palagi, PhD SIB Training SIB | Swiss Institute of Bioinformatics Quartier Sorge, Bâtiment Amphipôle - 1015 Lausanne - Switzerland patricia.palagi(a)sib.swiss <patricia.palagi(a)sib.swiss> - www.sib.swiss <http://www.sib.swiss> * -- Dr. Celia W.G. van Gelder Training Programme Manager DTL/ELIXIR-NL/Health-RI Network Manager TDCC-LSH tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl websites: https://www.dtls.nl/, https://www.health-ri.nl/, https://www.elixir-europe.org/platforms/training twitter: celia_vgelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours.

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EPB-ULB : full-time academic position
by GILIS Dimitri 17 Nov '22

17 Nov '22

Dear all, The Brussels School of Engineering will open a full-time academic position in Computational Modeling of Biomolecular systems. The job description is summarised below, and the full vacancy will be published on the following site from 1/12/2022 : https://www.ulb.be/fr/vacances-d-emplois-academiques-et-scientifiques/liste… Best regards. ---------------------------------------------------------- Dimitri Gilis Professeur 3BIO-Bioinfo École polytechnique de Bruxelles Phone: +32 2 650 36 15 E-mail: dimitri.gilis(a)ulb.be<mailto:dimitri.gilis@ulb.be> ------------------------------- Job description A mechanistic understanding of complex biological systems requires the consideration of multiple spatial and temporal scales, and their integration into holistic models or networks. Fluctuations play a major role in the dynamics of many of these processes and have to be considered to obtain a realistic description of these systems and their evolution. The large amounts of high-throughput biological data that are currently being produced, from the molecule to the organism scales, are an unprecedented source of information and a stepping stone to advance these issues. To address the key challenges of biomolecular modeling, innovative mathematical, computational and modeling approaches need to be developed. In this context, the candidate should be an expert in the modeling of: * Biomolecular systems (proteins, DNA, RNA, …) * Biological networks (interactome, gene regulatory networks, disease networks, …) and this expertise should cover multiples molecular scales He/she should also have a solid expertise in several of the following techniques: * Physics-oriented multi-scale modeling * Structural bioinformatics and biomolecular design * Dynamical and stochastic modeling of complex systems * Data-driven modeling of biological networks * State-of-the-art machine learning techniques * Evolutionary and coevolutionary techniques Area of Research: Transdisciplinary – bioinformatics, computational molecular biophysics, computational biology Educational and scientific goals: The successful candidate is expected to integrate into the existing teaching activities of the Schools of Engineering and Bioengineering, and to develop new, top-level, scientific activities in collaboration with other groups of the Schools of Engineering and Bioengineering and the Faculty of Sciences, in particular with the ULB/VUB Interuniversity Institute of Bioinformatics in Brussels ((IB)²). Courses covered at the time of recruitment: The appointed academic will take the responsibility of parts of the following courses: * In the Master 1 in Bioengineering and in the Master 2 in Biomedical Engineering * Introduction à la bioinformatique et à ses applications (partim of 18h in a 5 ECTS course) * In the Master 1 in Bioinformatics and Modeling * Biophysics and structural bioinformatics I (partim of 18h in a 5 ECTS course) * Biophysics and structural bioinformatics II (partim of 12h in a 5 ECTS course) After one year, the appointed academic will also take responsibility of a part of the following course: * In the Bachelor 1 in Bioengineering * Connaissances fondamentales et éléments de physique (partim of about 48h in a 10 ECTS course She/he will also have the opportunity in the future to contribute to other existing courses in the chemistry, bioengineering, physics, biomedical or informatics departments of the School of Engineering. Qualifications required : PhD Degree (with doctoral thesis) in Engineering or in Sciences. Skills required * Applicants should have at least 4 years of research experience at the time of their recruitment. * Post-doctoral experience and an excellent scientific record are required. * Exchange periods outside of the applicants’ home institution (during or after their PhD) will be taken into consideration when evaluating applications. * Experience in master and PhD thesis supervision, and grant submission and management are a plus. * Applicants who do not speak French (level C1) may be granted a period of adaptation, but they must be able to teach in French at the end of the 3rd year following their appointment. * Level C1 in English is expected. Candidates must be capable of teaching in English at the time of their appointment.

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