- BBClist - maillist.psb.ugent.be

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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Summer School on Design and Control of Microbial Communities, Leuven 11-13 Sep 2023
by BeNeLux bioinformaticians forum 28 Feb '23

28 Feb '23

Dear colleagues, We are pleased to announce our summer school on the design and control of microbial communities taking place in Leuven from 11-13th September 2023. The school will introduce students at the Master and PhD level to different computational methods to engineer microbial communities. Several well-known experts have confirmed their presence, including Ophelia Venturelli, Shiri Freilich, Hidde de Jong, Lutz Becks, Alex Fedorec, Beatriz Jiménez, Teppo Hiltunen, Ville Mustonen, Frank Delvigne, Steffen Waldherr and Aura Raulo. The latest developments in the field will be covered through research talks, while tutorials will give participants hands-on experience with selected methods. For more information and registration, please visit: http://msysbiology.com/microbedesign/ Kind regards, The organising team Karoline Faust, Didier Gonze & Leo Lahti http://msysbiology.com<http://msysbiology.com/> https://utc.ulb.be/dgonze.html http://datascience.utu.fi

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Re: [BBC] two Junior Lecturers VU/UvA master Bioinformatics and Systems Biology JD open till April 1st
by BeNeLux bioinformaticians forum 27 Feb '23

27 Feb '23

Dear all, I am delighted to announce that we are hiring two junior lecturers, and will extend the deadline till April 1st (it may be offline for some days due to administrative reasons). Hope to hear from you soon! Sincerely, Anton. On 15/02/2023 17:19, Anton Feenstra wrote: > Dear all, > > Just a kind reminder for the below vacancy, which is open for > applications till 1st of March. > > Groetjes, > Anton. > > > On 27/01/2023 13:22, BeNeLux bioinformaticians forum wrote: >> Dear all, >> >> We have another junior lecturer position available within the VU/UvA >> joint degree master programme Bioinformatics & Systems Biology in >> Amsterdam. >> >> For details and application procedure, please see >> https://workingat.vu.nl/ad/junior-lecturer-juniordocent-masters-programme-b… >> > -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1111 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +312059 87783 - skype: kafeenstra - room NU 12A31| | | Feenstra(a)few.vu.nl - www.few.vu.nl/~feenstra/ | | | "Do You Have a Mind of Your Own ?" (Garbage) | |_____________|_______________________________________________________|

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Fifth X-omics festival "the future of multi-omics research is now!"
by BeNeLux bioinformaticians forum 27 Feb '23

27 Feb '23

Dear, We would like to invite you to the fifth edition of the X-omics festival “the future of multi-omics research is now!”, which will be organized as a live event in Nijmegen, the Netherlands with the possibility to follow the program online via live stream on Monday April 17th 2023. The event will include: * Two keynote lectures * Lectures from X-omics investigators on multi-omics data integration and spatial omics * Pitches about new omics technologies and applications * Scientific posters * Networking opportunities Please find the final program for this day attached, full titles are displayed on our website: X-omics - Festival 2023<https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fx-omics.n…>. If you would like to attend the X-omics festival, make sure to register before April 3. Registration is open and free of charge via X-omics festival 2023 - Individual Registration<https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fx-omics.n…>. Researchers are highly encouraged to submit a poster abstract and present it during the X-omics festival. Poster abstract submission deadline is March 27. For more information please visit our website. <https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fx-omics.n…> We hope to see you all at the X-omics festival on April 17! Met vriendelijke groet, Kind regards, X-omics project management team www.x-omics.nl<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.x-omic…> info(a)X-omics.nl<mailto:info@X-omics.nl> [cid384481*image004.jpg(a)01D94A99.ACFD3F70]

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Summer School - From pathway modelling tools to cell-level simulations - Registration until 6th March 2023
by BeNeLux bioinformaticians forum 23 Feb '23

23 Feb '23

Dear all, >From the PerMedCoE project (https://permedcoe.eu/) we are organizing a Summer School that may be of your interest or to students or junior researchers you may know. The course is on 25-30th June 2023 in Seva, in a mountain region north from Barcelona. The deadline for registration is 6th March. Participants will gain first-hand experience using diverse biomedical modelling tools and how such tools could be used as part of workflows on high performance computing environments. Audience: Researchers from Computational Biology, Systems Biology, or Life Sciences. There are grants available, but application may take some days, so it is advisable not to wait until the very last moment for that. I am attaching a flyer and a summary below, this is the link for registration and further information: https://permedcoe.eu/training/permedcoe-summer-school-on-cell-level-simulati ons/. Thank you, Alba -- Alba Jené Sanz, PhD Bioinformatics Unit Coordinator Barcelona Supercomputing Center (BSC) <https://goo.gl/maps/q46T2oJf29t5mStp9> Plaça Eusebi Güell, 1-3, 08034-Barcelona, Spain <http://life.bsc.es/compbio> http://life.bsc.es/compbio

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10 Open Positions MSCA DN - Single cell in inflammatory autoimmune diseases (SIGNATURE)
by BeNeLux bioinformaticians forum 21 Feb '23

21 Feb '23

Dear colleagues, Within the framework of a new Marie Curie Training network (SIGNATURE), we currently have 10 open PhD positions in the field of single-cell omics for inflammatory diseases. These fellowships come with a lot of opportunities for mobility between many of the top labs in Europe in the field of single cell omics. More information can be found at https://euraxess.ec.europa.eu/jobs/69084 I would be happy if you could distribute this further to interested candidates, Best regards, Yvan Saeys *SIGNATURE will offer* * A thorough scientific education in the frame of a doctoral training program. * The possibility to participate in specific international courses, workshops and conferences. * Strong involvement in a European research project with high international visibility. * The opportunity to perform research visits to internationally renowned research labs in Europe. * A prestigious three-year MSCA Fellowship. * The positions receive funding for 36 months by the Marie-Sklodowska-Curie Doctoral Network within the Horizon Europe Program of the European Commission. *PhD Employments* We are looking for 10 highly motivated doctoral candidates, starting at the earliest possible dates. * Eligibility to enrol in a doctoral programme at the time of the recruitment. * MSc degree in life sciences/molecular biology or engineering/computer sciences (Please check each individual project for more information). * Supporting trans-national mobility (i.e. No residence or main activity (work, studies, etc.) in the country of the recruiting beneficiary for more than 12 months in the 36 months before their recruitment date). * Secondments - availability to travel as per each individual project requirements. *Job description* You will be performing all research activities in your respective Doctoral Candidate Project. This includes literature search, preparation of methodological design, study execution, data analysis, and dissemination through publication in highly ranked journals, as well as presentations at international conferences. You will be working closely with each other, as well as with other members of the SIGNATURE project and3TR project <https://3tr-imi.eu/>. International collaboration will be facilitated through short-term research stays at SIGNATURE partner institutions. You will actively participate in all training activities of the SIGNATURE network. You must have good communication skills in English (oral and written), be team-oriented and willing to work in an interdisciplinary and international environment. We expect the ability to take responsibility and meet deadlines, prioritizing where necessary. The review of applications will begin on March 2023. Questions regarding individual projects should be directed to the Principal Investigators. -- =============================================================================== Prof. dr. Yvan Saeys VIB Group Leader Data mining and modeling for biomedicine UGent Department of Applied Mathematics, Computer Science and Statistics Krijgslaan 281, S9, B-9000 Gent Inflammation Research Center, a VIB-UGent Department Technologiepark-Zwijnaarde 71 , B-9052 Zwijnaarde , Belgium Tel : +32(0)9 331 37 40 Fax : +32(0)9 221 76 73 Mailto:yvan.saeys@ugent.be http://www.dambi.ugent.be ===============================================================================

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10 Open Positions MSCA DN - Single cell in inflammatory autoimmune diseases (SIGNATURE)
by BeNeLux bioinformaticians forum 21 Feb '23

21 Feb '23

To whom it might concern, We are looking for 10 highly motivated doctoral candidates, starting at the earliest possible dates. * Eligibility to enrol in a doctoral programme at the time of the recruitment. * MSc degree in life sciences/molecular biology or engineering/computer sciences (Please check each individual project for more information). * Supporting trans-national mobility (i.e. No residence or main activity (work, studies, etc.) in the country of the recruiting beneficiary for more than 12 months in the 36 months before their recruitment date). * Secondments - availability to travel as per each individual project requirements. SIGNATURE will offer: * A thorough scientific education in the frame of a doctoral training program. * The possibility to participate in specific international courses, workshops and conferences. * Strong involvement in a European research project with high international visibility. * The opportunity to perform research visits to internationally renowned research labs in Europe. * A prestigious three-year MSCA Fellowship. * The positions receive funding for 36 months by the Marie-Sklodowska-Curie Doctoral Network within the Horizon Europe Program of the European Commission. Check it out! - https://euraxess.ec.europa.eu/jobs/69084<https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Feuraxess.…> https://www.linkedin.com/posts/signature-eu_10-open-positions-msca-dn-singl…<https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.linke…> [B41ECA9C] María Bazuelo Roldán | Área de Gestión de Proyectos Fundación Pública Andaluza Progreso y Salud Dirección Postal: Centro de Investigación GENYO Av. de la Ilustración, 114, 18016 Granada T +34 958 71 55 00 | Ext 209 M +34 680 980137 www.juntadeandalucia.es/fundacionprogresoysalud<http://www.juntadeandalucia.es/fundacionprogresoysalud> Este correo electrónico y, en su caso, cualquier fichero anexo, contiene información confidencial exclusivamente dirigida a su(s) destinatario(s). Toda copia o divulgación deberá ser autorizada por la Fundación Pública Andaluza Progreso y Salud. This e-mail and any attachments are confidential and exclusively directed to its adressee(s). Any copy or distribution will have to be authorized by Fundación Pública Andaluza Progreso y Salud. Protección de datos: de conformidad con la legislación vigente en materia de protección de datos personales, se le informa de que sus datos derivados del intercambio de correos electrónicos, serán tratados con la finalidad de llevar a cabo comunicaciones futuras, quedando almacenados durante el tiempo necesario para cumplir con las obligaciones legales estipuladas. Así mismo, se le informa que sus datos personales no serán cedidos a terceros, salvo que se disponga en una obligación legal. El responsable de este tratamiento de sus datos personales es la Fundación Pública Andaluza Progreso y Salud. Podrá contactar con el Delegado de Protección de Datos en la dirección electrónica dpd.csalud(a)juntadeandalucia.es<mailto:dpd.csalud@juntadeandalucia.es>. En todo caso, podrá ejercer en cualquier momento, sus derechos de acceso, rectificación, supresión, limitación del tratamiento, portabilidad y oposición, los cuales podrá ejercer dirigiéndose a la siguiente dirección de correo electrónico: lopd.fps(a)juntadeandalucia.es<mailto:lopd.fps@juntadeandalucia.es> o bien mediante escrito a: Fundación Pública Andaluza Progreso y Salud, avd. Américo Vespucio, 15, edificio S-2. 41092 Sevilla. For information on data protection in English please click here<http://www.juntadeandalucia.es/fundacionprogresoysalud/es/la-fundacion/lopd>. [4F5D370A] No imprimas este mensaje si no es necesario. El medio ambiente está en nuestras manos. Do not print this message if it is not necessary. The environment is in our hands.

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