October 2018 - BBClist - maillist.psb.ugent.be

Fwd: CENTURI is recruiting a lead data analyst/scientist - Marseille, France
by BAUDOT Anaïs 24 Oct '18

24 Oct '18

> Begin forwarded message: > > From: <info(a)centuri-livingsystems.org> > Subject: CENTURI is recruiting a lead data analyst/scientist > Date: 22 October 2018 at 11:03:45 CEST > To: undisclosed-recipients:; > > Dear Colleagues, > > CENTURI is recruiting a lead data analyst/scientist within CENTURI’s technology transfer platform. The lead data analyst will help shape the data sharing and analysis platform and will be able to learn from, as well as distribute his/her knowledge in the CENTURI community. > > More information about the offer: http://centuri-livingsystems.org/job-offer-data-analyst/ <http://centuri-livingsystems.org/job-offer-data-analyst/> > > > CENTURI offers a three-year contract from the Aix-Marseille Université. > > Deadline for application: November 23, 2018 > > > We invite you to share this this call with your professional network. > > Best regards, > CENTURI management team --------------------------------------------------------- Anaïs BAUDOT MMG, Marseille Medical Genetics U 1251, Faculté de Médecine de La Timone, 27 Bd Jean Moulin 13385 Marseille Cedex 5 0491324948 France anais.baudot(a)univ-amu.fr

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Data scientist position at Eindhoven University of Technology
by Bosnacki, D. 22 Oct '18

22 Oct '18

Eindhoven University of Technology has a vacancy for a data scientist at the Biomedical Engineering Department and the Institute for Complex Molecular Systems (ICMS). For more information please go to: https://jobs.tue.nl/nl/vacature/data-scientist-materialsdriven-regeneration…

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1-week course single-cell transcriptomics and epigenomics in Roscoff (France)
by Morgane Thomas-Chollier 19 Oct '18

19 Oct '18

Date : 3rd February 2019 – 8th February 2019 Place : Roscoff, France Deadline registration: 15th November This one-week class focuses on the large-scale study of heterogeneity across individual cells from the genomic, transcriptomic and epigenomic points of view. New 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 Student and Post Doc 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. It is not necessary to have personal single-cell data to analyse. Deadline registration: 15th November http://www.france-bioinformatique.fr/en/evenements/sincellTE_2019 -- The organizing committee: Erwan Corre, Marc Deloger, Marie-Agnès Dillies, Agnès Paquet, Antonio Rausell, Nicolas Servant, Morgane Thomas-Chollier Morgane

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Exciting postdoc opportunity in Bordeaux
by Nikolski Macha 19 Oct '18

19 Oct '18

Three more weeks to apply to this computational postdoc position in epigenomics with exciting methylation data and more ! Check it out and/or spread the word: https://www.sfbi.fr/content/investigating-methylome-grape-and-oak-under-wat… If you have questions about our group, please contact me. Looking forward to hearing from you, Macha Nikolski ======= Investigating the methylome of grape and oak under water stress Global climate changes that includes several environmental constraints including drought, is a major concern that affects plant survival both in agro-systems and forest ecosystems. Indeed plants have evolved a wide range of mechanisms to cope with adverse environmental conditions that often lead to rapid and integrated reprogramming of gene expression patterns. Recent works have evidenced that epigenetic regulations, including DNA methylation, are essential to the responses of plants to environmental constraints, and may contribute to their long term adaptation to adverse conditions. In this context the METDRY project addresses the question of the potential involvement of genomic DNA methylation in the adaptation and responses to drought in woody perennial plants using grape and oak as representatives of cultivated plants and forest ecosystems respectively. It is based on the comparative analysis of methylomes, transcriptomes and small RNA populations in a drought sensitive and drought tolerant species in grapevine and oak and aims at identifying differentially methylated regions (DMRs) and gene expression profiles linked to long term adaptation to drought. The main objectives of the project are: 1. To analyze the genome wide distribution of 5mC in a drought sensitive and tolerant species in oak and grapevine, and determine similarities and differences between these contrasted phenotypes in each genus. 2. To determine changes in DNA methylation landscape induced by drought in the sensitive and tolerant species in each genus. 3. To investigate if DNA methylation contributes in a similar way to the responses to drought stress and to long term adaptation to drought in plants from natural population (oak), and in plants that have been selected by breeders over several generation (grapevine). 4. To implement a robust bioinformatics data analysis pipeline for BS-seq data and integrative approaches including BS-Seq, RNA seq, and Small RNA seq data. Applicants should be highly motivated and have a PhD with expertise in bioinfomatic and strong background in (epi)genomics . Knowledge in plant sciences is strongly recommended. Qualifications: We seek a bright, highly motivated, and enthusiastic bioinformatician with a background in epigenomics or genomics and an interest for plant biology. Candidates with other backgrounds such as molecular biology, with a strong interest in bioinformatics, are also invited to apply. Experience with NGS technologies and pipeline development is required. Applicants should have demonstrated abilities to work in a Linux environment and have experience in handling NGS data. Programming (Python, Perl, etc.) is required and knowledge of biostatistics is appreciated. A high standard of spoken and written English is appreciated, as are good communication skills. Ability to work autonomously, as well as part of a team, and to interact with scientist from different background including molecular biologist, plant physiologist and bioinformaticians is required. Applicants will have to share their time between three different laboratories. Contact: philippe.gallusci(a)inra.fr <mailto:philippe.gallusci%40inra.fr> (0557575847/0680945152) gregoire.le-provost(a)inra.fr <mailto:gregoire.le-provost%40inra.fr> (0557122773) macha.nikolski(a)u-bordeaux.fr <mailto:macha.nikolski%40u-bordeaux.fr> (0557571247) Links: UMR EGFV: https://www6.bordeaux-aquitaine.inra.fr/egfv/ <https://www6.bordeaux-aquitaine.inra.fr/egfv/> CBIB: https://cbib.u-bordeaux.fr/ <https://cbib.u-bordeaux.fr/> UMR BIOGECO: https://www6.bordeaux-aquitaine.inra.fr/biogeco <https://www6.bordeaux-aquitaine.inra.fr/biogeco> -- Head of Bordeaux Bioinformatics Center Research Director LaBRI / CNRS CBiB - Université Bordeaux 146, rue Léo Saignat, 33076 Bordeaux www : http://www.labri.fr/perso/macha/ <http://www.labri.fr/perso/macha/> tel : +33 (0)5 57 57 12 47

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EuBIC Winter School 2019
by Bittremieux Wout 18 Oct '18

18 Oct '18

We kindly invite you to participate in the EuBIC Winter School 2019 on January 15th-18th 2019 in Zakopane, Poland on proteomics bioinformatics [1]. It is the third of its kind and has proven to successfully bring together scientists in the field of proteomics and bioinformatics for proteomics to discuss challenges specific to this field. The registration is opened [2] until November 16th (early bird) / December 16th (regular). The Winter School will start with an educational day dedicated to workshops and trainings in established proteomics tools and workflows. The following days, internationally renowned invited speakers will give lectures and practical workshops covering the aspects of identification, quantification, result interpretation, and integration of MS proteomics data. This year’s special focus is the Challenges in Quantification and DIA. In order to share and discuss our work, we invite all interested conference attendees to submit an abstract for a poster. A selection of abstract submissions will additionally be chosen for short talks. Yours sincerely, on behalf of the organization committee, Wout Bittremieux [1] https://www.proteomics-academy.org/eubic-winter-school-2019 [2] https://www.proteomics-academy.org/registration

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(IB)2 Research Day, 16th November 2018
by Matthieu Defrance 18 Oct '18

18 Oct '18

(IB)2 Research Day 2018 16th November 2018, 9.30-5 pm U-Residence, Congrescentrum, green room, Campus VUB, Brussels Registration: https://goo.gl/forms/bDFUQyXp8R6baKIQ2 We are pleased to announce that the annual "(IB)2 Research Day 2018" will be held November 16th 2018 from 9.30am to 5.00pm at the VUB Congrescentrum U-Residence (VUB Campus Generaal Jacqueslaan 271, 1050 Brussels). This one-day meeting is organized by (IB)2 or Interuniversity Institute of Bioinformatics in Brussels is a interdisciplinary research institute and supported by ULB and VUB universities. 9.30 9.35 Welcome 9.35 10.35 Keynote 1 - Carl Herrmann, University of Heidelberg Multi-omics data integration for single-cell genomics 10.35 11.05 Charlotte Nachtegael, Unraveling the oligogenic potential of developmental disorders (IB)2, ULB 11.05 11.30 Coffee Break 11.30 12.00 Youssef Bouysran, Bioinformatic investigations of missense mutations in the FBN1 gene (IB)2, ULB 12.00 12.30 Nathaniel Mon Père, Quantitative Models for Cell Differentiation in Hematopoiesis (IB)2, ULB 12.30 12.45 Flash presentations 12.45 14.00 Lunch break and poster session 14.00 15.00 Keynote 2 - Hervé Isambert, Institut Curie Paris Learning causal and non-causal networks from large scale genomic and clinical data 15.00 15.30 Gipsi Lima Mendez, Ocean Eco-system biology through integration of heterogeneous data (IB)2, ULB 15.30 16.00 Closing remarks / Future of the (IB)2 16.00 17.00 Musical Coffee Up to date version of the program: https://ibsquare.be/research-day This meeting is free and open to every researcher or student but a quick online registration is required: https://goo.gl/forms/bDFUQyXp8R6baKIQ2 If you have any questions regarding this meeting please feel free to contact: Sophie de Buylsophie.de.Buyl(a)vub.be or Matthieu Defrance matthieu.dc.defrance(a)ulb.ac.be On behalf the (IB)2, Sophie de Buyl and Matthieu Defrance

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Job: Research software engineer at the de Duve Institute, UCLouvain (Brussels, Belgium)
by Laurent Gatto 18 Oct '18

18 Oct '18

The Computational Biology (CBIO) unit at the de Duve Institute in Brussels, Belgium, seeks to appoint a full time research software engineer. The successful candidate will join the research group of Professor Laurent Gatto and will have the opportunity to work on projects across a broad range of biomedically relevant topics in collaboration with researchers from the de Duve institute as well as other institutes on the biomedical campus of UCLouvain. The focus of the position is on rigorous research software engineering, analysis pipeline development and high-throughput biology data analysis, with the possibility of engaging in teaching activities. If you recognise yourself in any of the following profiles, please consider applying. - You have created/maintained/used software to address research problems in high throughput biology (such as, for example genomics, transcriptomics, epigenetics, proteomics and/or metabolomics). - You can rapidly assimilate understanding of new biomedical questions, and quickly connect research needs to software requirements. - You are committed to open source software development best practices and know how to adapt these to biomedical research contexts. Duties and activities The research software engineer will be expected to contribute to various activities, including : - Research projects: support and advise collaborators with their data analyses and contributed to scientific reports and publications. - Maintain and develop research software and repositories linked to the ongoing research in the group and collaborative projects. - Participate in the administration of the computing and data storage infrastructure. - Attend scientific conferences to present their research and development and workshops to improve and learn new sets of skills. - Contribute to bioinformatics teaching, both within the institute and the School of Biomedical Sciences. Required skills The ideal candidate would be either a researcher with a focus on research software and data analysis, or a software developer with an interest in research and biomedical sciences. We are looking for a motivated candidate with a PhD or a Master's degree in bioinformatics or equivalent, possessing computational and quantitative skills such as : - Good knowledge of the R programming language and the Bioconductor infrastructure (important). - Experience with the processing and analysis of omics data (important). - Experience in open and reproducible research, open source software and open data (important). - Experience in C/C++ (desirable). - Experience in JavaScript, specifically the development of online visualisation applications (desirable). - Experience in teaching, ideally the Data and Software Carpentry curricula or interest in training to become an instructor (desirable). - Experience in high performance computing (desirable). - Experience with code versioning and collaborative tools such as, for example, git, and GitHub/GitLab (desirable). - Experience with other languages commonly used in computational biology and bioinformatics like Python or Julia (optional). - Knowledge of French and English is desirable. Contract on external resources, full time, with initial duration of 3 years (1 year renewable twice) - available immediately. We value equality, diversity and an open, collaborative and welcoming work environment. Please send your application by email to Laurent Gatto referencing this position, including a CV, 3 academic references, and a motivation letter. Don't hesitate to contact me for additional information. Original post advert: https://jobs.uclouvain.be/PersonnelAdministratif/job/Research-software-engi… Prof Laurent Gatto de Duve Institute - UCLouvain Avenue Hippocrate, 75 - bte B1.74.10 1200 Brussels, Belgium Tel: +32 (0)2 764 74 15

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Help Shape the Future of Training at Edinburgh Genomics.
by TRAIN edgenomics-training 17 Oct '18

17 Oct '18

Dear all At Edinburgh Genomics, we are always looking at ways we can improve the services we offer to you, the scientific community. We currently provide training courses covering a range of different genomics topics using the latest bioinformatics techniques. We want to keep these courses as relevant and as useful to you as possible, tailoring our training to best meet your needs. But, to do this we need your help! We want you to have your say in shaping the future of training provision at Edinburgh Genomics. Do you need more training in a particular programming language? Are you moving to a new type of analysis that feels bewildering without some expert advice? Let us know by completing this quick survey (20 short questions) and help us to better understand your needs: https://www.surveymonkey.co.uk/r/7M6QB2D The survey is completely anonymous unless you chose to share your contact details, your responses are used for developing training courses only, and are never shared with a third party. Thank you in advance: we value your opinions and preferences very highly. Kind Regards Nathan Medd Training and Outreach Manager Edinburgh Genomics' Privacy Notice can be viewed at: http://genomics.ed.ac.uk/about-us/privacy-notice This email and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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FW: Professorship KU Leuven Applied Bioinformatics in Microbial Ecology and related fields
by Hans Rediers 16 Oct '18

16 Oct '18

Dear, At KU Leuven's Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), there is an open position for a professor (Junior/Senior) in the field of 'Applied Bioinformatics in Microbial Ecology and related fields'. I dare to bring this vacancy to your attention. More information on the PME&BIM lab can be found on: https://iiw.kuleuven.be/onderzoek/pme-bim For all information regarding the job profile, consult: https://www.kuleuven.be/personeel/jobsite/jobs/54649637?hl=en&lang=en We are offering full-time employment in an intellectually challenging environment. KU Leuven is a research-intensive, internationally oriented university that carries out both fundamental and applied scientific research. You will work at Campus Group T in Leuven, a historic, dynamic and lively city located in the heart of Belgium, within 20 minutes from Brussels, the capital of the European Union, and less than two hours from Paris, London and Amsterdam. Feel free to pass on this announcement to all possibly interested researchers (including former PhD students, post-docs, colleagues etc). The deadline is February 1st, 2019. A concise research plan defining main lines of research is requested as an annex to the application tool. For all your questions, please feel free to contact me Yours sincerely, Hans Rediers ------------- Prof. dr. ir. Hans Rediers Programme coordinator Master IW: Biotechnology Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM) Cluster for Bioengineering Technology (CBeT) Department of Microbial and Molecular Systems (M2S) Faculty of Engineering Technology KU Leuven - Campus De Nayer Fortsesteenweg 30A | BE-2860 Sint-Katelijne-Waver | Belgium Tel. +32 (0)15 30 55 90 Fax. +32 (0)15 30 55 99 Website: www.kuleuven.be/pme-bim<http://www.kuleuven.be/pme-bim> E-mail: hans.rediers(a)kuleuven.be<mailto:hans.rediers@kuleuven.be>

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Second Announcement NSBM Fall Meeting
by Nicolaes, G (BIOCH) 15 Oct '18

15 Oct '18

Second Announcement [ogo.png] NETHERLANDS SOCIETY ON BIOMOLECULAR MODELLING Fall meeting 3D Protein Structures: what sequences cannot tell you November 16th 2018 Venue: Boothzaal, University Library De Uithof, Utrecht The Netherlands Society on Biomolecular Modelling (NSBM) is an independent society that brings people together in The Netherlands and beyond, that work on three dimensional structures of biomolecules and biomolecular simulations. This is a first announcement of our Fall meeting to which you are cordially invited. During the meeting, the floor will be given to students, PhD students, post-docs and a number of invited guest speakers who study protein structure and/or structural bioinformatics or related topics. Location and dates * Date: November 16th, 2018, 10:00-17:00 * Venue: Boothzaal, University Library De Uithof, Heidelberglaan 3, 3584 CS Utrecht * http://www.uu.nl/universiteitsbibliotheek/locaties<http://www.uu.nl/universiteitsbibliotheek/locaties%20> Deadlines * Registration deadline for posters or to be considered for a short talk: November 5th * Registration deadline (including lunch): November 9th Application procedure * Participants should send an email to register (required but free registration) to: g.nicolaes(a)maastrichtuniversity.nl<mailto:g.nicolaes@maastrichtuniversity.nl> * Submission of an abstract is required if you want to present a poster. * Indicate in your email if you want to be selected for a short oral presentation. Note: The maximum number of participants is limited to 75! So please register on time. Lead contact * Dr. Gerry Nicolaes - g.nicolaes(a)maastrichtuniversity.nl<mailto:g.nicolaes@maastrichtuniversity.nl> http://www.3dstructure-function.nl/nsbm-fall-meeting/<http://www.3dstructure-function.nl/?page_id=912&preview=true> Confirmed speakers are: o Dr. Vlad Cojocaru (Hubrecht Institute) - "Molecular simulations of DNA recognition by transcription factors" o Dr. Marc Baaden (Institut de Biologie Physico-Chimique) - " 3D protein structures in virtual molecular reality" o Dr. Chris Oostenbrink (Institute of Molecular Modeling and Simulation, BOKU Vienna) - "Binding molecules in free-energy calculations" o Prof. Peter Peters (Maastricht University) - "Beauty and Benefits of cryo-EM; our new endeavors in vitrification of proteins and cells" Abstract submission is still open and we have several free slots in the sessions for students, PhD students and post-docs Costs Attendance is free of charge but registration is required. Lunch and coffee will be provided thanks to the financial support of the Nijmegen Centre for Molecular and Biomolecular Informatics. A flyer is enclosed. With kind regards, Gerry Nicolaes [cid:image001.jpg@01CC2F5C.EA047880] Gerry Nicolaes, PhD Associate Professor Cardiovascular Research Institute Maastricht Biochemistry Department g.nicolaes(a)maastrichtuniversity.nl<mailto:g.nicolaes@maastrichtuniversity.nl> www.maastrichtuniversity.nl <http://www.maastrichtuniversity.nl/> Universiteitssingel 50, 6229 ER Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 3881688 F +31 43 3884159 http://www.3dstructure-function.nl<http://www.3dstructure-function.nl/> [cid:image002.jpg@01CC2F5C.EA047880]Please consider your environmental responsibility before printing this e-mail.

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