May 2019 - BBClist - maillist.psb.ugent.be

NERC Bursaries for Edinburgh Genomics Courses
by TRAIN edgenomics-training 02 Mar '22

02 Mar '22

Dear All We are pleased to announce we have a number of bursaries available to cover up-to the full fees of any of our upcoming bioinformatics courses. These bursaries are available to UK based students or researchers funded by the NERC or working on research that falls under the remit of the NERC (https://nerc.ukri.org/research/portfolio/remit/) Bursaries are available for any of our courses (see below) but are available for a LIMITED TIME ONLY: They are available for any course booked BEFORE 27th MARCH. So please don't wait to sign up! Our upcoming courses: Linux for Genomics, 13th March - An introduction to working on the command line, running commands and handling data relevant to bioinformatics. https://genomics.ed.ac.uk/services/linux-genomics R for Genomics, 14-15th March - An introduction to the statistical environment R, taking you from the very basics to writing basic functions and creating beautiful figures with ggplot2 https://genomics.ed.ac.uk/services/r-genomics Introduction to Python for Biologists, 18-22 March - This introductory course gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. https://genomics.ed.ac.uk/services/introduction-python-biologists-0 Data Manipulation and Visualisation with Python, 08 - 12 April - Python has a many high-quality libraries for working with scientific data. In this workshop we will see how to leverage these libraries to efficiently work with and visualise large volumes of data. https://genomics.ed.ac.uk/services/data-manipulation-and-visualisation-pyth… Introduction to RNA-seq Data Analysis, 9-10th May - This two-day course takes you through a tried-and-tested workflow for analysing RNA-seq data, from read mapping and QC to differential expression and result visualisation. https://genomics.ed.ac.uk/services/introduction-rna-seq-data-analysis If you think you are provably eligible for one of these bursaries, sign up to your desired course through the link provided and we will be in contact regarding fees. Kind Regards Nathan Medd Training and Outreach Manager - Edinburgh Genomics G.06, Ashworth Laboratories, Charlotte Auerbach Road, The King's Buildings, The University of Edinburgh, EH9 3FL, Edinburgh, Scotland 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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Open PostDoc Position in Computational Biology - Marseille, France
by BAUDOT Anaïs 16 Nov '19

16 Nov '19

Dear colleagues, We have an opening position for a postdoctoral fellow in the network and systems biology group, in the Marseille Medical Genetics Unit. The project is dedicated to network modeling for rare genetic diseases. Please see attachement for more details, and feel free to forward this message to potential candidates. Best regards, Anaïs --------------------------------------------------------- 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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Bioinformatics position available at the Erasmus MC Cancer Computational Biology Center
by Harmen van de Werken 04 Oct '19

04 Oct '19

A bioinformatics position is currently available at the Erasmus MC Cancer Computational Biology Center. http://www.erasmusmc.nl/vacature/?num=21578 Please apply, if you are enthusiastic and eager to improve our knowledge on cancer biology. Harmen van de Werken

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COMPUTATIONAL BIOLOGIST - TUMOR IMMUNOLOGY
by Lodewyk Wessels 25 Jul '19

25 Jul '19

VACANCY COMPUTATIONAL BIOLOGIST - TUMOR IMMUNOLOGY YOUR ROLE WITHIN THE INSTITUTE The research groups of Dr Karin de Visser, dr Marleen Kok and Prof dr Lodewyk Wessels, are looking for a motivated and talented Computational Biologist to join their teams at the Netherlands Cancer Institute (NKI). The Inflammation and Cancer group of dr. Karin de Visser is studying the impact of the immune system on metastatic breast cancer utilizing sophisticated mouse tumor models and state-of-the art ex vivo and in vitro immunological and molecular assays. The lab of de Visser closely collaborates with the translational research group of medical oncologist dr Marleen Kok. The mission of this team is to discover novel mechanisms underlying the crosstalk between breast cancer and the immune system, to optimize immunotherapy for breast cancer patients using novel combination treatments in clinical trials and the discovery of predictive biomarkers. The Computational cancer biology group of Prof dr Lodewyk Wessels is focused on quantifying and understanding treatment response in model systems and patients. To this end we develop bespoke and novel computational methods focusing on data integration and tailored to new technologies. We actively collaborate with many research groups in the NKI and strongly believe in the power of 'team science'. PROJECTS You will be involved in the following projects: 1. MOUSE MODELS FOR METASTATIC ESCAPE FROM IMMUNE CONTROL. To study the causal relationship between immune cells and metastatic breast cancer, we utilize state-of-the art genetically engineered mouse tumor models. We have extensive RNA-sequencing datasets of isolated immune cell populations, as well as RNA-sequencing and exome sequencing data of primary breast tumors and organ-specific metastases from these mouse models. You will be responsible for the computational analyses of the data, and to extract candidate pathways/genes from these datasets that can subsequently be tested in follow up experiments in the lab. Moreover, you will link these pre-clinical data to human datasets. 2. SYSTEMIC AND INTRA-TUMORAL IMMUNOMONITORING FOR PRECISION IMMUNE-MODULATION. We are performing extensive immunomonitoring studies in human breast cancer patients treated with immune checkpoint blockade, with the ultimate aim to validate hypotheses derived from our preclinical research in human cancer patients, and to stratify breast cancer patients for immunomodulatory therapies. We are setting-up multiplex immunohistochemistry with antibody panels that audit intratumoral lymphoid and myeloid cell populations and their functional state. In parallel, we have established an extensive multiplex flow cytometry pipeline to monitor the systemic immune landscape of breast cancer patients and healthy controls. These analyses generate a substantial amount of data which require thorough computational analyses. 3. MAPPING IMMUNO-GENOMIC INTERACTIONS. We are interested in dissecting the impact of the genetic make-up of breast tumors on the intra-tumoral and systemic immune landscape. You will be responsible for the identification and validation of genotype-immunophenotype associations by connecting DNA exome sequencing data, RNA sequencing data and immune profiles derived from our mouse tumor models and cancer patients. You will use both publicly available datasets and newly generated datasets. You will be embedded in the collaborative and enthusiastic international research groups of dr. Karin de Visser, dr Marleen Kok and Prof. dr. Lodewyk Wessels, providing a unique environment that combines computational cancer biology with pre-clinical and translational research into immune-oncology. YOUR PROFILE We seek to recruit an ambitious postdoc, capable of independent thinking, with a strong commitment to translational research. Candidates should hold a degree in bioinformatics, computer science or a related discipline, have experience in statistics and/or machine learning and be proficient in bioinformatics programming languages (e.g. R, Python). We expect candidates to be highly self-motivated, creative, and a team-player with strong communication skills. General background knowledge in biology and immunology is essential, and experience with projects involving the use of genomics and immune profiling data to identifying candidate targets and biomarkers is a plus. WANT MORE INFORMATION? Please visit our home pages https://www.nki.nl/divisions/tumor-biology-immunology/de-visser-k-group/ https://ccb.nki.nl or contact Karin de Visser: k.d.visser(a)nki.nl Marleen Kok: m.kok(a)nki.nl Lodewyk Wessels: l.wessels(a)nki.nl

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Postdoc position: In silico exploration of microbial community dynamics
by Karoline Faust 31 May '19

31 May '19

Dear all, The Lab of Microbial Systems Biology (http://tinyurl.com/MicrobialSysBio) is looking for a motivated postdoc with a passion for microbial community dynamics. The young lab, started in 2016, is part of the Molecular Bacteriology unit at the Rega Institute and aims at improving our understanding of microbial community structure and dynamics. The postdoc position is funded through an ERC starting grant. Project Microorganisms interact with one another and with the environment, thereby forming complex systems. While a number of mathematical models have been proposed to describe, analyze and predict microbial community dynamics, their application to microbial communities in vitro and in vivo is in its infancy. The Lab of Microbial Systems Biology strives to address this knowledge gap. Thus, the postdoc will focus on model-informed analysis of microbial sequencing data (time series in particular) and/or modelling of synthetic communities, working with data generated in-house and/or in collaborations. Profile The candidate should hold a doctoral degree in an area related to Systems Biology, Theoretical Biology or Bioinformatics and should have strong programming skills. The candidate should also have some background knowledge or at least a strong interest in theoretical ecology. Proficiency in English is necessary, experience with population models is a plus. Interested? Please submit a cover letter, a CV (including publication record) and a list with at least two references (with name, function, email, address and phone number) through the online application tool at https://www.kuleuven.be/personeel/jobsite/jobs/55121641 You can apply for this position until 31st August, 2019. The position will start in December 2019 or January 2020 (at the choice of the candidate). Please do not hesitate to contact me in case of questions. Kind regards, Karoline Karoline Faust --------------------------------------------------- Email: karoline.faust(a)kuleuven.be<mailto:karoline.faust@kuleuven.be> Web: http://tinyurl.com/MicrobialSysBio --------------------------------------------------- Room 7.A130, Rega Institute Laboratory of Molecular Bacteriology Department of Microbiology and Immunology KU Leuven, Campus Gasthuisberg Herestraat 49, postbus 1028 3000 Leuven Belgium ---------------------------------------------------

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Group leader positions, stem cell & development, Copenhagen
by Magali Michaut 31 May '19

31 May '19

Dear all, 2 group leader positions are open at DanStem in Copenhagen, Denmark. It would be great to recruit someone with computational expertise. https://www.nature.com/naturecareers/job/group-leaders-to-danstem-copenhage… <https://www.nature.com/naturecareers/job/group-leaders-to-danstem-copenhage…> Cheers, Magali

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Last call: Data Steward Knowledge and Skills Workshops 11 and 12 June 2019, Utrecht
by Celia van Gelder 31 May '19

31 May '19

Dear colleagues, We are happy to announce that the registration is now open for our two one-day Data Steward Knowledge and Skills workshops on June 11 and 12, 2019 in Utrecht. Registration is free of charge and we hope to welcome many of you there for a working meeting with and for the Data Steward Community! Dates: Two one-day workshops. First one June 11 & the second one on June 12 June 2019. Maximum participants per day: 25. Location: Holland Heart House, Utrecht, <https://www.hollandhearthouse.nl/Routedescription_HHH.pdf> https://www.hollandhearthouse.nl/Routedescription_HHH.pdf Registration: https://docs.google.com/forms/d/e/1FAIpQLSccCFvNqcA-3fmBqelUXN2EMGHUq68W0Xfb BGt46tSOP7Govg/viewform Registration is free of charge. Lunch is included. Time: 10-16 hrs Programme: https://www.dtls.nl/events/data-steward-knowledge-and-skills-workshop/ and https://www.dtls.nl/events/data-steward-knowledge-and-skills-workshop-2/ Target audience Data stewards, data managers, policy makers, HR persons, funders and all other stakeholders that are interested to share their expertise in Data Stewardship, want to get updated about the work that is going on, and want to contribute to the next steps that will be taken. Although the main focus is for the Life Sciences domain, our work on the competencies and skills of the data stewards is rather generic and also useful for other disciplines. Therefore participants from other disciplines are very welcome to join. Goal of the meeting In a ZonMw- funded project where we are working on defining the profession, skills and training needs of Data Stewards in the life sciences. All the output of the project produced so far can be found on <https://zenodo.org/communities/nl-ds-pd-ls/> https://zenodo.org/communities/nl-ds-pd-ls/. It is our ambition to produce tangible outputs, that can be used and implemented in the organisations. To achieve these goals it is crucial to get input from the community. In this way we make further steps in defining community-endorsed outcomes and decide together which next steps are needed to improve data stewardship function descriptions, capacity, visibility, recognition and training. As a data steward, you will meet your peers, expand your network, and will be able to get insight in the current status of Data Stewardship in the Netherlands and beyond. Concept Programme for both June 11 and June 12 Please note that it will be an interactive day, with working sessions and we invite you to bring your own materials with you, for example your current job description, job advertisements from your organisation, the data management policy of your organisation, information about trainings that you have attended and found useful, etc. 9.30 Registration open 10.0 Welcome & Introduction (Celia van Gelder, DTL/ELIXIR-NL) * Introduction of the project * Who is in the audience? 10.30 Working session 1: Your job description & role (Salome Scholtens, UMCG) * Introduction of the Function Matrix and the Venn Diagram for the Data Steward roles * Interactive session to positioning yourself in the Data Stewardship landscape. Do you recognize your own role, what is your position in your organisation, does your job description match our derived function profile? What are you missing? 11.30 Coffee break 12.00 Working session 2: Your knowledge, skills and abilities (Mijke Jetten, Radboud University) * Introduction of the Knowledge, skills and learning objectives * Interactive session in groups to analyze specific parts of the KSA table * Report back from breakout groups. 13.00 Lunch 13.45 Working session 3: Your training * Introduction of the Training related plans * Working session 14.30 Coffee break 15.00 Working session 4: What's next * What are the next steps to be taken by the policy makers in organisations/institutes, funders, HR etc? 15.45 Wrap up * Conclusions of the meeting & next steps 16. 00 End of meeting Best regards on behalf of the project team, Celia Dr. Celia W.G. van Gelder Programme Manager DTL Learning Training Coordinator ELIXIR-NL ELIXIR Training Platform Leader tel. +31613375327 e-mail: <mailto:celia.van.gelder@dtls.nl> celia.van.gelder(a)dtls.nl websites: <https://www.dtls.nl/> https://www.dtls.nl/, <https://www.elixir-europe.org/platforms/training> https://www.elixir-europe.org/platforms/training skype: celia.van.gelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht Postal address: Postbus 8500 | 3503 RM 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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Galaxy meets The Carpentries: join our pilot workshop!
by Mateusz Kuzak 28 May '19

28 May '19

Dear all, The Gallantries team is offering its first RNA-seq workshop for beginners on June 11&12. This workshop will be delivered simultaneously at two locations across Europe (Rotterdam, NL and Freiburg, DE). Registration is free, but limited spots are available, first come, first serve! More information about this course can be found here: galaxy-carpentries.github.io/gallantries/event/2019-03-25-first-galantries-workshop/ Please feel free to forward this information in your network. Best regards, Mateusz — Mateusz Kuzak Scientific Community Manager | Dutch Techcentre for Life Sciences e-mail: mateusz.kuzak(a)dtls.nl | Tel. +31 643707254 twitter: @matkuzak | GitHub: mkuzak | skype: mkuzak orcid: orcid.org/0000-0003-0087-6021 Visiting address: DTL | Jaarbeurs Innovation Mile (JIM) | 6th-floor Beatrixgebouw Jaarbeursplein 6 | 3521 AL Utrecht

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PhD position - modeling integrin-cell interactions
by Carlier, Aurélie (MERLN) 25 May '19

25 May '19

Dear all, If you know interesting candidates for this modeling position, feel free to forward! https://www.academictransfer.com/nl/54915/modeling-life-at-the-cell-matrix-… Best wishes Aurélie [Lustrumlogo 2016] MERLN Institute for Technology-Inspired Regenerative Medicine dr. Aurélie Carlier Assistant Professor a.carlier(a)maastrichtuniversity.nl <mailto:a.carlier@maastrichtuniversity.nl> M +31 (0)6 39 60 21 38 Universiteitssingel 40, 6229 ER Maastricht / Room C3.577 PO Box 616, 6200 MD Maastricht http://merln.maastrichtuniversity.nl<http://merln.maastrichtuniversity.nl/> https://sites.google.com/view/aureliecarlier/homepage https://be.linkedin.com/in/aureliecarlier

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Job posting: Postdoc in Environmental Genomics & bioinformatics
by Filip Volckaert 25 May '19

25 May '19

Dear all, Please find attached and at the bottom of this message our latest open position for the Genomics Core and Department of Biology at the KU Leuven. We would appreciate it if you could post this up in your job portals. Please do not hesitate to contact me if in need of further assistance. Thank you! Kind regards Filip Volckaert Professor of marine ecology and evolution Laboratory of Biodiversity and Evolutionary Genomics KU Leuven Ch. Deberiotstraat 32, box 2439 B-3000 Leuven, Belgium Phone: +32 16 32 39 72 Fax: +32 16 32 45 75 Email: filip.volckaert(a)kuleuven.be URL: bio.kuleuven.be/eeb/lbeg Skype: filipvolckaert1 Postdoctoral fellow in Blue Biotech The Department of Biology and The Genomics Core of the KU Leuven are currently looking for a postdoctoral fellow in Environmental genomics & bioinformatics to lead independent population genomic research and develop ESFRI-EMBRC bioinformatics services. The successful candidate will join two international teams that study the molecular evolution of marine organisms and develop analytical tools for NGS data for research purposes, and transitions them to/towards marine scientists. The successful candidate will focus on independent scientific research in evolutionary genomics and the development of bioinformatic toolkits for external users. We also offer the possibility to develop our ongoing consultancy in marine genomics. We are looking for a motivated and scientifically excellent candidate in environmental genomics/ bioinformatics with a problem-solving attitude to work in a collegial environment pervaded with intellectual rigor. Strong communication skills complemented with innovative and analytical thinking are important assets. Applicants must hold a PhD in a related field such as (Applied) Biology, Bioinformatics or Computational Biology. The individual we are looking for will have to be confrontable with common bioinformatics software and programming languages (Python, Perl, Java, R), and be highly motivated to solve biological problems. The successful applicant will also be adapting and implementing existing bioinformatics pipelines in an automated cloud-based analysis platform to make these algorithms available for marine biological and other fundamental biological questions. The candidate will also have an opportunity for the teaching and mentoring of students. We look forward to receiving a motivation letter (max. 1 page), short CV (max. 3 pages), a scientific achievements track-record (max. 2 pages) including a list of your five most important publications, and three names of referees. We offer an initial 18 Months contract (extendable with national or EU funds) a competitive salary and interactive work environment in collaboration with the European Marine Biological Resource Center (www.embrc.eu<http://www.embrc.eu>), a well-established marine research team (bio.kuleuven.be/eeb/lbeg) and the largest Genomics Service core (www.genomicscore.be<http://www.genomicscore.be>) in Belgium. KU Leuven is a research-intensive, internationally oriented university that has been elected Europe's most innovative university by Reuters and consistently ranks and features in Europe's top-15 universities within the Times Higher Education ranking. Leuven is a historic, dynamic and lively city located in the heart of Belgium, within 20 min from Brussels, the capital of the European Union, and less than 2 h from Paris, London and Amsterdam. Working site: Leuven, Belgium Application deadline: The application must be sent as a single PDF by email to conny.coeckelberghs(a)kuleuven.be with as subject 'eGenomics/bioinformatics postdoc position' by midnight June 25th 2019. For further information contact dr. Gregory Maes, phone +32 16 37 25 22, gregory.maes@ kuleuven.be<mailto:gregory.maes@%20kuleuven.be> and/or prof. Filip Volckaert, phone: +32 16 39 72, filip.volckaert(a)kuleuven.be<mailto:filip.volckaert@kuleuven.be>.

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