February 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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Bioinformatics Summer School - July 2019 - UCLouvain
by Laurent Gatto 25 Feb '19

25 Feb '19

Dear all, We would like to announce the international bioinformatics summer school that will take place at the UCLouvain, in Louvain-la-Neuve, Belgium, from the 1 - 5 July 2019. This one-week intensive summer school in bioinformatics will focus on data analysis and high throughput biology, with a special focus on R/Bioconductor and its application to a wide range of topics across bioinformatics and computational biology. Participants will benefit from the expertise of renowned experts in the field of omics data analysis. The course is intended for researchers who are familiar with omics experimental technologies and their applications in biology, have had some exposure with R, and who want to learn or expand their bioinformatics skills. The material will cover underlying theory and practical hands-on exercises. At the end of the course, participants should be able to run analysis workflows on their own omics data, adapt and combine different tools and make informed choices about bioinformatics data analysis strategies. The summer school will accept up to 50 participants and offers 20 scholarships to students and early career researchers. Further details, preliminary schedule and registration details are available on the summer school’s webpage at https://uclouvain-cbio.github.io/BSS2019/. On behalf of the organising committee, Laurent Prof Laurent Gatto 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/

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Postdoc Bioinformatics Vacancy @Amsterdam UMC (AMC)
by Koster, J.J.B. (Jan) 22 Feb '19

22 Feb '19

Dear all, The Bioinformatics team at Oncogenomics is looking for a bioinformatics postdoc to further extend the R2 platform (http://r2.amc.nl) towards personalized genomics applications. https://werkenbijamc.nl/vacatures/bioinformatician-postdoc/ We are looking forward to meet you Jan Koster Ph.D. Group leader Bioinformatics Department of Oncogenomics, M1-132 Academic Medical Center (AMC) University of Amsterdam Meibergdreef 9 1105 AZ Amsterdam the Netherlands Tel: +31 20 56 67536 Mobile: +31 6 49628872 Email: j<https://webmail.amc.nl/owa/r2-support@amc.uva.nl/redir.aspx?SURL=ilk7fUTz3G…>ankoster(a)amc.uva.nl ________________________________ AMC Disclaimer : https://www.amc.nl/disclaimer ________________________________

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Job vacancy @ Amsterdam UMC
by Sie, D.L.S. (Daud) 22 Feb '19

22 Feb '19

Dear all, The bioinformatics team Clinical Genetics Amsterdam UMC is looking for a senior bioinformatics specialist: https://www.werkenbijvumc.nl/vacatures/senior-bioinformaticus-genoomanalyse/ Are you the one to join our team? Let me know if you have any questions. Regards, Daoud [cid:image002.png@01D40E30.3E299A80] Dr. Daoud Sie | Head Bioinformatics | Coordinator Core Facility Genomics Department of Clinical Genetics Location VUmc | MF-J391 | Van der Boechosrtstraat 7, 1081 BT Amsterdam Location AMC | K2-211 | Meibergdreef 9, 1105 AZ Amsterdam T: (+31)20-4442428 | E: d.sie(a)amsterdamumc.nl www.amsterdamumc.nl<http://www.amsterdamumc.nl/> | www.vumc.nl<http://www.vumc.nl/> / www.amc.nl<http://www.amc.nl/> ______________________________________________________ VUmc disclaimer: www.vumc.nl/disclaimer<http://www.vumc.nl/disclaimer> ______________________________________________________ VUmc disclaimer : www.vumc.nl/disclaimer AMC disclaimer : www.amc.nl/disclaimer

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Course Flowcytometrie 2, 9 & 16 April 2019
by Sari van Heel - Vauhkala 22 Feb '19

22 Feb '19

Dear Member of BBClist, We would like to draw your attention to our upcoming course Flowcytometrie that will be organized by the Research Group Analysis Techniques in the Life Sciences in April 2019: Name course: Flowcytometrie, van kalibratie tot applicatie Course date: Tuesday 2, 9 & 16 April 2019 Location: Erasmus MC, Rotterdam Registration fee: €600,- Website: http://www.alsavans.nl/cursussen/avans-training-2541.html The digital registration form is available on our website. Should you have any questions, please do not hesitate to contact us by email at: info.ALS(a)avans.nl<mailto:info.ALS@avans.nl> Kind regards, Ms. Sari van Heel-Vauhkala Secretary Research Group Analysis Techniques in the Life Sciences Breda, the Netherlands

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SCIENTIFIC PROGRAMMER IN DATA VISUALISATION (KU Leuven)
by Vera van Noort 21 Feb '19

21 Feb '19

Vera van Noort (KU Leuven) and Jan Aerts (KU Leuven/UHasselt) are looking for a Scientific programmer in data visualisation. In this project we will build a framework for creating custom visualisations and combining these in a dashboard-setting. The aim is to create the necessary front- and backend to allow for (1) easily creating and incorporating new visual modules (conceptually similar to https://github.com/jandot/bio-graphics) (2) combining these visual modules in a single interface, and (3) incorporating a biological ontology which links biological concepts to features in the visuals. The applicant needs to have demonstrable experience in web-development and software management. This includes strong programming skills in javascript and if possible python, and/or clojurescript. https://www.kuleuven.be/personeel/jobsite/jobs/55033629 For more information please contact Prof. dr. Vera van Noort mail: vera.vannoort(a)kuleuven.be or Prof. dr. ir. Jan Aerts mail: jan.aerts(a)kuleuven.be.

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MOPGP 2019 in the Magical city of Marrakech
by El-ghazali Talbi 21 Feb '19

21 Feb '19

Dear Colleague, I would like to invite you to submit an abstract for the 2019 International Conference on Multiple Objective Programming and Goal Programming (MOPGP) <http://mopgp.org/> in Marrakech, Morocco. Selected extended-abstracts will be considered as potential full-paper publications, subject to peer reviews in Annals of Operations Research (Call for Papers: <http://rutcor.rutgers.edu/CfPMOPGP%202019.pdf>Recent Advances in Multiobjective Optimization <http://rutcor.rutgers.edu/CfPMOPGP%202019.pdf>). The submission Deadline is on May 30, 2019. Thank you in advance and we look forward to welcoming you in the oasis of the magical city of Marrakech. Best regards -- *********************************************************************** MOPGP'2019 Int. Conference on Multiple Objective Programming and Goal Programming 28-31 Oct 2019, Marrakech, Morocco http://www.mopgp.org *********************************************************************** Prof. El-ghazali TALBI Polytech'Lille, University Lille - INRIA CRISTAL - CNRS

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