March 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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2 years Post-doc bioinformatiics positions in London
by nicos_mlists_06＠yahoo.co.uk 29 Mar '19

29 Mar '19

Two Post-doc positions in bioinformatics at the March of Dimes, Prematurity Research Centre at Imperial College London. To work with Dr David MacIntyre on understanding the biology of, and predict preterm births from clinical datasets. 1. focus on working with microbiomic, metabolomic and glycomic datasets https://www.imperial.ac.uk/jobs/description/MED01132/research-associate-bio… 2. focus on RNAseq analyses https://www.imperial.ac.uk/jobs/description/MED01113/research-associate-bio… The group is fully and well embedded in the research within the department with access to excellent clinical datasets, clinicians and biologists. It fosters commitment and provides an environment appreciative of elegant bioinformatics work. The positions are full time and for fixed term of two years in the first instance. Salary is 37,486 - 46,4999. See adverts for contact details. --- Nicos Angelopoulos http://stoics.org.uk/~nicos/

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Invitation for BDB-E seminar on May 23, 2019
by Avans Hogeschool 29 Mar '19

29 Mar '19

Big Data in Biology Education (BDB-E) Thursday May 23, 2019 09.00 - 18.00 hrs. Dear business relation, We are happy to invite you for our Big Data in Biology Education (BDB-E) seminar on Thursday May 23 coming. Next generation sequencing (NGS) revolutionizes the work field of DNA technology and DNA information, and so does our education and our research! ATGM and the lectorate ALS move forward in teaching and research related to innovative DNA techniques, generating large numbers of data, and the subsequent big data analysis. At this seminar, experts and students will share their experience and views why it is important to invest in teaching the ‘dry-lab’ analyses to our students. Preliminary program 09:30 - 10:45 Morning Session 1 Data-driven Bio-medical research Pieter-Jan van der Zaag from Philips Health Care, Harmen van de Werken from Erasmus MC, and ATGM student Derek van Tilborg 11:00 - 12:15 Morning Session 2 Development of Data intensive Bio-technology Ali May from Baseclear, Victor de Jager from BASF Vegetable Molecular Breeding and ATGM student Chun Tang 12:15 - 13:00 Lunch 13:00 - 14:30 Afternoon session 3 Big data in the Microbiology Aldert Zomer UU, Natacha Monge Gomes Do Couto UMCG, Brian van der Veer MUMC+ and ATGM/ALS student Marco Ivens 15:00 - 16:30 Three parallel workshops Workshop 1: MinION hands-on trouble shooting Workshop 2: Employers meets Educators Workshop 3: Student poster presentation 16:30 - 16:45 Closure by Erik van Seventer 17:00 - 18:00 Drinks For whom? This seminar is for Hogescholen/Universities (teachers and students) from the Bioinformatics and Biology and Medical Laboratory Research programs. Additionally, organizations/researchers interested in the different topics, which are related to big-data that are highlighted during this conference, are welcome. Registration You can register for the BDB-E until the 17th of May. Do you have questions or want more information? Please contact BDBE.seminar(a)avans.nl We hope to welcome you. Kind regards, Eefje Schrauwen Miaomiao Zhou Kees Rodenburg ============================================================ ** Sign up (http://) This is a text block. You can use it to add text to your template. ** (https://avans.us20.list-manage.com/track/click?u=a6a3b6f4fc55883e2d6114ed3&…) This email was sent to bbclist(a)psb.ugent.be (mailto:bbclist@psb.ugent.be) why did I get this? (https://avans.us20.list-manage.com/about?u=a6a3b6f4fc55883e2d6114ed3&id=4b1…) unsubscribe from this list (https://avans.us20.list-manage.com/unsubscribe?u=a6a3b6f4fc55883e2d6114ed3&…) update subscription preferences (https://avans.us20.list-manage.com/profile?u=a6a3b6f4fc55883e2d6114ed3&id=4…) Avans Hogeschool . Lovendsdijkstraat 63 . Breda, Nb 4818 AJ . Netherlands Email Marketing Powered by Mailchimp http://www.mailchimp.com/monkey-rewards/?utm_source=freemium_newsletter&utm…

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Software Carpentry course: Computing skills for reproducible research - still slots available
by Alexander Botzki 28 Mar '19

28 Mar '19

Dear all, I would like to send you more information about our next ELIXIR training course taking place 16 and 17th of April in Brussels. Computing skills for reproducible research: Software Carpentry Software Carpentry<https://email.vibconferences.be/t/r-l-jillfa-shyuuqkd-d/> aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. Date: 16 and 17 April Location: Brussels Trainer: Malvika Sharan, Stijn Van Hoey, Christof De Bo Registration: https://training.vib.be/computing-skills-reproducible-research-software-car… Please feel free to spread further in your network if you see fit. Best regards, Alex Alexander Botzki - Head of VIB Bioinformatics Core | Training Coordinator ELIXIR-BE VIB Bioinformatics Core Rijvisschestraat 126, 9052 GENT, Belgium | +32 9 248 16 00 www.bits.vib.be<http://www.bits.vib.be/> | @vibbioinfocore | https://corefacilities.vib.be<https://corefacilities.vib.be/> [signatureFooter (002)]

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Upcoming HPC training events for life scientists organised by SURFsara and ELIXIR-NL: 23-24 April and May 9 2019 , Utrecht, the Netherlands
by Celia van Gelder 27 Mar '19

27 Mar '19

Dear all, On behalf of Mateusz Kuzak and ELIXIR-NL please find below the announcements of two upcoming HPC courses targeted at Life Science researchers. Please spread in your organisation as you see fit. Thank you! Celia ++++++++++++ Dear all, SURFsara in collaboration with ELIXIR-NL and DTL is organising two High-Performance Computing workshops targeted at life science researchers. Both workshops will take place in Utrecht in SURF offices. <https://carlos-tb.github.io/2019-04-23-Cluster-Computing-ELIXIR/> "Cluster Computing for Life Sciences" is a two-day workshop. On the first day, participants will learn the basics of the Unix shell and how to work on the command line efficiently and how to access resources with more computing power (computer cluster) and run the computations remotely. On the second day, they will learn the basics of Python programming language and build a simple analysis pipeline with Snakemake and execute it on the computer cluster. Website and registration <https://carlos-tb.github.io/2019-04-23-Cluster-Computing-ELIXIR/> Time and Date: 9 am - 5 pm, 23 - 24 April, 2019 Registration fee: Registration is free of charge Location: SURF Utrecht. Kantoren Hoog Overborch (Hoog Catharijne), Moreelsepark 48, room 3.5, 3511 EP Utrecht ------------------------------- <https://carlos-tb.github.io/2019-05-09-Deep-Learning-ELIXIR/> "Deep Learning for Life Sciences" is a one day workshop. In the morning, participants will learn the basics of machine learning and artificial neural networks. In the afternoon they will gain hands-on experience with applying newly acquired skills to analyse imaging data with Python in Jupyter Notebooks. Website and registration <https://carlos-tb.github.io/2019-05-09-Deep-Learning-ELIXIR/> Time and Date: 9 am - 5 pm, May 9, 2019 Registration fee: Registration is free of charge Location: SURF Utrecht. Kantoren Hoog Overborch (Hoog Catharijne), Moreelsepark 48, room 3.5, 3511 EP Utrecht kind regards, Mateusz -- .

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3 years PhD bioinformatics position in Paris
by Eric Bonnet 26 Mar '19

26 Mar '19

Dear all, A 3 years CEA funded PhD position in bioinformatics is open in Paris to study the role of glial cells in Huntington disease. For a detailed description see: https://drive.google.com/open?id=1MAdftl9y-HJe8ufNDMA-yPmawLdV5cc1YDmsxTmAH… Best regards, Eric Bonnet, PhD. CEA/DRF/JACOB/CNRGH/LBA 2 rue Gaston Crémieux 91057 EVRY Cedex

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Two-year postdoc position for a Bioinformatician in multi-omics
by Morgane Pierre-Jean 26 Mar '19

26 Mar '19

Dear all, Please find attached a two-year postdoc opportunity at CNRGH (Centre National de Recherche en Génomique Humaine). Best regards, Morgane PIERRE-JEAN, PhD. CEA/DRF/JACOB/CNRGH 2 rue Gaston Crémieux 91057 EVRY Cedex

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