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

VIB job offering: Instructional Designer for Life Sciences
by Alexander Botzki 16 Dec '19

16 Dec '19

Dear members of the BBC list, At VIB, we are recruiting an Instructional Designer (e-learning) for Life Sciences based at the VIB Bioinformatics Core. More information can be found on this web site: https://jobso.id/cav5 Please feel free to spread in more e-learning focused networks 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/>

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opening for a jr. bioinformatician @ Orionis (Ghent)
by Lieven Sterck 13 Dec '19

13 Dec '19

wkr, Lieven Lieven Sterck - Senior Postdoctoral Scientist Bioinformatics VIB Department of Plant Systems Biology Ghent University Technologiepark-Zwijnaarde 71 - 9052 Ghent - Belgium Tel. +32(0)9 331 38 21 [ http://bioinformatics.psb.ugent.be/ | http://bioinformatics.psb.ugent.be ] "Facts are meaningless. You could use facts to prove anything that's even remotely true" - H. Simpson

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PhD Candidate/Postdoc position at NKI on cellular regulation
by Alba Jene 12 Dec '19

12 Dec '19

Dear all, There is an open position in our collaborator Lodewyk Wessels lab at NKI, please find further details here: https://ccb.nki.nl/open-positions/ Best, -- Alba Jené Sanz, PhD Bioinformatics Unit Coordinator Barcelona Supercomputing Center (BSC) <https://maps.google.com/?q=C/+Jordi+Girona+29,+08034-Barcelona,+Spain&entry =gmail&source=g> C/ Jordi Girona 29, 08034-Barcelona, Spain Tel: +34 93 413 7572 nodelay http://bsc.es/disclaimer

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Winter research school "Networks and molecular biology" - Luminy, Marseille, France
by Anaïs BAUDOT 11 Dec '19

11 Dec '19

Dear all, We are organising a research school "Networks and molecular biology” on March 2 - 6, 2020. The global aim of the school is to present network theoretical models, algorithms, and their applications to biomedecine. The school will be held in the CIRM international meeting center in Luminy, Marseille. Pre-inscriptions are now open https://conferences.cirm-math.fr/2305.html <https://conferences.cirm-math.fr/2305.html>. Call for contributions: send your abstract (1 page) to mathsbiomonth-week5(a)sciencesconf.org <mailto:mathsbiomonth-week5@sciencesconf.org> , indicating in your email if you submit for a selected talk, a poster or both. Deadline January, 5th, 2020. Topics of interest include: - Network inference - Dynamical modelling of regulatory networks - Network mining - Machine Learning - Cancer and Rare diseases applications of Network approaches Speakers-Teachers: Chloé-Agathe Azencott (Mines ParisTech - Institut Curie, Paris) Christine Brun (TAGC, Marseille) Hervé Isambert (Institut Curie, Paris) Boris Kholodenko (Systems Biology Ireland, and Conway Institutes at University College Dublin) Edda Klipp (Humboldt University, Berlin) Kim-Anh Le Cao (University of Melbourne) Antonio Rausell (Clinical Bioinformatics, Imagine Institute) Maria Rodriguez-Martinez (IBM, Zurich) Julio Saez-Rodriguez (European Bioinformatics Institute, Cambridge) Marta Sales-Pardo (Chemical Engineering, Tarragona, Spain) Jana Wolf (Max Delbrück Center, Germany) Scientific Committee Alain Barrat (CNRS - CPT, Aix-Marseille Université) Christine Brun (CNRS - TAGC, Aix-Marseille Université) Laurence Calzone (Institut Curie, Paris) Claudine Chaouiya (I2M, Aix-Marseille Université) Florence Forbes (INRIA Grenoble Rhone-Alpes) Denis Thieffry (IBENS Paris) Organizing Committee Anaïs Baudot (MMG, Aix-Marseille Université) Brigitte Mossé (I2M, Aix-Marseille Université) Élisabeth Remy (I2M, Aix-Marseille Université) Laurent Tichit (I2M, Aix-Marseille Université) Matthieu Vignes (Massey University) This event is organised in the context of the thematic month on Mathematical Issues in Biology at the Centre International de Rencontres Mathématiques (CIRM, Marseille, https://conferences.cirm-math.fr/2141.html <https://conferences.cirm-math.fr/2141.html>). The meeting & housing are free of charge but subjected to selection of the applications. --------------------------------------------------------- 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 <mailto:anais.baudot@univ-amu.fr>

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Cursusaanbod
by Lectoraat ALS-Avans 09 Dec '19

09 Dec '19

Beste, Bij deze wil ik graag onze cursussen onder de aandacht brengen: Titel: Medische Immunologie Data: 12+19 februari, 4+11+18+25 maart 2020 van 16.00u tot 18.30u Locatie: LUMC, Leiden Kosten: €850,- (inclusief cursusmateriaal; leerboek Medische Immunologie) Titel: Cursus Mohs micrografische chirurgie, Een praktische benadering voor analisten. Data: 12 en 19 mei 2020 Locatie: Avans Hogeschool, Lovensdijkstraat 63, 4818 AJ Breda Kosten: €750,- (inclusief cursusmap, cursusboek ‘introduction to Mohs Cryotomy, drank en lunches) Titel: Course Variant effect prediction Data: 30 Juni – 3 July 2020 (4-daagse cursus) Locatie: Avans Hogeschool, Lovensdijkstraat 63, Breda Kosten: €900,- (including course materials and lunch) Voor meer informatie over deze cursus mag verwezen worden naar onze website: http://www.alsavans.nl. Contactgegevens: Mevr. Kelly van Boheemen, Tel: +31 (0)88 525 6728; e-mail: info.als(a)avans.nl<mailto:info.als@avans.nl>

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Fwd: Master 2 internship (Brest, France)
by Lieven Sterck 09 Dec '19

09 Dec '19

Hi, colleagues in the Ifremer Centre in Brest are looking for a master 2 student to do an internship in genome assembly and annotation of the oyster genome. More info in the attached advert. with kind regards, lieven > From: "Alexandre Cormier" <cormieralexandre(a)gmail.com> > To: "Lieven Sterck" <lieven.sterck(a)psb.vib-ugent.be> > Sent: Friday, 6 December, 2019 16:01:40 > Subject: Master 2 internship

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Workshop CNRS Single-Cell 2020 (Roscoff, France)
by Morgane Thomas-Chollier 05 Dec '19

05 Dec '19

Training : Single-Cell Transcriptomics and Epigenetics: Theory and Practice (sincellTE) // Ecole thématique CNRS Single-Cell 2020 Date : 22 March 2020 – 27 March 2020 Place : Roscoff, France Deadline pre-registration: 15th January 2020 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. Requirements : Understanding of bioinformatics tools and pipelines for next generation sequencing data (RNA-seq or Hi-C or ATAC-seq bulk). Participants must have prior experience on NGS data analysis with everyday use of R and good knowledge of Unix command line. It is not necessary to have personal single-cell data to analyse. All information and pre-registration: https://www.france-bioinformatique.fr/en/evenements/ecole-single-cell-2020 Share our leaflets: English : https://www.france-bioinformatique.fr/sites/default/files/Plaquette_sincell… French : https://www.france-bioinformatique.fr/sites/default/files/Plaquette_sincell…

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message for BBC mailing list
by Puck Knipscheer 04 Dec '19

04 Dec '19

Hi, The research groups of Juan Garaycoechea and Puck Knipscheer at the Hubrecht Institute in Utrecht have a position available for a bioinformatician. Attached you will find the advertisement. Would it be possible to post this on the BBC list? Many thanks, Puck -- Puck Knipscheer Group leader, Hubrecht Institute Oncode Institute Hubrecht Institute Uppsalalaan 8 3584 CT, Utrecht The Netherlands Phone: +31(0)30-2121 875 Email: p.knipscheer(a)Hubrecht.eu<applewebdata://B6A43367-B3E9-4EE4-9FAF-EDD3ECC44A9C/p.knipscheer@Hubrecht.eu>

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Postdoc position:
by Lodewyk Wessels 03 Dec '19

03 Dec '19

POSTDOC POSITION: Mapping cellular regulation from 130 genome-wide phenotype screens Are you a computational biologist with a fascination for cellular regulation? This project is a unique opportunity to unravel cellular regulation and discover new biology and therapeutic strategies. THE PROJECT Human cells perform highly complex tasks but the map of cellular regulation that controls these processes is surprisingly poorly known. In diseases, these processes are disturbed and targeted interference is required to rebalance disease. Such interference can only result in effective disease eradication with minimal side effects when the map of cellular regulation is known in sufficient detail. We will employ Phenosaurus, a large collection ~130 genome-wide haploid screens and advanced computational inference to reconstruct this map. Phenosaurus is a genotype to phenotype map that contains the strength of association between every gene and 130 (phopho)protein readouts in HAP1 cells. We envisage charting the regulatory map using two approaches. First, we will identify functional units. We will determine gene-gene similarity based on Phenosaurus phenotypic profiles and fuse these similarities with independent co-data sources such as protein-protein interaction maps, co-expression maps and gene ontologies to identify high confidence functional units (complexes and pathways). Second, we will identify regulatory interactions between functional units and genes. As many associations in Phenosaurus are indirect i.e. mediated by e.g. ‘master regulators’, we will employ network inference approaches, such as the PC algorithm, guided by co-data sources to identify (master) regulators and their associated interactions. High confidence predictions emerging from these analyses, such as protein complex or pathway membership (first approach) and new putative regulatory interactions with master regulators (second approach) will be validated experimentally. Importantly, this project provides the opportunity to develop novel computational approaches associated with data fusion, network inference and effective application of co-data. YOUR WORKING ENVIRONMENT You will research and benchmark the latest algorithms, develop new algorithms and help design validation and follow-up experiments. You will be working closely with fellow computational scientists of the Wessels group (ccb.nki.nl) experimentalists in the Brummelkamp group and scientists of Scenic Biotech BV (scenicbiotech.com) a biotech startup. You will be part of the Netherlands Cancer Institute (NKI), a world-class cancer research institute residing under the same roof as the Antoni van Leeuwenhoek cancer hospital in the vibrant city of Amsterdam. The NKI provides an open, lively and stimulating environment with access to top-notch facilities, including high-performance computing and with many opportunities to interact with colleagues at social events, attend high-quality seminars and perform translational research. WHAT WE ARE LOOKING FOR: Highly motivated postdocs with: - A degree or advanced skills in bioinformatics, or a related discipline - A degree or a high level of proficiency in (molecular) biology - Proficiency in R, Python and data base management - Experience in interacting with molecular biologists INTERESTED? Please send applications by email to Lodewyk Wessels and use “#application #postdoc” in the subject line. Include a CV, motivation letter and the names and contact information of at least two references in your application. DEADLINE: 20 January 2020

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