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

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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Save the date: Boost Your Visibility - Improving F of FAIR for Dutch Training and Data Resources through Bioschemas, Hackathon, 7-8 February 2019, Utrecht, the Netherlands
by Mateusz Kuzak 10 Jan '19

10 Jan '19

-- apologies for cross posting -- Dear colleague, Are you a training provider/organizer with a catalogue of training events and/or training materials or a data provider, curator or manager of Life Science resources such as Biobanks, Proteins, Samples, Beacons, Tools? Then this hackathon may be very relevant for you! DTL and ELIXIR-NL are organising a workshop/hackathon for content providers of Life Science resources such as Proteins, Samples, Beacons, Tools, and Training events and materials. Join this event to learn how to make your resources rank higher on (Google, Bing, Yahoo and other) search result pages or include your resource in relevant registries (like TeSS, the ELIXIR Training Portal) and receive more web traffic can raise the exposure of your work to be found by larger audiences. The event will start at lunch time on Thursday February 7 and will finish on Friday February 8 at 4pm. In the first half day of this 1.5 day event participants will learn about schema.org and bioschemas from experts working on Bioschemas definitions and implementations for ELIXIR resources and they will get some examples of successful Bioschemas implementations in Life Science resources, both from within and outside the Netherlands. The second day will have the form of a hackathon during which participants will work on adding Bioschemas metadata to their resources with the help of the experts. For training materials and events we will also add them to the ELIXIR’s Training Portal TeSS. Please find more information and the draft agenda here and mark the dates in your agenda if you are interested. The registration will open at the beginning of January. Looking forward to seeing you at the hackathon! On behalf of DTL/ELIXIR-NL, Celia van Gelder and Mateusz Kuzak — 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 Visting address: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw Jaarbeursplein 6 | 3521 AL Utrecht

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Opening: Sr Bioinformatician in one of the largest next-gen sequencing service providers in Europe
by Ali May 27 Dec '18

27 Dec '18

Hello, I am writing to let you know that there's an opening for a very interesting position at BaseClear (Leiden), one of the largest next-generation sequencing service providers in Europe. In short, we are looking for a Sr. Bioinformatician who can run the place and build new services for 1000+ clients. More info at: https://www.baseclear.com/career-jobs/senior-bioinformatician-m-f/ Don't hesitate to apply if you think there might be a fit, or otherwise to share with anyone who may be interested. Best wishes, Ali

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Computational Biologist Single Cell Analysis @Janssen Belgium
by Joke Reumers 26 Dec '18

26 Dec '18

Dear all, We have a job opening (permanent position) for a computational biologist at the Janssen campus in Beerse, Belgium. While the focus of the job will lie heavily on single cell (seq) analysis, application is open with anyone with relevant experience in the context of ‘omics or related areas. Applications can be submitted via: https://jobs.jnj.com/jobs/1805706109W?lang=en-us <https://jobs.jnj.com/jobs/1805706109W?lang=en-us> Please feel free to share to other channels. For more information, please contact me at jreumers(a)its.jnj.com <mailto:jreumers@its.jnj.com> Happy holidays! Joke Reumers

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Edinburgh Biomedical Data Science School
by Van Anh Huynh-Thu 19 Dec '18

19 Dec '18

Dear all We are organising a week-long school on biomedical data science at the MRC Institute of Genetics and Molecular Medicine on March 11-15; details and registration here https://www.ed.ac.uk/igmm/news-and-events/events/latest-events/biomedical-d… <https://www.ed.ac.uk/igmm/news-and-events/events/latest-events/biomedical-d…>. We have a fantastic line-up of lecturers and it should be a great opportunity for students/ postdocs who want to learn about modern machine learning applied to large-scale genomic/ post-genomic data. We are limited to 25 participants by the capacity of the computer room and it will be first-come-first-served. Let me take this opportunity to wish you all a serene festive break and a great 2019. Dr Guido Sanguinetti Professor of Computational Bioinformatics, School of Informatics & SynthSys 10 Crichton St Edinburgh EH8 9AB tel: +44(0)131 6505136 email: gsanguin(a)inf.ed.ac.uk <mailto:gsanguin@inf.ed.ac.uk>

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Post-doc and PhD positions in computational biology in Munich
by Laurent Gatto 19 Dec '18

19 Dec '18

Simon Anders' group is currently seeking computational people to fill three positions (two post-docs, one PhD student), for projects related to developing methods to use single-cell assays in vascular biology and in haematology research: https://www.zmbh.uni-heidelberg.de/anders/open.shtml All three projects have close ties to experimental and clinical research and hence are a great opportunity to get to know all sides of life science research, not only for bioinformaticians but also for computational scientists from other fields.

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2 years post-doc in integrative omics at the Louvain Drug Research Institute
by Laurent Gatto 19 Dec '18

19 Dec '18

Summary: The laboratory of integrated Pharmacometrics, pharmacokinetics and pharmacogenomics (PMGK) at the Louvain Drug Research Institute (LDRI, UCLouvain), is seeking for a post-doctoral researcher focus on integrating multiple types of –omics data (mainly microbiomics, transcriptomics and genomics) to identify biological determinants of drug pharmacokinetics and their interaction in the context of kidney transplantation and immunosuppressive treatments. This project is financed through an Incentive grant for scientific research founded by the Fonds National de la Recherche scientifique (FNRS). Ideally, the candidate will have a strong data science background and knowledge in pharmacokinetic modelling, statistical/bioinformatic methods to integrate multiple biological data types. Details in the attached document. Please contact Laure Elens for additional information - laure.elens(a)uclouvain.be

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Post Doc Position Computational Bladder Cancer Genomics
by Harmen van de Werken 17 Dec '18

17 Dec '18

Dear All , Those who are interested in a challenging post-doc position in Computational Biology, Bioinformatics and Bladder Cancer please apply to our vacant position https://www.werkenbijerasmusmc.nl/en/vacancy/23002/postdoc-computational-bi… and make a huge leap forward in unraveling cancer biology and in your career. Kind regards, Harmen van de Werken -- Harmen van de Werken, Ph.D. Assistant Professor in Computational Biology at Department of Urology & Managing Director Cancer Computational Biology Center (CCBC) both at Erasmus MC P.O. Box 2040, Be-355 3000 CA Rotterdam, the Netherlands Visiting address: Josephine Nefkens Building Dr. Molewaterplein 40, office Be-330a 3015 GD Rotterdam, the Netherlands Tel: +31-10-7044467 (office) Tel: +31-10-7044488 (department) Fax: +31-10-7044661 https://ccbc.erasmusmc.nl/ Email: h.vandewerken(a)erasmusmc.nl Skype: harmen.vandewerken

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