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

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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One-day course on Public Proteomics Data Reprocessing
by Kim DE RUYCK 27 Sep '18

27 Sep '18

Dear all I would like to highlight the " [ http://www.vib.be/en/training/research-training/courses/Pages/Elixir-Tabloi… | Public Proteomics Data Reprocessing and the Tabloid Proteome ] " course organized by the Computational Omics and Systems Biology Group and ELIXIR Belgium (Wednesday 10 October 2018, Ghent). If you are, or during your project will be, working with larger amounts of proteomics data, this course provides a good introduction to facilitate this. The course provides an introduction to public proteomics resources and tools, followed by a practical exercise in which the reprocessing of MS data from PRIDE will be handled. The Tabloid Proteome will be introduced as a use case of public proteomics data re-use, followed by a second practical investigating protein association using Tabloid Proteome database. Within one day, you will get a good view of the possibilities of re-using proteomics data. Kind regards, Kim De Ruyck Kim De Ruyck PhD Coordinator ELIXIR Belgium VIB, Technologiepark 927, 9052 Gent | +32 (0)9 33 13 694 [ http://www.elixir-belgium.org/ | www.elixir-belgium.org ] [ https://twitter.com/ELIXIRnodeBE | @ELIXIRnodeBE ] [ http://eepurl.com/cl-xOX | Subscribe to our mailing list ]

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+++ RSG BIOHACKATHON - BRUSSELS 16/11/2018 +++
by Daniele Parisi 26 Sep '18

26 Sep '18

Dear colleagues, RSG Belgium is excited to announce the FIRST RSG BELGIUM HACKATHON, which will take place in Brussels on 11th November. This event represents a good opportunity for MSc/PhD students from all scientific backgrounds to Improve PROBLEM SOLVING, TEAMWORK AND CODING SKILLS BY WORKING TOGETHER AS A MULTIDISCIPLINARY TEAM. You can read about the FOUR DIFFERENT SHORT PROJECTS selected by the RSG Belgium team on the registration form, and EXPRESS YOUR PREFERENCE. The most voted ones will be part of the challenge of the Hackhaton. Do not hesitate, REGISTER HERE: https://docs.google.com/forms/d/e/1FAIpQLSdmv3Jroj1m0e_Edk2oCgLktZttmIp686X… DATE AND TIME: 16/11/2018, 09:00 until 18:00 PLACE: Université Libre de Bruxelles, La Plaine campus, Building NO, 9th floor, room: 2NO906 ("Salle des professeurs"), Brussels, Belgium REGISTRATION DEADLINE: 27 October 2018 More information will be available on our web page http://www.rsg-belgium.iscbsc.org/ Best regards -- DANIELE PARISI PhD student at ESAT - STADIUS, Yves Moreau's group President of RSG Belgium Chair of ESCS 2018 Kasteelpark Arenberg 10 - box 01.34 3001 Leuven, Belgium Tel: +32488794394

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byteMAL2018: Last call to register and submit a poster abstract
by Loïc 26 Sep '18

26 Sep '18

Dear all, Concerning the byteMAL2018 conference (Bioinformatics for Young inTernational researchers Maastricht - Aachen - Liège), we remind you that you must register and submit a poster abstract before Monday, October 1 to have a chance to be selected for a flash talk, and until Wednesday, October 3 to simply present a poster. Date: October 5 at 9.30am Location: B22, Chemin de la Vallée 4 (Sart Tilman Campus) 4000 Liège https://www.campus.uliege.be/cms/c_5799509/en/b22-institut-de-botanique We look forward to welcoming you! The Liège byteMAL team

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1 Phd position available - Deep learning/Computer vision/Bioimaging (Belgium)
by Raphaël Marée 26 Sep '18

26 Sep '18

Dear colleagues, The Montefiore Institute (http://www.montefiore.uliege.be) at the University of Liège, Belgium has an opening for a PhD candidate to work on the development of novel deep/machine learning algorithms for quantitative multimodal biomedical image analysis. More specifically, this PhD project entails the development of novel algorithms to automatically locate, measure, and classify elements in multimodal biomedical images with a specific focus on skeletal development applications. These algorithms will be disseminated to a wide audience through the open-source Cytomine web-based software platform (http://uliege.cytomine.org) The ideal candidate should have a Master in Computer Science or Biomedical Engineering, with a taste for deep/machine learning and modern software programming. The candidate will be supervised by senior scientific staff with a background in computer science (Prof. Wehenkel, Prof. Geurts, Dr. Raphaël Marée) in collaboration with biomedical researchers (Dr. Marc Muller) and other project partners. The candidate will actively participate in PhD training activities within the BioMedaqu consortium. It is a Marie Sklodowska-Curie Innovative Training Network (MCSA-ITN) with the primary research aim to create an innovative expertise combining research in skeletal biology of aquaculture fish species with that in biomedical models and humans. In total, 15 Early Stage Researchers (ESRs) will be appointed by the BioMedaqu consortium for 36 months each. There are strict eligibility requirements for the ESR PhD positions in MSCA-ITN. Please ensure that you qualify before applying, as ineligible candidates cannot be considered. See more details here: http://www.giga.uliege.be/cms/c_279692/en/biomedaqu-open-positions https://euraxess.ec.europa.eu/jobs/315826 The position starts before January 2019. Interested and eligible candidates should send their résumé and application letter to Dr. Raphaël Marée (raphael.maree(a)uliege.be) and Dr. Marc Muller (m.muller(a)uliege.be) as soon as possible. Best regards, Raphaël. -- Raphaël Marée (PhD) http://www.montefiore.ulg.ac.be/~maree/ http://www.cytomine.org/ Tél.: +32 4 366 26 44

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Assistant Professor Bioinformatics for personalized Medicine, Nijmegen, The Netherlands
by Celia van Gelder 26 Sep '18

26 Sep '18

On behalf of Peter-Bram ‘t Hoen please find this interesting job opening below: Do you have the ambition to build your own bioinformatics research group and are you passionate about personalised medicine? If so, consider the vacancy in the Centre for Molecular and Biomolecular Informatics (CMBI) at Radboudumc Nijmegen, The Netherlands. https://www.radboudumc.nl/en/vacancies/60641-assistant-professor-bioinforma… Best regards Celia Dr. Celia W.G. van Gelder Programme Manager DTL Learning Training Coordinator ELIXIR-NL ELIXIR Training Platform Leader tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl <mailto:celia.van.gelder@dtls.nl> websites: <http://www.dtls.nl/> www.dtls.nl, <http://www.biosb.nl/> www.biosb.nl 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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Postdoctoral position - Mathematical modeling in network biology
by REMY Elisabeth 25 Sep '18

25 Sep '18

Please find hereafter a job offer for a 2 years interdisciplinary post-doc position in Marseille (France). ------- Project The aim of the project is to characterize molecular pathways deregulated in myelofibrosis development and define predictive factors of disease evolution. Hematopoietic tissue is sensitive to aging, which results in senescence and haematological age-related diseases like myelofibrosis. We propose an interdisciplinary approach focused on the understanding of the hematopoietic stem cell (HSC)/stromal cell cross-talk that evolves during aging and favors myelofibrosis. The applicant will be in charge of the establishment and analysis of mathematical models centered on bone marrow and HSC aging in order to better understand haematological age-related disease onset. We have developed a unique mouse model, which recapitulates physiological and pathological aging that will be used to generate single cell transcriptomic data. The generated data, together with an extensive literature study, will be the base to address the complexity of the network deregulated upon HSC/stromal cell aging by mathematical modeling approaches. Environment The successful applicant will work in the Mathematics and Algorithms for Systems Biology (Mabios, http://mabios.math.cnrs.fr/index.html) group in the Marseille Institute of Mathematics (I2M, Aix-Marseille University) an interdisciplinary team of mathematicians and computational biologists, in close collaboration with the E. Duprez team (http://crcm.marseille.inserm.fr/en/researchteams/estelle-duprez) specialised in Epigenetic Factors in Normal and Malignant Hematopoiesis in the Centre de Recherche en Cancérologie de Marseille (CRCM). Expected profile The applicant should have a formation (PhD) in Computer Science, Applied Mathematics, Computational Biology (or related fields). He/she should have a strong interest in biology and interdisciplinary approaches to decipher biological processes. Skills in programming/scripting and/or bioinformatics (for *-seq data processing) would be an advantage. Offer Fully-funded position for 2 years in Marseille. The starting date is expected in January 2019. Application can be sent directly to “elisabeth.remy(a)univ-amu.fr<mailto:elisabeth.remy@univ-amu.fr>” and “estelle.duprez(a)inserm.fr<mailto:estelle.duprez@inserm.fr>”. Please make sure your application includes a letter of motivation, a list of publications, a detailed CV and the contact information of 2 references (including email addresses and phone numbers). Keywords: Mathematical modeling, Single cell, Data Analysis, Systems Biology --------- --------------------------------------------------------------------- Élisabeth REMY Institut de Mathématiques de Marseille (I2M) Campus de Luminy- Case 907 13288 Marseille cedex 09 +33 (0)4 91 26 95 65 http://mabios.math.cnrs.fr/index.html

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Job: lecturer bioinformatics at Hogeschool van Arnhem en Nijmegen (Dutch)
by Bruggen Martijn van der 25 Sep '18

25 Sep '18

Dear all, We have an opening for a lecturer bioinformatics/informatics and for an instructor bioinformatics. Note: vacancies are only for Dutch-speaking candidates. Please also forward to any potentially interested candidates you might know. https://www.han.nl/start/corporate/werken-bij-de-han/vacatures/_detail/inde… https://www.han.nl/start/corporate/werken-bij-de-han/vacatures/_detail/inde… Martijn. Drs. M.H.H. van der Bruggen Docent bioinformatica / Opleidingscoördinator bioinformatica Hogeschool van Arnhem en Nijmegen (HAN) Instituut voor Toegepaste Biowetenschappen en Chemie Postadres: postbus 6960 | 6503 GL NIJMEGEN | Nederland Bezoekadres: Laan van Scheut 2 | Kamer 0.07 | 6525 EM NIJMEGEN | Nederland | +31-6-55206344 Aanwezig: maandag – dinsdag – woensdag – donderdag - vrijdag [1512978560569_PastedImage] [cid:c8979e1a-6e02-48b0-9801-f1d99ff2285e]

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PhD position: Metabolic modeling of bacterial interactions
by Karoline Faust 24 Sep '18

24 Sep '18

PhD position: Metabolic modeling of bacterial interactions The Laboratory of Microbial Systems Biology (http://tinyurl.com/MicrobialSysBio) is looking for a motivated PhD candidate who is interested in investigating microbial communities through metabolic modeling. 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 PhD position is funded through an ERC starting grant. Project While metabolic models have been successfully applied to describe the behavior of bacteria grown in mono-culture, their extension to several interacting bacterial strains is a field of active research. The goal of this PhD is to develop and evaluate approaches based on metabolic modeling to predict bacterial interactions. In addition, we want to apply metabolic modeling to predict the behavior of bacterial communities growing in well-defined conditions. Profile The candidate should have a solid background in systems biology. Knowledge of metabolic modeling or metabolic network analysis is a plus. Applicants should have a Master degree in systems biology, bioinformatics or equivalent with at least a distinction, obtained in January 2019 at the latest. A proof of proficiency in English is a requirement. Offer -full-time 4-year contract -enrolment at one of the top universities in Europe -exciting research environment -competitive salary Interested? Please submit a cover letter, a CV including obtained grades, and a list with at least two references (with name, function, email, address and phone number) through the online application tool (https://www.kuleuven.be/personeel/jobsite/jobs/54798210) You can apply for this position no later than 1st December, 2018. The PhD will start in January 2019. For more information, please contact Karoline Faust at: karoline.faust(a)kuleuven.be

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