March 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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Anniversary RSAT / GINsim : Workshop and tutorial
by Morgane Thomas-Chollier 30 Mar '18

30 Mar '18

Workshop Anniversary 20th RSAT/ 15th GINsim ----------------------------------------------------------------- Computational biology softwares tend to be a relatively short life. RSAT (http://rsat.eu/) and GINsim (http://ginsim.org/) are notable exceptions, in large part thanks to active and friendly networks of collaborators. Indeed, 2018 marks the 20th anniversary of the first publication on RSAT, as well as the 15th anniversary of the first publication on GINsim. We propose to celebrate this joint event at IBENS in Paris, on May 16-17, 2018. The first day will be devoted to a series invited talks on the computational modelling and analysis of ci-regulatory regions and cellular networks. The second day will be devoted to tutorials on RSAT and GINsim for biologists. Invited speakers: • Samuel Collombet, Institut Curie, Paris • Claudine Chaouiya, IGC, Lisbon, Portugal • Bruno Contreiras Moreira, Estación Experimental de Aula Dei-CSIC, Zaragoza, Spain • Carl Herrmann, Universität Heidelberg, DKFZ, Heidelberg, Germany • Anthony Mathelier, NCMM, Oslo Norway • Pedro Monteiro, INESC-ID / IST - Universidade de Lisboa, Portugal • Elisabeth Remy, Institut de Mathématiques de Marseille • Hugues Roest Crollius, IBENS, Paris • Jacques van Helden, TAGC Marseille Program and registration (free but compulsory) : https://www.ibens.ens.fr/spip.php?article350 Looking forward to meeting you at this event ! Morgane Thomas-Chollier and Denis Thieffry

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Upcoming Bioinformatics Training Sessions of VIB and ELIXIR Belgium
by Alexander Botzki 29 Mar '18

29 Mar '18

Dear all, We would like to let you know that EBI trainers are coming to Belgium to give workshops on Ensembl Browser and Ensembl REST API in May 2018. Furthermore, ELIXIR Belgium is organising a Data Carpentry workshop in Brussels in June 2018. If you like to have more info and register to any of the courses, please visit https://bit.ly/1PkrdsU Thanks a lot. Best regards, Alexander ________________________________ Ensembl Browser Workshop This workshop offers participants hands-on experience in the use of the Ensembl vertebrate genome browser and provides them with the necessary background information. Ensembl genomes can also be covered if participants are working with bacteria, plants, fungi, protists or (invertebrate) metazoa. Date: 4 May Location: Park Inn, Leuven Trainer: Erin Haskell, EBI ________________________________ Ensembl REST API Workshop This workshop will introduce the basics of working with the Ensembl REST API, including an introduction to the main endpoints, exploring the documentation and writing sample clients. Participants will write their own scripts. Requirements Basic knowledge of a programming language. While any language can be used to access the REST API in practice, the support in this course will be limited to Python and Perl. Date: 14 May Location: BioAccelerator Trainer: Benjamin Moore and Matthew Laird, EBI ________________________________ ELIXIR Data carpentry workshop This is an introductory workshop to data management, databases, and data analysis in R. Researchers can perform simple to complex data management through open source tools and techniques which do not require highly specialist skills. This hands-on workshop will assist you to learn more about basic concepts and tools, including program design, version control, data management, and task automation. Requirements We recommend participants to have a basic understanding of R and its data types. Date: 12 and 13 June Location: Brussels Trainer: Paula Andrea Martinez, Stijn Van Hoey, Tina O'Grady, Christof De B

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Vacancies in Bioinformatics & Data Science @ KeyGene
by Roeland van Ham 28 Mar '18

28 Mar '18

We have vacancies available in Bioinformatics & Data Science at KeyGene, Wageningen, The Netherlands. Check them out at: http://www.keygene.com/scientist-genome-bioinformatics/ http://www.keygene.com/data-scientist-quantitative-genetics/ Interested in a postdoc position in sequence analysis instead? Contact me at rvh(a)keygene.com<mailto:rvh@keygene.com> Prof. Dr. Roeland van Ham Vice President Bioinformatics & Modeling Keygene N.V. | P.O. Box 216 | 6700 AE Wageningen | The Netherlands T (+31) 317 46 68 66 | F (+31) 317 42 49 39 | CoC. 09066631 | http://www.keygene.com<http://www.keygene.com/> [http://www.keygene.com/images/keygenegeneral.jpg]<http://www.keygene.com> Stay up-to-date! Subscribe to our bimonthly newsletter here<http://www.keygene.com/newsletter> [http://www.keygene.com/images/linkedin-grey.png]<https://www.linkedin.com/company/KeyGene> [http://www.keygene.com/images/twitter-grey.png] <https://twitter.com/KeyGeneInfo> [http://www.keygene.com/images/facebook-grey.png] <https://www.facebook.com/KeyGeneNV> The information contained in this message, and attachments if any, may be privileged and/or confidential and is intended to be received only by persons entitled to receive such information. Use of any part of this message and/or its attachments if any, in any other way than as explicitly stated by the sender is strictly prohibited. Should you receive this message unintentionally please notify the sender immediately, and delete it together with all attachments, if any. Thank you. The transmission of messages and/or information via the Internet is not secured and may be intercepted by third parties. KeyGene assumes no liability for any damage caused by any unintentional disclosure and/or use of the content of this message and attachments if any.

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Tenure track Computational Biology vacancy at CCA (Amsterdam)
by Ylstra, B 27 Mar '18

27 Mar '18

Anyone interested in a Tenure track Computational Biologist / PI-position? Please apply within the coming 2 weeks via https://www.werkenbijvumc.nl/vacatures/assistant-professor-computational-on…

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Registration open: Workshop Applying bioinformatics and data science competency frameworks to ELIXIR Training, 5-6 April 2018, Amsterdam
by Celia van Gelder 27 Mar '18

27 Mar '18

Workshop Applying bioinformatics and data science competency frameworks to ELIXIR Training, 5-6 April 2018, Amsterdam Date: 5-6 April 2018 (preceded by an optional seminar on April 4) Venue: Amsterdam Science Park Congress Centre, Science Park 123, 1098 XG Amsterdam Website & registration: <https://www.eventbrite.co.uk/e/applying-bioinformatics-and-data-science-com petency-frameworks-to-elixir-training-registration-43087835877> Eventbrite page. Registration is free of charge and you can register for each day separately. Full Programme: <https://www.dtls.nl/wp-content/uploads/2018/03/Full-Programme-120318.pdf> https://www.dtls.nl/wp-content/uploads/2018/03/Full-Programme-120318.pdf Organizers: Celia van Gelder (DTL/ELIXIR-Netherlands), Gabriella Rustici (University of Cambridge, ELIXIR-UK), Vera Matser (BioExcel), Allegra Via (ELIXIR-Italy) Target audience: Individuals working in training and education who are interested in learning the state of the art about bioinformatics and data science competency frameworks and their application to date. Description Much work is currently being done in developing and applying competency frameworks, both in bioinformatics and in data science. In the context of ELIXIR Training, we aim to build on the existing expertise in this area and, together with the training stakeholders, to derive a proper implementation strategy. This international workshop will bring together individuals from organisations and projects who have expertise in defining and in applying competency bioinformatics and data science frameworks in their own organisations. In a series of interactive sessions, we will build on the existing knowledge and work towards the following workshop goals: * Identify competency frameworks that are relevant to the ELIXIR user community and learn about successful implementation examples of these frameworks * Further define the relevant "personas" we are targeting with (ELIXIR) training * Extract from the existing work a set of core competencies and sets of KSAs (knowledge, skills and abilities) that can subsequently be used: * to map courses in TeSS, the ELIXIR Training Portal * to build a curriculum for a one-week Advanced Bioinformatics Workshop (which will be part of the CODATA RDA Research Data Science Summer school series) * to set the first steps towards defining routes through a specific set of courses (learning paths) Workshop Speakers: Implementing a competency-based training strategy for biomolecular researchers with high computational needs - Vera Matser (BioExcel) ISCB competencies and their implementation in H3ABioNet - Nicola Mulder (Computational Biology Division, University of Cape Town, H3ABioNet PI) Mapping bioinformatics competencies to University of Cambridge trainings - Gabriella Rustici (University of Cambridge) Application of EDISON Data Science Framework (EDSF) for customisable Data Science curricula development - Yuri Demchenko (University of Amsterdam, EDISON project) The curriculum of the CODATA-RDA Research Data Science Summer School - Hugh Shananan (Royal Holloway University of London) A critical look at competencies (Allegra Via, CNR-IBPM, ELIXIR-Italy) Learning Paths in the ERUDITE portal - John van Horn (University of Southern California, BD2K Training Coordination Center) Workflows in TeS - Niall Beard (ELIXIR-UK, University of Manchester) Seminar April 4, 14.40-16.30 Designing effective instruction and interpretable assessment by Allegra Via (CNR-IBPM, ELIXIR-Italy). See https://www.dtls.nl/wp-content/uploads/2018/03/April-4-pdf-2.pdf for more info. More information? Please contact Celia van Gelder ( <mailto:celia.van.gelder@dtls.nl> celia.van.gelder(a)dtls.nl) if you need more information. Dr. Celia W.G. van Gelder Programme Manager Learning DTL/ELIXIR-NL Training Education Manager BioSB ELIXIR Training Platform Leader tel. +31613375327 e-mail: <mailto:celia.van.gelder@dtls.nl> celia.van.gelder(a)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

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steward FAIR big research data in genomics & health
by Morris Swertz 23 Mar '18

23 Mar '18

Dear bio-data-science friends, We are searching for FAIR data managers or stewards to join our team of 25 data scientists, engineers and data managers to accelerate research in genomics and health via FAIR and reproducible data, methods and software and improve researchers and patients lives. Please apply here: https://www.umcg.nl/NL/UMCG/Werken_in_het_UMCG/Vacatures/Externe_vacatures/… (sorry for dutch vacancy text). Best wishes to all Morris -- Prof.dr. Morris A. Swertz - Adjunct professor Big data in Biomedicine -Lead UMCG Research IT programme - Head Genomics Coordination Center, UMCG Dept of Genetics - Lead MOLGENIS data science software - FAIR Data/IT leader in BBMRI-NL and Health-RI - Phone +31 50 3617100 - Fax + 31 50 3617230 - email m.a.swertz(a)rug.nl

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Data Steward position at UMC Utrecht
by Beek-4, D.M. van 23 Mar '18

23 Mar '18

Dear all, We have a job opening for a Data Steward at the Center for Molecular Medicine at the UMC Utrecht. Please find the details below and online at: http://www.werkenbijumcutrecht.nl/vacatures/Paginas/data-steward%20(2018-03… With kind regards, Daphne van Beek [cid:image001.png@01D357C3.DA1DC660] Data Steward UMC Bioinformatics Expertise Core - www.ubec.nl<http://www.ubec.nl/> | Department of Genetics | Center for Molecular Medicine | University Medical Center Utrecht | Universiteitsweg 100, 3584 CG, Utrecht | Huispostnummer: Str 1.305 | Office: Stratenum 0.304 | T: +31 88 75 682 04 | M: +31 6 2018 37 77 | www.umcutrecht.nl<http://www.umcutrecht.nl> | Office Hours: Mon, Tue, Thu, Fri [cid:image002.png@01D357C3.DA1DC660] LinkedIn<http://www.linkedin.com/in/daphnevanbeek> This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. P Please think of the environment before printing this email. Job opening: Data Steward The primary focus of the data steward, is to function as a ‘spider in the web’, link researchers to available resources within the UMCU, the UU and nationally. You will be responsible for the big data for research agenda and develop a strategy for FAIR data stewardship in the UBEC/CMM. You will provide best practices and develop training programs to create awareness about FAIR data stewardship. You will initiate and maintain contacts within the institute, the campus and nationally on everything related to data stewardship. Department The Section of Genetics [http://www.umcutrecht.nl/en/Research/Research-centers/Center-for-Molecular-…] of the Center for Molecular Medicine (CMM) uses genomics and bioinformatics approaches to understand the genetic basis of disease. Expertise and state-of-the-art infrastructure is available for next-generation DNA sequencing, single molecule sequencing, genotyping, metabolomics, bioinformatics and a broad range of model systems, including patient-derived primary cultures, iPS cells and organoid culturing. You will join the recently established UMCU Bioinformatics Expertise Core (UBEC) [http://www.ubec.nl] The UBEC provides bioinformatics services and support to researchers on the Utrecht Science Park campus. Data stewardship services is a part of the portfolio of the UBEC [https://datastewardship.ubec.nl] Profile You are educated as a data steward, bioinformatician or computational biologist (or related discipline) with a data analysis mindset. You should be able to function as a spokesperson of the researchers. The maximum salary for this position (100%) is € 4.216,00 gross per month based on full-time employment (work week 36 hours). This job is based on a temporary position for 1 year; possibility extension max 4 years. In addition, we offer an annual benefit of 8.3%, holiday allowance, travel expenses, career opportunities and personal budget. The terms of employment<http://www.werkenbijumcutrecht.nl/international/Pages/Terms-of-employment.a…> are in accordance with the Cao University Medical Centers (UMC). More information If you have any questions about this vacancy, please contact Mr.Dr. Jeroen de Ridder, PI, phone 088 7550406. Email j.deridder-4(a)umcutrecht.nl<mailto:j.deridder-4@umcutrecht.nl>. Acquisition based on this jobopening is not appreciated. Apply online: http://www.werkenbijumcutrecht.nl/vacatures/Paginas/data-steward%20(2018-03… ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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4 tenure track positions Bioinformatics/Data Science/Computer Science in Amsterdam
by Sanne Abeln 23 Mar '18

23 Mar '18

Dear all, Please find below four open tenure track positions in Bioinformatics, Data Science or more generally Computer Science in Amsterdam, one at the VUmc and three at the VU. VU - deadline 12 April: https://www.vu.nl/en/employment/vacancies/2018/18068ThreeAssistantProfessor… VUmc - deadline 10 April: https://www.werkenbijvumc.nl/vacatures/assistant-professor-computational-on… Best regards, Sanne -- -- Sanne Abeln Assistant Professor Bioinformatics - VU University Amsterdam s.abeln(a)vu.nl +31 20 59 87816 www.few.vu.nl/~abeln <http://www.few.vu.nl/%7Eabeln>

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