- BBClist - maillist.psb.ugent.be

Position available: Applied Bioinformatics team leader at Wageningen Research
by Ridder, Dick de 20 Dec '16

20 Dec '16

Dear all, Wageningen Research is looking for a leader of the Applied Bioinformatics team, part of the Bioscience business unit: https://www.academictransfer.com/employer/WUR/vacancy/37747/lang/en/ Best regards, Dick de Ridder Bioinformatics Group, Wageningen University http://www.bif.wur.nl/

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Bioinformatics/metagenomics postdoc opening in Leiden, NL
by Leon Mei 20 Dec '16

20 Dec '16

Dear colleague, Please find below a new bioinformatics postdoc opening at LUMC department of Medical Microbiology. Please feel free to forward this link to people who might be interested in this position. https://www.lumc.nl/over-het-lumc/werken-bij/vacatures-solliciteren/researc… Best regards, Leon

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GATK workshop in Belgium - 22-22 February 2017
by Alexander Botzki 19 Dec '16

19 Dec '16

Dear Bert, dear All, Thanks a lot for your email about GATK - given a successful first edition end of 2015, we hoped that there is much interested in such a workshop and we asked the GATK team to come to Belgium for a second workshop. So, for those who would like to join us in February 2017, VIB is organising a 3 day GATK workshop in Leuven on 20-22 February 2017. More information and registration (opens on 26th of December): http://www.vib.be/en/training/research-training/courses/Pages/GATK-Best-pra… Best regards, Janick and Alex Alexander Botzki - Manager BITS | Training Coordinator ELIXIR-BE VIB - BITS Rijvisschestraat 126, 9052 GENT | +32 9 248 16 00 www.bits.vib.be<http://www.bits.vib.be/> | @bitsatvib<https://twitter.com/bitsatvib> | https://corefacilities.vib.be<https://corefacilities.vib.be/> [signatureFooter (002)]

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Bioinformatics position available at the Erasmus MC Human Genomics Facility
by J.A.M. Verlouw 15 Dec '16

15 Dec '16

The Human Genomics Facility (HuGe-F) of the Department of Internal Medicine of the Erasmus MC will be leading one of Europe's largest human genome projects using Illumina's Global Screening Array (GSA). As such we are seeking an enthusiastic bio-informatician to perform post-processing of the genotyped GSA data. Other tasks would include implementing a Laboratory Information Management System (LIMS) and supporting other HuGe-F activities such as RNA-Sequencing, microbiome sequencing, DNA methylation arrays and Genome-Wide Association Analyses. For more information please see: http://www.erasmusmc.nl/vacature/?num=21671 Best regards, Joost Verlouw Bioinformatic Genetic Lab, Department of Internal Medicine Erasmus Medical Center, Rotterdam Room: Ee-579 Tel: 010-7038426

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Vacancy Senior Bioinformatician
by Beek, Daphne van 15 Dec '16

15 Dec '16

Dear all, The Clinical Genetics department at the VUmc Amsterdam is looking for a Senior Bioinformatician: https://www.werkenbijvumc.nl/vacatures/senior-bioinformaticus/ The following job description is in Dutch. If you would like to know more please contact Daoud Sie (e: d.sie(a)vumc.nl<mailto:d.sie@vumc.nl> or +31 (0)20 444 30 92). ---- Senior Bioinformaticus Ben jij de bioinformaticus die ons onderzoeksteam verder vorm gaat geven? * 36 uur * Salarisindicatie: 3527 tot 4842 euro * Vast contract, bepaalde tijd Werkomgeving Het laboratorium voor genoomdiagnostiek van de afdeling klinische genetica is ontstaan uit een fusie van het laboratorium voor chromosoomdiagnostiek en het laboratorium voor DNA- en eiwit diagnostiek. Onze hoofdtaak bestaat uit genetisch onderzoek naar erfelijke ziektes zoals bindweefselziektes, verstandelijke beperking en erfelijke vormen van kanker. Binnen het laboratorium wordt het hele genetische spectrum van chromosomale aberraties tot aan single nucleotide-mutaties geanalyseerd. De resultaten van deze analyses worden gebruikt voor erfelijkheidsadvies en advies aan medisch specialisten over de behandeling en follow-up van patiënten. Naast de implementatie van Next Generation Sequencing (NGS) technieken zoals targeted en whole exome sequencing (WES) zijn we bezig met het valideren en implementeren van whole genome sequencing (WGS) waarbij zowel snv, indels als CNV analyse op whole genome data uitgevoerd wordt. Daarnaast zijn we bezig met de implementatie van een landelijk project waarbij NIPT (niet invasieve prenatale test) grootschalig ingevoerd wordt. De hierboven genoemde werkzaamheden gaan gepaard met de afhandeling en analyse van grote hoeveelheden data. Werkzaamheden De geschikte kandidaat zal een centrale positie innemen in de bioinformatica groep van onze sectie en leiding geven aan 3 FTE bioinformatici. Daarnaast zal er intensief samengewerkt worden met andere (research)secties en klinische afdelingen. De werkzaamheden bestaan uit het ontwikkelen en beheer van de huidige data-analyse pipelines en het verder opzetten van infrastructuur. Hieronder vallen: * Ontwikkelen, valideren en implementeren van nieuwe bioinformatische tools in de diagnostiek; * Faciliteren van diagnostiek productie (o.a. runnen van pipelines, troubleshooten); * De organisatie van data flow en opslag * Het samenwerken met en ondersteunen van clinici en onderzoekers * Hulp bij onderhoud van de servers en databases. * Optimaliseren van de diagnostische workflow (o.a. door te automatiseren); * Onderhouden van contacten binnen de kaders van nationale projecten (bijv. implementatie NIPT en WGS) * Jouw profiel We zoeken een zelfstandige en gemotiveerde Bioinformaticus/Software Engineer met interesse in moleculaire biologie, voorkennis van genetica is wenselijk. * Afgeronde WO opleiding of gepromoveerd in de (bio)informatica met bij voorkeur relevante werkervaring; * Ervaring met het ontwikkelen/runnen/onderhouden van een (geautomatiseerde) pipeline; * Kennis van en ervaring met Python en bash in een Linux omgeving; * Ervaring met het werken met HPC is een pré; * Goede communicatieve vaardigheden. * Management ervaring Daarnaast ben je analytisch sterk, inventief in het vinden van passende oplossingen, stressbestendig en neem je initiatief. Wij bieden Salarisschaal 11: 3527 tot 4842 euro bruto bij een fulltime dienstverband (afhankelijk van opleiding en ervaring). Naast een uitstekend basissalaris bieden we onder andere 8,3% eindejaarsuitkering en 8% vakantietoeslag. Klik hier voor meer informatie over onze arbeidsvoorwaarden<http://www.werkenbijvumc.nl/arbeidsvoorwaarden/>. Het is voor nieuw aangestelde medewerkers verplicht om bij indiensttreding een VOG (Verklaring Omtrent Gedrag) aan te vragen. Je dient hiervoor in het bezit te zijn van een DigiD. Bijzonderheden Wij bieden een contract voor 12 maanden, met een mogelijkheid tot verlenging. Interesse? Wil je meer informatie over de functie dan kun je contact opnemen met mw. J. Weiss via 0204448355 of met R.van Latum via 0204444435. Je kunt uiterlijk tot en met 4 januari 2017 solliciteren via de button. Acquisitie naar aanleiding van deze vacature wordt niet op prijs gesteld. Vriendelijke groet, ir. Daphne van Beek Bioinformaticus Klinische Genetica E: d.vanbeek(a)vumc.nl<mailto:d.vanbeek@vumc.nl> Bioinformatici E: bioinf-klingen(a)vumc.nl<mailto:bioinf-klingen@vumc.nl> T: +31 (0)20 444 30 92 [http://www.vumc.nl/corporate/5489865/8393215/VUmc_E_logo+payoff.jpg] Bezoekadres: Van der Boechorststraat 7 (MF J-391), 1081 BT Amsterdam Postadres: Secretariaat laboratorium voor Genoomdiagnostiek, Polikliniek, PK-0X-011, VUmc Afdeling Klinische Genetica, Postbus 7057, 1007 MB Amsterdam www.vumc.nl<blocked::www.vumc.nl> www.vumc.nl/socialemedia<http://www.vumc.nl/socialemedia> www.vumc.nl/steun-ons<http://www.vumc.nl/steun-ons> --------------------------------------------------- Disclaimer Deze e-mail is vertrouwelijk en alleen bestemd voor de geadresseerde. Als deze e-mail niet voor u bestemd is, wordt u verzocht dit aan de afzender te melden, het bericht niet verder te verspreiden en direct te vernietigen. VU medisch centrum staat niet in voor de juiste en volledige overbrenging van de inhoud van deze e-mail. ---------------------------------------------------

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Fixed position computational biology Janssen Belgium
by Joke Reumers 14 Dec '16

14 Dec '16

Introduction / Description Janssen Discovery Sciences is a center of excellence focused on small-molecule drug discovery at Janssen R&D. Our scientists, together with a deep network of partners and collaborators, perform cutting-edge research from target & lead discovery through pre-clinical safety assessment to discover and develop transformational medicines. Every day we use our deep scientific expertise in drug discovery and development and our integrated suite of enabling technologies, platforms and tools to advance the research portfolio of Janssen’s five Therapeutic Areas: Cardiovascular & Metabolism, Immunology, Infectious Diseases & Vaccines, Neuroscience and Oncology. Within Discovery Sciences, the department of Computational Sciences provides expertise in computational/systems biology and big data analytics to support all aspects of drug discovery and development. The team provides a variety of complementary computational methodologies to extract meaningful and actionable information from biomedical data to facilitate the identification and validation of new targets in partnership with disease area experts in the therapeutic area discovery groups. The team is heavily engaged in deploying bioinformatics, machine learning and cutting-edge computational modeling and simulations techniques to advance our understanding of disease. The in silico activities are complemented and experimentally validated by wet lab capabilities within the team, utilizing stem cell, molecular genetics, gene editing, next generation sequencing and a variety of ‘-omics’ technologies We are looking for an enthusiastic candidate to join the European Computational Sciences team. The successful candidate will have a broad bioinformatics experience with a good working knowledge of genetics / pathway biology and deep scientific expertise in a number of disciplines including high-dimensional omics technologies and data analysis, methodologies for drug discovery and reverse translation coupled with the ability to work collaboratively with internal and external partners. Whereas the position will be based in Beerse (Belgium), it will support global teams in the different therapeutic areas and its Disease Area Strongholds. Furthermore, as the immune system plays a pivotal role in the progression of many diseases, background in immunology is a plus. Description of the function Work closely with therapeutic area teams to understand where bioinformatics approaches can best impact their scientific and technical challenges. Steer application of bioinformatics/genomics to benefit projects in therapeutic area projects. Work collaboratively with wet lab, IT and statistical specialists to deliver processes, tools and techniques to solve scientific problems. Application of a wide range of genomic technologies (RNAseq, WES, WGS) to target identification, validation and biomarker discovery. Development and application of approaches combining multi-omic data sets (including next-generation-sequencing) with phenotypic annotation to reveal actionable insights surrounding complex biological problems. Written and verbal communication of study results to project teams, including proposals for further experiments to validate key findings. Build and steer further development of small prototype tools for bench scientists to access and visualize project data. Play a key role in the interactions with other omics experts in functional areas such as Toxicology and Quantitative Sciences. Collaborate with industry and academia, and exploit external resources, to find the most effective solutions to complex biological problems. Qualifications PhD in bioinformatics, biostatistics, computational biology or similar. Alternately, a PhD in molecular biology, immunology, etc. combined with a very strong record of high-throughput data analysis, supported by publication in this area. Post-doctoral experience as well as exposure to wet lab activities in an academic or industrial setting is a plus. Ability to analyze and interpret complex omics datasets (e.g. microarrays, next-generation sequencing, flow cytometry, mass spectrometry proteomics, etc.). Proficiency in appropriate programming languages and software (e.g., R /Python/Perl/ Tableau/Spotfire) and data management. Strong written and oral presentation capabilities, with a convincing record of peer-reviewed publications and presentations at scientific conferences. Ability to clearly articulate scientific and operational concepts of biomarker research across functions, levels, and disciplines. High intrinsic motivation in combination with strong scientific curiosity and a high level of autonomy. Strong interpersonal skills and ability to work productively in a highly dynamic environment. Strong team orientation, highly collaborative and results-oriented. Good planning, prioritization, problem solving, and organizational skills. Knowledge and understanding of the regulatory, legal and operational requirements of sample collection and data handling for omics analyses in clinical studies is a plus.

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Gauging interest for a GATK workshop in 2017
by Bert Overduin 14 Dec '16

14 Dec '16

Dear all, As in 2015 and 2016, there is again in 2017 the possibility of getting the GATK (https://software.broadinstitute.org/gatk/) team from the Broad Institute in Boston over to Edinburgh for a workshop. To determine whether it's worthwhile to do this, I'd like to gauge the potential interest for this. If you're potentially interested, please carefully read the attached workshop description and then fill in the short survey you can find at: https://www.surveymonkey.co.uk/r/ZJ6CGKY As for the workshop fees, I would expect these to be approximately £75 / day. Please note that this just to gauge interest. If the workshop will go ahead, this will be advertised through the usual channels (Edinburgh Genomics website, mailing lists, Twitter etc.) and there will be a proper registration procedure put in place. With kind regards, Bert -- Bert Overduin, PhD TRAINING AND OUTREACH BIOINFORMATICIAN Bert.Overduin(a)ed.ac.uk orcid.org/0000-0002-5281-8838 EDINBURGH GENOMICS The University of Edinburgh Ashworth Laboratories The King's Buildings Charlotte Auerbach Road Edinburgh EH9 3FL Scotland, United Kingdom tel. +44(0)1316507403 http://genomics.ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Software Developer position available at the EISBM
by Johann Pellet 07 Dec '16

07 Dec '16

Software Developer in Computational Biology, Lyon, France. Employer: CNRS Location: CNRS-EISBM, Lyon, France Expires: 30 December 2016 Qualifications: BSc or MSc Salary: Depending on qualifications and experience, based on CNRS salary grid Duration: 6 months (funding opportunities to extend this position are being explored) Starting date: available immediately, not later than 15th March 2017 Keywords: programming, software development, open-source, web-based, computational systems biology, systems medicine We are looking for an enthusiastic JavaScript / HTML / CSS programmer to work on developing a plugin for an open-source web-based graph editor specialized for biological networks, whose functionality is based on Cytoscape.js. Specifically, the plugin will enable visualization of the biological networks found in different System Biology standards formats. The successful applicant will join a multidisciplinary collaborative environment: computational biologists, experienced software architects and software developers. Required qualification and skills: BSc or MSc in Computer Science, in Bioinformatics or related disciplines. Strong JavaScript, HTML and CSS skills and good communication skills in English with both technical and non-technical colleagues are required. The position involves collaboration with eTRIKS partners on Translational Medicine projects across Europe. The selected candidate will be based in Lyon-Gerland within the CNRS-EISBM team led by Dr. Charles Auffray, hosted by Claude Bernard University on the Charles Mérieux campus. Available as a part of the European Translational Research Information and Knowledge Management Services project (eTRIKS), funded by the Innovative Medicines Initiative (IMI) of the European Commission 7th Framework Programme and the European Federation of Pharmaceutical Industries and Associations (EFPIA). Enthusiastic and motivated candidates are encouraged to contact Alexander Mazein jobs(a)eisbm.org <mailto:jobs@eisbm.org> with a CV and a brief description of their programming skills. Many thanks! Best regards Johann

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Bioinformatics senior lecturer or associate professor position in Groningen
by Noback MA, Michiel 05 Dec '16

05 Dec '16

Dear all, A position is available at the Hanze University of Applied Sciences (Hanzehogeschool) in Groningen. Emphasis lies on research / research acquisition, but lecturing will also be part of your tasks. Possibility to advancement to professor (lector). See: https://www.academictransfer.com/employer/Hanzehogeschool-Groningen-/vacanc… You can contact me for additional information as well. Dr. M A. Noback | Bioinformatics senior lecturer & researcher | Institute for Life Science and Technology | Hanze University of Applied Sciences | Phone +31 50 5954691 | Postbus 3037 | 9701 DA Groningen | The Netherlands

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2 vacancies for bioinformatics at Intelligent Pharma
by Valerie Vanhooren 05 Dec '16

05 Dec '16

Dear Madam/Sir, We are currently looking to fill 2 bioinformatic job positions at Intelligent Pharma (www.intelligentpharma.com) First, we are looking for a PhD student, see information in attach Second, we are looking for a PhD in Bioinformatics or an experienced researcher in the field of protein modelling, in order to apply for a grant here in Barcelona. Info on the grant here: http://www.catalonia.com/en/innovate-in-catalonia/tecniospringplus/tecniosp… and in case of any questions you can always contact me. Many thanks! kind regards Valerie -- Valerie Vanhooren, PhD Business Development Manager Baldiri Reixac, 4 08028 Barcelona - Spain T: +34 934 034 551 www.intelligentpharma.com <http://www.intelligentpharma.com> La información contenida en este mensaje y/o archivo(s) adjunto(s) es confidencial y está destinada a ser leída solo por la(s) persona(s) a la(s) que va dirigida. Si usted lee este mensaje y no es el destinatario señalado, el empleado o el agente responsable de entregar el mensaje al destinatario, o ha recibido esta comunicación por error, le informamos que está totalmente prohibida, y puede ser ilegal, cualquier divulgación,distribución o reproducción de esta comunicación. El remitente no asume ningún tipo de responsabilidad si este correo electrónico pudiera contener algún virus informático que hubiese escapado a nuestro exhaustivo control. No imprimas si no es necesario. Protejamos el Medio Ambiente. The information contained in this e-mail is confidential and is intended for the recipient/s only. If you have received this e-mail by error, please notify us immediately by replying and then deleting it and the annexed material that it may contain from your system, not being allowed its modification, copy, distribution, storage and/or total or partial disclosure by any means. The sender does not assume any responsibility in case this e-mail could include any computer virus that may have escaped our exhaustive control. Print only if necessary. Protect the Environment.

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