December 2016 - 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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2 Postdoc opportunities in the de Ridder lab @UMC Utrecht
by Jeroen de Ridder 23 Dec '16

23 Dec '16

Dear all, There are two upcoming postdoc opportunities in my lab. Interested? Please contact me: j.deridder-4(a)umcutrecht.nl<mailto:j.deridder-4@umcutrecht.nl> Position 1 - Biomarker discovery for on-chip detection of methylated DNA sequences This will be a collaboration with Nanomed Diagnostics, a start-up company (starting in 2017) that has spun-off from the University of Twente (UT). The company is developing a chip and read-out device that can be used for the rapid detection of cancer from urine (The urine-chip). The technology is based on the on-chip detection of methylated DNA sequences enriched in the urine of cancer patients. You will be in charge of the discovery of novel methylation-based biomarkers from public data using cloud-based machine learning techniques. Position 2 - Googling the cancer genome: Identification and prioritization of relevant structural variations in whole genome sequencing data of cancer patients You will develop new analytical and computational methods that enable fast and cost-efficient detection of all structural variants in whole genome sequencing data. In addition, machine-learned ranking technologies will be employed to uncover clinically relevant structural variants among the vast numbers of irrelevant variants. The project will be carried out in collaboration with a team of eScience engineers from the Netherlands eScience Center. About the lab In the de Ridder lab we create and apply innovative data science methods to advance our understanding of disease biology. Our research efforts are always inspired by a biological question and typically deal with big data, such as large-scale genomics and epigenomics datasets. As a result, much of the research floats on machine learning and data integration algorithms. We also heavily rely on high-performance computing and statistics. Typical projects of the lab include the integration of genome conformation measurements (4C and Hi-C) with genome-wide screening data, annotation and prioritization of non-coding variations (SVs and SNVs) and interpretable classification models for patient cohort data. -- Jeroen de Ridder, PhD Associate professor / Principal Investigator | University Medical Center Utrecht - Center for Molecular Medicine | Address: Universiteitsweg 100, STR 1.305 | 3584 CG Utrecht, The Netherlands | Tel: +31 (0)88 7550406 | Mob: +31 (0)6 24288813 | Skype: j_de_ridder | Secretary: Monique van Schaik, M.A.H.vanSchaick(a)umcutrecht.nl<mailto:M.A.H.vanSchaick@umcutrecht.nl>, +31 (0)88 7568312 ------------------------------------------------------------------------------ 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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Bioinformatics position at Enza Zaden
by Joachim Bargsten 21 Dec '16

21 Dec '16

Dear all, Enza Zaden is an independent vegetable seed company, breeding, producing and marketing varieties all over the world. We have an open bioinformatics position, you can find more information at http://www.enzazaden.nl/Vacatures/vacatures/bioinformatician Best regards, Joachim Bargsten -- Joachim Bargsten, PhD Senior Bioinformatician Enza Zaden Research and Development B.V. P.O. Box 7 | 1600 AA Enkhuizen | The Netherlands web: http://www.enzazaden.nl | phone: +31 (0)228 350 100 trade register: 37116112 ________________________________ [Enza Zaden] [Enza Zaden Familiebedrijven Award] The information in this electronic mail message is private and confidential, and only intended for the addressee. Should you receive this message by mistake, you are hereby notified that any disclosure, reproduction, distribution or use of this message is strictly prohibited. Please inform the sender by reply transmission and delete the message. No legal consequences can be derived from the contents of the e-mail. Enza Zaden will accept no responsibility for any damage as a result of the use and/or acceptation of the contents of this e-mail. Always scan attachments before opening them.

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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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