- BBClist - maillist.psb.ugent.be

Vacancy Coordinator Bioinformatics
by Sie, D.L.S. (Daud) 29 Jun '20

29 Jun '20

Dear all, The clinical genetics department of the Amsterdam UMC has an open position, senior level, to coordinate bioinformatics activities within the department. Your job is to supervise a young and growing bioinformatics team, to develop new pipelines, maintain existing pipelines and tend to the bioinformatics procedures in our clinical lab. If you think you are the right person for this job, apply via the following link: https://www.werkenbijvumc.nl/vacatures/coordinator-bioinformatica-genoomana… Let me know if you have any questions. Kind regards, Daoud [cid:image002.png@01D40E30.3E299A80] Dr. Daoud Sie | Head Bioinformatics | Consultant Core Facility Genomics Department of Clinical Genetics Location VUmc | MF-J391 | Van der Boechosrtstraat 7, 1081 BT Amsterdam Location AMC | K2-211 | Meibergdreef 9, 1105 AZ Amsterdam T: (+31)20-4442428 | E: d.sie(a)amsterdamumc.nl www.amsterdamumc.nl<http://www.amsterdamumc.nl/> | www.vumc.nl<http://www.vumc.nl/> / www.amc.nl<http://www.amc.nl/> ______________________________________________________ VUmc disclaimer: www.vumc.nl/disclaimer<http://www.vumc.nl/disclaimer> ______________________________________________________ VUmc disclaimer : www.vumc.nl/disclaimer AMC disclaimer : www.amc.nl/disclaimer

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Vacancy: Bioinformatics Community Project Manager at EMBL Heidelberg
by Sander Wuyts 29 Jun '20

29 Jun '20

Dear, � The European Molecular Biology Laboratory (EMBL) is looking for a Bioinformatics Community Project Manager. � The successful candidate will work as part of the Bio-IT core team and with stakeholders across all EMBL research units to coordinate new and existing project activities; encourage and empower community members to engage with and contribute to these activities; and develop project strategy. � Bio-IT project activity includes: * delivering training in computational research skills; * creating connections between community members; * developing and maintaining resources and supporting infrastructure; * and disseminating relevant information throughout the community. More info here: https://www.embl.de/jobs/searchjobs/index.php?ref=HD01778 Or in this Twitter thread: https://twitter.com/tbyhdgs/status/1276516550619598850 Kind regards, Sander Wuyts, PhD

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Funded PhD position on "Artificial intelligence and machine learning for e-health Applications"
by Francesco FONTANELLA 26 Jun '20

26 Jun '20

The Artificial intelligence and machine learning group at the University of Cassino and Southern Lazio (ITALY), is looking for an excellent candidate for a funded PhD position on the following topic: *Artificial Intelligence and Pattern recognition for e-Health applications* If you are interested please send an email to fontanella(a)unicas.it with your CV and your interests. Francesco Fontanella -- Francesco Fontanella, PhD Assistant Professor The University of Cassino and Southern Lazio, Italy web: http://webuser.unicas.it/fontanella Voice: (+39) 0776 299 3382 Fax: (+39) 0776 299 4358

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Computational biologist position available at Princess Maxima Center for Pediatric Oncology
by Patrick Kemmeren 26 Jun '20

26 Jun '20

Dear all, We have an opening in our institute for a computational biologist working in the context of childhood kidney cancers using various advanced technologies such as organoids, single-cell sequncing and genomics. Interested in a great opportunity to work in an environment that matters, please look at: https://werkenbijprinsesmaximacentrum.nl/vacature/computational-biologist-g… Regards, Patrick -- Patrick Kemmeren, PhD Principal Investigator & head Big Data Core T +31 (0)88 972 90 00 | M +31 (0)6 53 11 25 53 * * *Princess Máxima Center for Pediatric Oncology* **Heidelberglaan 25 | 3584 CS Utrecht | T +31 (0)88 972 90 00 |***> Website* <https://research.prinsesmaximacentrum.nl/en/research-groups/kemmeren-group>

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IT/Bioinformatics job opening at Hartwig Medical Foundation
by Daphne van Beek 19 Jun '20

19 Jun '20

Dear all, We have an IT/bioinformatics job opening at Hartwig Medical Foundation. Do you want to make a contribution to the advancement of research and treatment of cancer? Join our team! For details, please see below or the web-version (in Dutch): https://www.hartwigmedicalfoundation.nl/8232-2/ Vacature IT-er/Bioinformaticus binnen een high tech lab Hartwig Medical Foundation helpt vanuit het Science Park in Amsterdam de zorg voor patiënten met kanker te verbeteren. We hebben hiervoor een high-tech lab met state-of-the-art whole genome sequencing<https://www.oncoact.nl/hoe-werkt-oncoact/#wholegenomesequencing> apparatuur.[cid:0773F30B-7ADA-42B2-9DE4-19370B70306A]<https://www.hartwigmedicalfoundation.nl/wp-content/uploads/2020/06/novaseq-…> * Voor de analyse van de data heeft ons internationale team van IT-specialisten, bioinformatici en lab-analisten zeer geavanceerde bioinformatische software ontwikkeld, die ze iedere dag verbeteren. * Voor de patiënt met kanker van vandaag hebben we een patiëntrapport<https://www.hartwigmedicalfoundation.nl/inhoud-rapport/> ontwikkeld dat alle mogelijke behandelopties “op maat” (personalised healthcare) in beeld brengt. * Voor de patiënt van morgen hebben we in samenwerking met onderzoekers een database opgebouwd met de DNA-data en de behandelgegevens van meer dan 4.500 patiënten. Die data worden nu al voor meer dan 130 onderzoeken wereldwijd, gericht op de verbetering van behandeling, gebruikt. * Wij werken samen met academische instellingen, ziekenhuizen en experts uit binnen- en buitenland. We zoeken een gedreven allround IT-er/bioinformaticus die lid wil worden van ons high tech sequencing lab team. Als IT-er/bioinformaticus kun je natuurlijk vrij snel terecht bij verschillende bedrijven met jouw specifieke skillset. Echter, wij kunnen ervoor zorgen dat je met jouw skills ook daadwerkelijk een impact hebt op het verbeteren van de behandeling van kankerpatiënten. * Kandidaten zijn gedreven, hebben ervaring met het werken met klanten, zijn teamspelers en vinden het leuk en zijn in staat om snel en goed nieuwe dingen te leren. * Ze zijn enthousiast om mee te werken aan kankeronderzoek en diagnostiek. * Ze kunnen gestructureerd werken, nemen initiatief en maken zelfstandig rapportages. * Ze zijn in staat om zelfstandig te scripten om informatie te verzamelen en structureren, nieuwe databases op te tuigen en hieromheen een gebruikersvriendelijk systeem te bouwen. Hiervoor is het nodig om analytisch te kunnen denken en om bij gebruikers specifieke eisen voor het systeem te inventariseren. We hebben geen voorkeur voor een specifieke programmeertaal om dit voorgaande te realiseren. * Ze vinden het geen probleem om binnen onze specifieke werkomgeving (we werken natuurlijk met patient data) te werken binnen ISO 17025 en ISO 27001 normen. Dit betekent voornamelijk dat je secuur en volgens bepaalde protocollen werkt. Inhoudelijke kennis van de norm is voor deze functie niet noodzakelijk. Je activiteiten bestaan onder andere uit: * Controleren, verwerken en opsturen van sequencing data ten behoeve van research en Hartwig Medical OncoAct<https://www.oncoact.nl/>. * Bijdragen aan de ontwikkeling, verbetering en ondersteuning van ons Lab Informatie Management Systeem (LIMS). * Ontwikkelen en ondersteunen van lab-innovatie voor sample en data logistiek. * Ontwikkelen en beheren van research website en sample registratie portal. * Beheren van intern computernetwerk en IT-apparatuur gebruikt in lab en office. Je voldoet aan zoveel mogelijk van onze wensen: * HBO/WO-(bio)informatica. * Kennis van programmeren en een programmeertaal (we werken zelf met meerdere talen). * Bekwaam in Nederlands en Engels in woord en geschrift. * Kunnen werken met databases (bijvoorbeeld Microsoft Access of andersoortig) is een pré. * Ervaring met Next Generation Sequencing is een pré. Ons aanbod * Een baan voor 32-40 uur per week met diverse werkzaamheden. * Een aanstelling voor in eerste instantie een jaar, met kans op verlenging. * Je salaris bepalen we op basis van je (werk)ervaring en achtergrond. * Je kunt direct beginnen. * Je bent onderdeel van het proces voor het verbeteren van behandeling voor kankerpatiënten. Je faciliteert hoogstaand onderzoek en een Whole Genome DNA test die wereldwijd voorloper is. Zie ook onze repository op https://github.com/hartwigmedical<https://github.com/hartwigmedical>. * Je bent onderdeel van zowel het lab-team als het bioinformatica/IT team, en daarbij ook uitdagingen van beide werelden moeten aangaan en oplossen. * Je kunt je in verschillende richtingen ontwikkelen; we hebben veel ervaring in huis op diverse gebieden: IT, bioinformatica, lab automatisering en onderzoek. * Je hebt contact met interne en externe klanten, zowel nationaal en internationaal. * Je werkt op ons moderne kantoor op Amsterdam Science Park, naast/onder/boven andere innovatieve bedrijven. Tijdens de COVID-19 periode kun je natuurlijk thuis werken. * Leuke collega’s<https://www.hartwigmedicalfoundation.nl/organisatie/>, kantoor-lunches, regelmatig borrelen en gezelligheid. [cid:50D0F8F4-C73C-4346-B098-34EC0A94D538]<https://www.hartwigmedicalfoundation.nl/wp-content/uploads/2020/06/je5a2687…> Reageer Stuur je curriculum vitae naar info(a)hartwigmedicalfoundation.nl<mailto:info@hartwigmedicalfoundation.nl>. De sollicitatieprocedure zal bestaan uit twee tot drie (video)gesprekken en ongeveer twee weken in beslag nemen. Voor vragen over de functie of over onze organisatie kun je contact opnemen met onze Lab Manager Ewart de Bruijn: e.debruijn(a)hartwigmedicalfoundation.nl<mailto:e.debruijn@hartwigmedicalfoundation.nl> of via telefoonnummer 020 – 235 2640. Locatie: Amsterdam Science Park 408, 1098 XH Amsterdam Kind regards / Met vriendelijke groet, Daphne van Beek Projectmanager/Senior Bioinformaticus <https://www.hartwigmedicalfoundation.nl/> [cid:image001.png@01D522AA.72291F60] A Science Park 408, 1098 XH Amsterdam T +31 (0)20 235 2640 W hartwigmedicalfoundation.nl<https://www.hartwigmedicalfoundation.nl> <https://www.facebook.com/HartwigMedicalFoundation> [cid:image002.png@01D522AA.72291F60] <https://www.linkedin.com/company/hartwig-medical-foundation> [cid:image003.png@01D522AA.72291F60] <https://twitter.com/hartwigmedical> [cid:image004.png@01D522AA.72291F60] <https://www.instagram.com/hartwigmedicalfoundation/?hl=nl> [cid:image005.png@01D522AA.72291F60] <https://www.youtube.com/channel/UCK8juCiUGC1OsEXPtdEEwPA> [cid:image006.png@01D522AA.72291F60] Onze missie is dat elke patiënt met uitgezaaide kanker een gepersonaliseerde behandeling krijgt met behulp van een uitgebreide DNA-test<https://www.hartwigmedicalfoundation.nl/dna-test/>.

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Job opening: VIB Postdoc in Plant Single Cell Biology
by Yvan Saeys 17 Jun '20

17 Jun '20

A postdoctoral research position in the De Rybel lab (VIB) in the area of single cell transcriptomics in crop plants is available. This position is a close collaboration between the De Rybel and Saeys labs at VIB in collaboration with BASF as industrial partner in the framework of an approved VLAIO project. The successful candidate will adapt existing wet lab single cell transcriptomics methodologies to crop plant species and initiate statistical analysis of this data. As such, this position entails the integration of both wet lab and dry lab into one collaborative project. About the Partners The De Rybel lab at the VIB‐UGent Center for Plant Systems Biology (PSB) has a key interest in understanding cell division orientation in plants and how this process contributes to vascular proliferation. The lab has a long-standing expertise in using bulk RNA-sequencing to uncover transcriptional networks during plant developmental processes. More recently, a strong investment was made to establish single cell RNA-seq (scRNA-seq) workflows to further increase resolution at spatial and temporal level. In this case, the wet-lab expertise was developed by the De Rybel lab, while the bio-infomatics expertise and all data analysis was optimised in the Saeys lab. The Saeys lab at the VIB-UGent Center for Inflammation Research (IRC) studies the design and application of data mining and machine learning techniques for biomedical applications. The lab is renowned for its research on single-cell technologies, including flow and mass cytometry, single-cell RNA sequencing, and is currently pioneering novel single-cell technologies including spatial transcriptomics and single-cell multi-omics (e.g. CITE-seq). The BASF Innovation Center in Gent aims to deliver innovative solutions for BASFs seed business by developing valuable traits for various crops through biotechnology solutions and modern breeding techniques. The activities of the Innovation Center cover all aspects involved with the R&D process, from the initial stages of research to life cycle management, or as we call it, from the lab to the field. The Innovation Center employs a workforce of approximately 400 from 20 different countries at state-of-the-art laboratories space for plant biotechnology research in Zwijnaarde and greenhouse and breeding installations in Astene, Zwijnaarde, and Bottelare. Your project Embedded in the De Rybel lab at VIB and in close collaboration with the Saeys lab at VIB and BASF as industrial partner, you will support the implementation, analysis and ongoing development of single cell transcriptome data-sets in the context of plant biotechnology. As a true go-between these collaborative groups, you will work at the intersection between the experimental scientists and the computational scientists. You will be involved in the wet lab data generation pipeline with the De Rybel lab, BASF and VIB core facilities to further optimize the existing workflows. You will be involved in the dry lab data analysis pipeline with the Saeys lab and BASF to establish and optimise the bio-informatic workflows. Profile * You have a PhD in Plant biotechnology with a strong interest or experience in bioinformatics/computational biology; OR you have a PhD in bioinformatics/computational biology with a clear experience in plant biotechnology. * You have good Linux/command line skills and you are experienced with R and/or python programming * You have hands-on experience with (single cell) RNA sequencing or other NGS workflows. * Attention to detail, accurate reasoning and problem-solving skills are needed. * You must be able to communicate effectively (written and spoken) in English and act as go-between person between the research groups and the company * Ability to work well independently and within a team environment * You have strong time management and communication skills to balance multiple experiments between several collaborators * Having a multidisciplinary background in laboratory work and bioinformatics is requested. Experience with web technologies (such as PHP, HTML, CSS, Javascript, vue.js or Laravel) is a plus but not required. We offer * A full time post-doc position in the De Rybel lab for 3 years within the framework of a successful VLAIO grant application between the De Rybel lab, the Saeys lab and BASF (Starting Date: September 2020) * Working at the interface between Academic (VIB) and Industrial (BASF) teams with a can-do-attitude and a strong on-going collaboration * Entrance into our Plant Single Cell Platform with access to state-of-the-art VIB Core Facilities. * The opportunity to develop as a single-cell transcriptomics expert in the plant field and within a strong network of both scientific and industrial collaborators. How to apply? For more information contact Bert De Rybel. Please complete the online application procedure <https://jobso.id/cqo6> and include a detailed CV incl. list of publications, a motivation letter and the contact information of three referees. -- =============================================================================== Prof. dr. Yvan Saeys VIB Group Leader Data mining and modeling for biomedicine UGent Department of Applied Mathematics, Computer Science and Statistics Krijgslaan 281, S9, B-9000 Gent Inflammation Research Center, a VIB-UGent Department Technologiepark-Zwijnaarde 71 , B-9052 Zwijnaarde , Belgium Tel : +32(0)9 331 37 40 Fax : +32(0)9 221 76 73 Mailto: yvan.saeys(a)ugent.be http://www.dambi.ugent.be ===============================================================================

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Bioinformatician/Research Software Engineer position at de Duve Institute, UCLouvain
by Laurent Gatto 11 Jun '20

11 Jun '20

The Computational Biology (CBIO) unit at the de Duve Institute in Brussels, Belgium, seeks to appoint a full time research software engineer. The successful candidate will join the research group of Professor Laurent Gatto and will have the opportunity to work on projects across a broad range of biomedically relevant topics in collaboration with researchers of the biomedical campus of UCLouvain. The focus of the position is on rigorous research software engineering, analysis pipeline development and high-throughput biology data analysis, with the possibility of engaging in teaching activities. If you recognise yourself in any of the following profiles, please consider applying. - You have created/maintained/used software to address research problems in high throughput biology (such as, for example genomics, transcriptomics, epigenetics, proteomics and/or metabolomics). - You can rapidly assimilate understanding of new biomedical questions, and quickly connect research needs to software requirements. - You are committed to open source software development best practices and know how to adapt these to biomedical research contexts. Duties and activities The research software engineer will be expected to contribute to various activities, including : - Research projects: support and advise collaborators with their data analyses and contributed to scientific reports and publications. - Maintain and develop research software and repositories linked to the ongoing research in the group and collaborative projects. - Participate in the administration of the computing and data storage infrastructure. - Attend scientific conferences to present their research and development and workshops to improve and learn new sets of skills. - Contribute to bioinformatics teaching, both within the institute and the School of Biomedical Sciences. Required skills The ideal candidate would be either a researcher with a focus on research software and data analysis, or a software developer with an interest in research and biomedical sciences. We are looking for a motivated candidate with a PhD or a Master's degree in bioinformatics or equivalent, possessing computational and quantitative skills such as: - Good knowledge of the R programming language and the Bioconductor infrastructure (important). - Experience with the processing and analysis of omics data (important). - Experience in open and reproducible research, open source software and open data (desirable). - Experience in C/C++ (desirable). - Experience in JavaScript, specifically the development of online visualisation applications (optional). - Experience in teaching, ideally the Data and Software Carpentry curricula or interest in training to become an instructor (desirable). - Experience in high performance computing (desirable). - Experience with code versioning and collaborative tools such as, for example, git, and GitHub/GitLab (desirable). - Experience with other languages commonly used in computational biology and bioinformatics like Python or Julia (optional). - Knowledge of French and English is desirable. Contract on external resources, full time, with initial duration of 2 years (1 year renewable once). Position available mid August. We value equality, diversity and an open, collaborative and welcoming work environment. Please send your application by email to Laurent Gatto (laurent.gatto(a)uclouvain.be) referencing this position, including a CV, motivation letter and two references.

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ESCS 2020 | Abstract submission is open
by ESCS 11 Jun '20

11 Jun '20

[image: ESCS2020_banner-notPaint.png] Dear all, The abstract submission process for the *European Student Council Symposium 2020 (ESCS 2020)* is open! The ESCS 2020 will take place on *6th September 2020 in Sitges, Spain* directly preceding the opening of the European Conference on Computational Biology (ECCB 2020). The ESCS provides a forum for students and young researchers in the fields of Bioinformatics and Computational Biology to meet, present their work in front of an international audience, build a network within the computational biology community and obtain opportunities that can contribute to the development of their scientific career. In this scope, we invite all participants to submit *an abstract for an oral or poster presentation*. The submission deadline for abstracts is: *11th June 2020*. You can find all relevant information about ESCS 2020 here: *https://www.escs2020.iscbsc.org/ <https://www.escs2020.iscbsc.org/>*. For any further inquiries don't hesitate to contact us at *escs(a)iscbsc.org <escs(a)iscbsc.org>*. Best regards, Gabriel Olguín Orellana, chair ESCS 2020 Sofia Papadimitriou, co-chair ESCS 2020

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postdoc available in cancer pharmacogenomics modelling
by Pedro BALLESTER 09 Jun '20

09 Jun '20

Dear colleagues, A postdoc position in cancer pharmacogenomics modelling is available in my group. Further information, including how to apply, can be found at https://academicpositions.com/ad/aix-marseille-universite/2020/postdoc-in-p… Best wishes, Pedro -- (c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c) Dr. Pedro J. Ballester Group Leader at the Cancer Research Centre of Marseille Research scientist at INSERM http://crcm.marseille.inserm.fr/en/researchteams/pedro-ballester/ [1] https://publons.com/researcher/975063/pedro-j-ballester/ (c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c)¤(c) Links: ------ [1] http://crcm.marseille.inserm.fr/en/researchTEAMs/pedro-ballester/

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PhD position: Computational Early Cancer Diagnostics
by Lodewyk Wessels 09 Jun '20

09 Jun '20

PhD Position OVI-DETECT: ACCURATE IDENTIFICATION OF OVARIAN CANCER FROM LIQUID BIOPSIES COLLABORATING INSTITUTES The Netherlands Cancer Institute (NKI), Amsterdam. Delft University of Technology (TUDelft), Delft VU University Medical Center (VUMC), Amsterdam The Johns Hopkins University School of Medicine, Baltimore, USA. PROJECT DESCRIPTION In the Netherlands, 7600 women are diagnosed yearly with an ovarian tumor. Only about 5% of these tumors are malignant. It is very important to accurately identify these malignant tumors prior to surgery to ensure proper treatment. Unfortunately, this can be very challenging. In this project, we aim to find specific molecular biomarkers in liquid biopsies that can efficiently discriminate between benign and malignant ovarian tumors with a sensitivity of at least 90% and a specificity of at least 80%. We will determine genetic abnormalities (mutations, copy number aberrations and chromosomal abnormalities) in circulating tumor DNA and RNA profiles of tumor educated platelets (TEPs). We will develop novel computational approaches to analyze these unique datasets separately and jointly, to arrive at accurate predictors to identify malignant tumors from liquid biopsies. INTERDISCIPLINARY COLLABORATION The groups of Lodewyk Wessels and Marcel Reinders and (NKI and TUDelft) will develop advanced machine learning approaches to construct (integrative) predictors from the different data streams. The supervisory team will be strengthened by the pathology expertise of Hugo Horlings (NKI) and collaborations with Victor Velculescu at Johns Hopkins (circulating copy number profiles from circulating DNA) and Tom Wurdinger at the VUMC (TEPs). The project is embedded within broad oncological collaborations within the VUMC, LUMC, Catharina Ziekenhuis in Eindhoven and the NKI. The successful candidate will be employed at the NKI and will spend at least two days per week at the TUDelft. Regular meetings between project partners will be held to generate sufficient cohesion and momentum. CANDIDATE PROFILE We are seeking a highly motivated PhD candidate with: • A degree in bioinformatics, computer science or a related discipline • Experience in statistics, machine learning and/or pattern recognition • Proficiency in bioinformatics programming languages (e.g. R, Python) • Good cross-disciplinary collaborative and communication skills • Experience in analysing high-throughput molecular data is a plus • Experience in cancer biology and clinical applications is a plus INTERESTED? Please send your CV and motivation letter to Lodewyk Wessels (l.wessels(a)nki.nl) Please include the contact information of at least two references. DEADLINE 01 September 2020

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