- BBClist - maillist.psb.ugent.be

Bioinformatician / Data Scientist position available at NIZO
by Wels, Michiel 30 Jul '18

30 Jul '18

Currently we are looking for a Bioinformatician / Data Scientist to strengthen our Microbiomics team at NIZO. Best Regards, Michiel Wels [cid:image001.png@01D427EA.96C2B400]<http://www.nizo.com/news/courses/> M.W.W. (Michiel) Wels PhD Expertise Group Leader Microbiomics T: +31 318 659 674 M: +31 6 445 727 51 F: +31 318 650 400 E: Michiel.Wels(a)nizo.com<mailto:Michiel.Wels@nizo.com> P.O. Box 20, 6710 BA EDE, The Netherlands Kernhemseweg 2, 6718 ZB EDE, The Netherlands Visit our website at www.nizo.com<http://www.nizo.com/>. Follow us: [cid:image003.jpg@01D427EA.4231AF90] <https://www.linkedin.com/company/nizo-food-research/> [cid:image004.jpg@01D427EA.4231AF90] <https://twitter.com/NIZOfoodnews/> This message may contain information that is not intended for you. If you are not the addressee, intended addressee or if this message was sent to you by mistake, you are hereby notified that any disclosure, copying, distribution or taking action in reliance on the content of this email message is prohibited. You are kindly asked to inform the sender and delete the message. NIZO food research B.V. accepts no liability for damage of any kind resulting from the risks inherent in the electronic transmission of messages.

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job offer down under
by Stephane Rombauts 24 Jul '18

24 Jul '18

Anna Koltunow (CSIRO) is looking for a bioinformatician on her Gates project. She needs someone with capacity to do support work but also open to new fundamental stuff. The position is on the Waite campus, Adelaide based, and full time. Some information about Anna’s research can be found here: [ https://people.csiro.au/K/A/Anna-Koltunow | https://people.csiro.au/K/A/Anna-Koltunow ] , [ https://www.science.org.au/fellowship/fellows/dr-anna-mg-koltunow | https://www.science.org.au/fellowship/fellows/dr-anna-mg-koltunow ] . Stephane Rombauts - Senior staff scientist Bioinformatics VIB-UGent Center for Plant Systems Biology Ghent University Technologiepark 927 - 9052 Ghent - Belgium Tel. +32(0)9 331 38 21 [ http://www.psb.ugent.be/ | www.psb.ugent.be ]

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Postdoc position in (plant) genome biology
by Yves Van de Peer 24 Jul '18

24 Jul '18

Bioinformatics Postdoc Position in Evolutionary and Comparative Genomics A three-year postdoctoral position is available in the Van de Peer lab (http://bioinformatics.psb.ugent.be/beg/) at VIB/Ghent University, Belgium, starting October 1st, 2018. The Van de Peer lab is considered a center of excellence in gene prediction and genome annotation, and comparative and evolutionary genomics. As we are involved in several international plant genome and evolution projects, we are currently looking for a bioinformatician to strengthen our genome annotation and analysis team. You will also be involved in the study of gene and genome duplications, another major interest of the research group. *Required Qualifications* The ideal candidate holds a PhD degree in bioinformatics or computational biology (or equivalent through experience), is highly interested, ambitious, curiosity-driven and likes interdisciplinary work. He/she will need to interact productively with evolutionary biologists, genome biologists and computer scientists. Programming/scripting experience (e.g., Perl, Python, R, …) and experience working in a Linux environment are essential. A background in genomic, transcriptomic and/or epigenetic research and experience in evolutionary and/or comparative genomics is expected. Since English is the working language of the laboratory, excellent English communication skills are imperative. The candidate should have a proven track record with at least two publications as first author in renowned peer reviewed journals. *Working environment* The successful candidate will work in the Department of Plant Biotechnology and Bioinformatics/VIB Center of Plant Systems Biology, Ghent University, Belgium. VIB and Ghent University offer a supportive and stimulating environment, with access to excellent computer and academic facilities. More information on our research and research topics can be found at http://bioinformatics.psb.ugent.be/beg/. *Contact details* To apply, please send a single document including a letter of motivation describing your research motivation and experience, a detailed CV with a list of publications, summary of past research, and contact details for at least two referees to yves.vandepeer(a)psb.ugent.be. Review of applications will continue until a suitable candidate is found. Yves Van de Peer VIB Center for Plant Systems Biology Department of Plant Biotechnology and Bioinformatics Ghent University Belgium

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FW: call for group leader position in computational biology at institut Curie - update
by Alexander Botzki 23 Jul '18

23 Jul '18

To: Emmanuel Barillot <Emmanuel.Barillot(a)curie.fr> Subject: call for group leader position in computational biology at institut Curie - update Dear colleagues, We are recruiting group leader in computational biology at institut Curie (see attachment). I also add an URL in case you want to tweet it or share it this way: http://sysbio.curie.fr/texts/Call4GroupLeaderCurieU900-2018.pdf Could you please spread the word as widely as possible? Many thanks for your help Best wishes Emmanuel - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Dr Emmanuel Barillot Director of U900 Institut Curie - INSERM - PSL Research University / Mines ParisTech: "Bioinformatics and Computational Systems Biology of Cancer" Institut Curie 26 rue d'Ulm 75248 PARIS cedex 05 FRANCE Mail: Emmanuel.Barillot(a)curie.fr

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Open positions computational biology and data analyst at VIB
by Alexander Botzki 19 Jul '18

19 Jul '18

Dear all, VIB has several data science and computational biology-related openings Data Analyst https://vibvzw.jobsoid.com/j/13817/business-intelligence-analyst-bianalyst-… Single Cell Technology Specialist https://vibvzw.jobsoid.com/jobs/35bba14f-79b7-4388-b015-a4fb9d97ee41/14088/… Single Cell Bioinformatics Specialist https://vibvzw.jobsoid.com/jobs/35bba14f-79b7-4388-b015-a4fb9d97ee41/11971/… For more information and other jobs please visit http://www.vib.be/jobs Best regards, Alex Alexander Botzki - Head of VIB Bioinformatics Core | Training Coordinator ELIXIR-BE VIB Bioinformatics Core Rijvisschestraat 126, 9052 GENT, Belgium | +32 9 248 16 00 www.bits.vib.be<http://www.bits.vib.be/> | @vibbioinfocore | https://corefacilities.vib.be<https://corefacilities.vib.be/> [signatureFooter (002)]

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Registration Open for ELIXIR-NL Course Bioinformatics for Translational Medicine using Galaxy: see it, do it, teach it! - 17- 19 October 2018, Amsterdam
by Celia van Gelder 13 Jul '18

13 Jul '18

*ELIXIR-NL Course: * Bioinformatics for Translational Medicine using Galaxy: see it, do it, teach it! Please circulate this email to those who might be interested. Date: 17-19 October, 2018 Location: VU Amsterdam (O|2 Lab Building <https://goo.gl/maps/CphwJEFDegt>, Gustav Mahlerlaan 665, 1082 MK, 1082 MK Amsterdam) Organizers: This course is an ELIXIR-EXCELERATE course and is organised by ELIXIR-NL by Chao (Cico) Zhang (VU), Sanne Abeln (VU), Anton Feenstra (VU), Saskia Hiltemann (ErasmusMC), Mateusz Kuzak (DTL) and Celia van Gelder (DTL). Course page (incl. Application Form): https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translat… TARGET AUDIENCE 1) Biomedical & translational medicine researchers/students who are keen on bioinformatics and 2) educators in the “bio” domain who would like to start using Galaxy in their courses as an introduction to Bioinformatics. COURSE DESCRIPTION Analysing molecular data in translational medicine involves a multitude of computational steps. Here, we introduce the basics of how to design and run these steps within Galaxy, a free and easy-to-use web platform that enables users to connect bioinformatics tools into a workflow without any prior programming expertise. This course consists of two parts. Part 1 will let you get familiar with Galaxy; it will introduce some bioinformatics workflows used for RNAseq, variant detection and metagenomics; and how to easily connect different computational steps in Galaxy. Part 2 will focus on how to teach bioinformatics with Galaxy and to design bioinformatics courses using Galaxy. Participants can register for both parts separately. This course is also interspersed with a few keynotes, from recognised researchers in the fields of Biomedicine, Bioinformatics education and Galaxy workflows. The confirmed speakers include Jaap Heringa, who is the scientific director of the Netherlands Bioinformatics Centre; and Björn Grüning, who is the leader of Galaxy training network, also actively involved in Bioconda. PREREQUISITE KNOWLEDGE The attendees of Part I are assumed to have the basic knowledge of biomedicine (molecular biology and genomics) and be interested in analysing patient derived sequencing data. The attendees of Part II are assumed to have some teaching experience in the relevant field (e.g., bioinformatics, computational biology, systems biology, quantitative biology, etc.) COURSE SCHEDULE The course consists of six modules, as the table below shows, covering a list of topics as follows: - Introduction to Galaxy. Run bioinformatics tools and workflows in Galaxy without the need for any programming expertise. - Reference-based RNA-Seq data analysis - Module detection in differential gene expression in meta transcriptomics samples. - Microbiota Analysis: 16S rRNA sequencing analysis in Galaxy - How to teach bioinformatics workflows. - Galaxy setup for teaching and training material development. Day 1 - Wed Oct 17 Day 2 - Thur Oct 18 Day 3 - Frid Oct 19 Morning Galaxy 101 + Variant detection <http://galaxyproject.github.io/training-material/topics/introduction/> Network analysis with microbiota metatranscriptome <https://www.ncbi.nlm.nih.gov/pubmed/26342232> Teaching bioinformatics workflows Saskia Hiltemann <https://shiltemann.github.io/> Chao Zhang <https://hi-it.org/> Anton Feenstra <http://www.few.vu.nl/~feenstra/> Keynote Speech* I: About bioinformatics workflows II: About Galaxy and ELIXIR III: About bioinformatics teaching TBD Björn Grüning <https://galaxyproject.org/people/bjoern-gruening/> Jaap Heringa <https://www.cs.vu.nl/~heringa/> Afternoon BWA + RNAseq <http://galaxyproject.github.io/training-material/topics/transcriptomics/> 16S rRNA sequencing with mothur <http://galaxyproject.github.io/training-material/topics/metagenomics/> Galaxy training material development <http://galaxyproject.github.io/training-material/> Saskia Hiltemann <https://shiltemann.github.io/> Saskia Hiltemann <https://shiltemann.github.io/> Saskia Hiltemann <https://shiltemann.github.io/> Evening Social dinner About the instructors: Each session is led by one instructor listed in the table above but strongly supported by multiple co-instructors, including, but not limited to, Saskia Hiltemann (ErasmusMC), Chao Zhang (VU), Leon Mei (LUMC), Ruben Vorderman (LUMC) and Sanne Abeln (VU). Note: The course is held in a computer classroom, so you don’t need to bring your own laptop. COURSE FEE Course participation is free of charge. A workshop dinner will be organized on Thursday (at participants’ own expenses) Should you have any question about this course, please contact Celia van Gelder (celia.van.gelder(a)dtls.nl) 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 websites: www.dtls.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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Available (permanent) positions in Sweden
by Lieven Sterck 12 Jul '18

12 Jul '18

> From: "Henrik Lantz" <henrik.lantz(a)nbis.se> > To: "Lieven Sterck" <lieven.sterck(a)psb.vib-ugent.be> > Sent: Wednesday, 11 July, 2018 11:48:20 > Subject: Available positions in Sweden > Hi Lieven, > We have two new permanent positions available in Lund in the Southernmost part > of Sweden. The positions focus on support to Swedish researchers under a > fee-for-service model and will most likely involve working with RNA-seq data. > As the positions are permanent I was thinking that there might be an interest > also in other countries, and I would appreciate if you could spread the below > link to interested people in Belgium. > https://lu.mynetworkglobal.com/en/what:job/jobID:216986/ > Cheers, > Henrik

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Bioinformatician position: computational cancer biology
by Lodewyk Wessels 12 Jul '18

12 Jul '18

BIOINFORMATICIAN POSITION EARLY DETECTION OF OVARIAN CANCER and INTEGRATION OF TISSUE SPATIAL MAPS AND GENE EXPRESSION The research groups of Lodewyk Wessels, Frederic Amant and Christianne Lok are looking for a motivated and talented Computational Biologist to join their teams at the Netherlands Cancer Institute (NKI). PROJECT DESCRIPTIONS. Early detection of Ovarian cancer. Differentiation between benign growth and ovarian tumors before surgery is currently far from optimal. This leads to a significant fraction of ovarian tumors going undetected and also a large fraction of benign growths being unnecessarily treated in specialized settings. In this project we will be employing innovative non-invasive sampling of peripheral blood to develop a more accurate test for the detection of ovarian tumors. We will employ two strategies. First we will isolate and perform RNAseq profiling on tumor educated platelets (TEP). Second, we will perform DNA sequencing and to detect abnormal DNA copy number profiles from the circulating tumor DNA (ctDNA). For both datasets, the successful candidate will build classifiers to accurately distinguish ovarian cancer from benign growths. Integration of gene expression and tissue imaging to study post-partum breast cancer. Breast cancers that occur 1 to 2 years after childbirth (postpartum breast cancer) have a particularly poor outcome. It has been hypothesized that (immunological) changes in the breast, occurring after childbirth, are underlying the poor prognosis of postpartum breast cancer. In this project we will investigate postpartum breast cancer by combining two unique data sets across 400 patients. Tumors will be subjected to RNA-sequencing as well as spatial tissue profiling for a panel of immune markers employing the VECTRA technology. The spatial profiling provides the location of cells in a cross section of the tumor as well as the expression of the recorded markers in each cell. This allows a detailed characterization of the tumor and the surrounding stroma, indicating which cells occur in the stroma, their position with respect to each other and with respect to the tumor cells. The successful candidate will perform computational analysis of these datasets separately and in an integrated fashion to study the mechanisms that underlie postpartum breast cancer. CANDIDATE PROFILE. We are seeking a highly motivated bioinformatician with: • A degree in bioinformatics, computer science or a related discipline • Experience with high-throughput data analysis, especially sequencing data • Proficiency in bioinformatics programming languages (e.g. R, Python) • Good cross-disciplinary collaborative and communication skills • Experience in statistics, machine learning and/or image processing is a plus • Experience in cancer biology and clinical applications is a plus INTERESTED? Please send CV and motivation letter to Lodewyk Wessels (l.wessels(a)nki.nl) and Patty Lagerweij (p.lagerweij(a)nki.nl) Please include the names and contact information of at least two references. For further information on the Wessels group (Computational Cancer Biology) please visit our home page https://ccb.nki.nl/

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Discrete models and formal verification in biology - 29-31 August 2018 - open for registration!
by Anton Feenstra 11 Jul '18

11 Jul '18

Dear colleagues, You may be interested in a workshop on "Discrete models and formal verification in biology" that will be hosted by Ben Hall, from 29-31 August 2018, Murray Edwards College Cambridge For more information and registration, please refer to https://discretebiology.com/ Best, Anton. -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1081 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +31 20 59 87783 - skype: kafeenstra - room S404 | | | Feenstra(a)few.vu.nl - www.few.vu.nl/~feenstra/ | | | "Studying expands knowledge. Knowledge is power. | | | Power corrupts. Corruption is a crime. Crime doesn't | | | pay." (Anonymous) | |_____________|_______________________________________________________|

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October training workshops at Edinburgh Genomics: Linux for Genomics, Intro to RNAseq Analysis and Intro to Python
by DUNBAR Donald 10 Jul '18

10 Jul '18

Hello all, we have some new dates in October for our popular Edinburgh Genomics training workshops<https://genomics.ed.ac.uk/services/training>. We now offer registration, on a first come first served basis, to our Linux for Genomics, Introduction to RNAseq Data Analysis, and Introduction to Python for Biologists workshops developed and taught by our Edinburgh Genomics Bioinformaticians and our training partner Dr Martin Jones. 1. Linux for Genomics, Monday 1st October 2018 REGISTER NOW<https://www.surveymonkey.co.uk/r/L4G_011018> 2. Introduction to RNAseq Data Analysis, Tuesday 2nd to Wednesday 3rd October 2018 REGISTER NOW<https://www.surveymonkey.co.uk/r/I2R_021018><https://www.surveymonkey.co.uk/r/6QQVF7D> 3. Introduction to RNAseq Data Analysis, Thursday 4th to Friday 5th October 2018 REGISTER NOW<https://www.surveymonkey.co.uk/r/I2R_041018> 4. Introduction to Python for Biologists, Monday 22nd to Friday 26th October 2018 REGISTER NOW<https://www.surveymonkey.co.uk/r/ZBVFTQ3> Please use the links provided above to register for a place. These workshops are very popular and have limited places, so please do register as early as you can. After registration, you will be asked for payment and then your place will be confirmed. Cancellation up to one month before the workshop will allow a refund minus an admin fee. See course details on our training pages: * https://genomics.ed.ac.uk/services/training * https://genomics.ed.ac.uk/services/introduction-rna-seq-data-analysis * https://genomics.ed.ac.uk/services/linux-genomics * https://genomics.ed.ac.uk/services/introduction-python-biologists-0 Please let me know if you have any questions or comments. Feel free to share with colleagues and contacts. We plan to offer an 'R for Genomics' and an 'Advanced Linux: Cloud, Cluster and Pipeline Programming' early in 2019, and we will let you know when these are available. With best wishes and we look forward to welcoming you to Edinburgh Genomics. Donald --- Dr Donald Dunbar Bioinformatics Operations Manager Edinburgh Genomics, Genome Science Ashworth Labs, The King's Buildings The University of Edinburgh donald.dunbar(a)ed.ac.uk Edinburgh Genomics' Privacy Notice can be viewed at: http://genomics.ed.ac.uk/about-us/privacy-notice This email and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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