December 2017 - 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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COSMIC: 14 positions available
by A.H.C. van Kampen 28 Dec '17

28 Dec '17

COSMIC offers 14 research positions (www.cosmic-h2020.eu<http://www.cosmic-h2020.eu>) Applications are invited for 14 ESRs (Early Stage Researchers) funded by the Marie-Skłodowska-Curie Innovative Training Network COSMIC (COmbatting Disorders of Adaptive Immunity with Systems MedICine) within the European Horizon 2020 Programme. COSMIC is an international consortium of high profile universities, research institutions and companies. We are looking for 13 PhD positions and 1 industrial researcher with profiles in experimental immunology and computational modelling. COSMIC aims to deliver the next generation of leading, entrepreneurial, and creative systems medicine professionals having expertise, skills, and experience to successfully combat complex human disorders. In COSMIC we will focus on the role of the germinal center in B-cell lymphoma and rheumatoid arthritis, diseases that originate from abnormal functioning of immune cells. For more information please visit www.cosmic-h2020.eu. | Prof. dr. Antoine H.C. van Kampen | (1) Bioinformatics Laboratory | Clinical Epidemiology, Biostatistics and Bioinformatics (KEBB) | Academic Medical Center (AMC) | Visiting address: Meibergdreef 9, J1B-208 (J-building, floor 1B) | Postal address: PO Box 22700, 1100 DE Amsterdam, the Netherlands | www.bioinformaticslaboratory.nl<http://www.bioinformaticslaboratory.nl/> | (2) Biosystems Data Analysis | Swammerdam Institute for Life Sciences (SILS) | University of Amsterdam | Visiting address: Science Park 904, C2-206 | 1098 XH Amsterdam, The Netherlands | www.bdagroup.nl<http://www.bdagroup.nl/> |phone: ++31-20-5667096 (AMC) |Mobile: 06-41768067 | a.h.vankampen(a)amc.uva.nl<mailto:a.h.vankampen@amc.uva.nl> | Skype:antoine.van.kampen | ________________________________ AMC Disclaimer : https://www.amc.nl/disclaimer ________________________________

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Save the Date - Belgian-Dutch Transcriptomics Data Analysis Summer School August 2018
by Alexander Botzki 22 Dec '17

22 Dec '17

Dear all, Save the date! Together with our partners @DTL_nl<https://twitter.com/DTL_nl> @ELIXIRNL<https://twitter.com/ELIXIRNL> @LUMC_Leiden<https://twitter.com/LUMC_Leiden> @ELIXIRnodeBE<https://twitter.com/ELIXIRnodeBE> we organise the first Belgian-Dutch #Transcriptomics<https://twitter.com/hashtag/Transcriptomics?src=hash> Data Analysis Summer School 2018 from 26th to 31st of August in the quaint city of Leuven. More information and registration for future alerts at http://bit.ly/2B9d6GM <https://t.co/BpLsYdVvlY> Enjoy the holiday season! 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/> [MAIL SIGNATURE - ABLS2] [signatureFooter (002)]

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BioSB course: Optimisation techniques in Bioinformatics and Systems Biology - 12-16 February - Wageningen
by Femke Francissen 20 Dec '17

20 Dec '17

BioSB course: Optimisation techniques in Bioinformatics and Systems Biology Course coordinators: Jaap Kaandorp (UvA), Jaap Molenaar (WU), Hans Stigter (WU), Cajo ter Braak (WU) Date: 12-16 February 2018 Location: Wageningen Website link <http://biosb.nl/education/course-portfolio-2/optimisation-techniques-in-bio…>Registration link <http://biosb.nl/education/course-portfolio-2/optimisation-techniques-in-bio…> Course description Many problems in bioinformatics and systems biology require at a certain moment application of some optimisation technique. When facing optimisation problems, many researchers suffice with applying a simple algorithm in Excel, coming to the conclusion that it does not work properly or runs into convergence problems. It is not necessary to stick to that stage, since optimisation is a rapidly expanding field of research, that generates more and more efficient, successful, and easy-to-use algorithms. This course is intended to provide you with the main ideas underlying optimisation, and to get you acquainted with the optimisation techniques that are nowadays available and widely used. In addition, a great variety of examples of optimisation problems in life sciences will be presented and discussed. Course programme The course has the following structure: Day 1: Math refresher and univariate optimisation (Jaap Molenaar+ Hans Stigter) Dag 2: Local multivariate optimisation (Jaap Molenaar + Hans Stigter) Dag 3: Global stochastic optimisation (simulated annealing, evolutionary algorithms) (Jaap Kaandorp) Dag 4: Parameter estimation, systems control and optimisation (Hans Stigter + Jaap Molenaar) Dag 5: MCMC techniques (Cajo ter Braak) The first day is devoted to study simple problems that allow the use of algorithms that are intuitively clear. On day 2, we extend to problems that are bit more complicated. On day 3, we introduce techniques that are based on stochastic searching, while day 4 is spent on the frequently met problem of finding values for the parameters in a model, given a dataset. This challenging problem requires a bit more sophisticated optimisation tools. You will learn about uncertainty and identifiability of the parameters. In addition, you will get some experience with using appropriate parameter estimation tools. On the last day, the state-of-the-art will be presented, since then the popular and powerful Markov Chain Monte Carlo (MCMC) technique will be dealt with. This method is based on a Bayesian approach. So, you will learn about prior distribution, posterior distribution, likelihood, and how in MCMC likelihood and prior distribution are combined to arrive at a posterior distribution. Target audience We assume that the participants have some basic knowledge of modelling in the life sciences. However, it is not necessary to be an expert in mathematics, since the course starts with a session to refresh the mathematical background needed for optimisation. BioSB research school This course is part of the Education Programme of BioSB <http://biosb.nl/education/course-portfolio-2/>, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education for in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl <http://www.biosb.nl/>. Femke Francissen Community manager BioSB Research School

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BioSB/ELIXIR-NL course on Managing and Integrating Life Science Information: Approaches using Linked Data and Semantics (5th edition)
by Femke Francissen 19 Dec '17

19 Dec '17

BioSB/ELIXIR-NL course on Managing and Integrating Life Science Information:Approaches using Linked Data and Semantics (5th edition) With endorsements for FAIR* data stewardship ranging from Nature Genetics to the G7, and increasing pressure from funders for much stricter data management, FAIR data stewardship skills will be among the most wanted for the next decade. By following this course, you add these skills to your CV and learn cutting-edge semantic techniques to search and integrate health and life science data for efficient, reproducible data science. * FAIR: Findable, Accessible, Interoperable and Reusable for humans and computers Course coordinators: Marco Roos (LUMC), Katy Wolstencroft (LIACS, Leiden University) Date: 22-26 January 2018 Location: Amsterdam Science Park, The Netherlands Website link <http://biosb.nl/education/course-portfolio/course-managing-and-integrating-…> Registration link <http://biosb.nl/education/course-portfolio/course-managing-and-integrating-…> Target audience This course is for bioinformaticians who would like to learn about leading-edge data and knowledge integration solutions. You will learn (1) powerful and flexible approaches to data and information management for your bioinformatics application (Semantic Web and Linked Data), (2) how to work with data across remote locations, for instance by applying Web Services and workflows, (3) how to publish your own data to make it available and reusable for the rest of the community. We assume a basic understanding of bioinformatics programming for the hands on sessions. It would suit previous user participants of BYOD meetings <http://www.dtls.nl/fair-data/byod/> who would like more hands-on experience of data integration. It would also suit data providers who would like to explore new ways of serving their data or integrating it with other resources. Description The amount of Life Science data available in the public domain is a vast and growing resource for bioinformatics research. There are over 20 million papers in PubMed and over 1600 biological databases. In many cases finding and applying the information from these resources is far from trivial. Following this course will show you techniques for working with these distributed resources, which includes using the web of Linked data and scientific workflows. It will also focus on methods for using or linking your own data into this large distributed Semantic Web of resources, in order to ensure that your data is FAIR <http://www.dtls.nl/fair-data/> (Findable, Accessible, Interoperable and Reusable). This course introduces modern techniques for the management of life science data and knowledge for bioinformatics applications. After following this course students should be able to start creating their first applications based on these technologies or make more informed design decisions for their current application. In this course you will learn about: Linked Data and the Semantic Web technologies that underpin it How you can use Linked Data for data and knowledge integration in the Life Sciences Available Linked Data resources in the public domain and large-scale projects that use these resources How you can integrate your own data with Linked Data resources How you can combine data integration and analysis over distributed resources, using Web Services and workflows Confirmed lecturers: Frank van Harmelen (Vrije Universiteit Amsterdam), Andre Dekker (Maastricht University) Tentative programme: The program will include the following topics: Introduction to Semantic Interoperability and the Semantic Web; The Semantic Web in Use; The Semantic web in use – systems and guidelines; Data stewardship and making Data Understandable and Searchable (the FAIR principles); Using, Integrating and Analysing Data This course is part of the Education Programme of BioSB <http://biosb.nl/education/course-portfolio-2/>, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education for in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl <http://www.biosb.nl/>. Femke Francissen Community manager BioSB Research School

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ECCB 2018 Call for Tutorials, Workshops and SIGs
by Yves Moreau 18 Dec '17

18 Dec '17

> View this email in your browser <http://mailchi.mp/iscb/eccb-2018-call-for-tutorials-workshops-and-sigs?e=3f…> > > ECCB 2018 to be held in Athens, Greece, 8-12 September > The Hellenic Society for Computational Biology and Bioinformatics <https://iscb.us3.list-manage.com/track/click?u=4c0e7fa66594378a44ccd614e&id…> will organize the seventeenth edition of the European Conference on Computational Biology in association with the ELIXIR. > > It is one of the main computational event in 2018 and will welcome scientists working in a variety of disciplines, including bioinformatics, computational biology, biology, medicine, and systems biology. Participating in ECCB 2018 will be the perfect opportunity to keep pace with cutting edge research, and to network with members of ECCB community. > > Now Accepting Proposals for Workshops, Tutorials, and SIGs > The ECCB 2018 program commitee invites proposals for one or two day workshops or special interest group meetings (SIGs). > > Proposals are expected to provide participants with an informal setting to discuss technical issues, exchange research ideas, and to share practical experiences on a range of focused or emerging topics in bioinformatics. > > Each workshop/SIG should provide an interesting perspective on the cutting edge of a selected research field. Workshops may include any form of presentation such as talks or panel discussions. > > Call for Workshops/SIGs > <https://iscb.us3.list-manage.com/track/click?u=4c0e7fa66594378a44ccd614e&id…> > Key Dates > <https://iscb.us3.list-manage.com/track/click?u=4c0e7fa66594378a44ccd614e&id…> > Call for Tutorials > <https://iscb.us3.list-manage.com/track/click?u=4c0e7fa66594378a44ccd614e&id…> > ECCB 2018 > 17th European Conference on Computational Biology > September 8-12, 2018 > Athens, Greece - Stavros Niarchos Foundation Cultural Center > > > > > > > > This email was sent to yves.moreau(a)esat.kuleuven.be <mailto:yves.moreau@esat.kuleuven.be> > why did I get this? <https://iscb.us3.list-manage.com/about?u=4c0e7fa66594378a44ccd614e&id=04453…> unsubscribe from this list <https://iscb.us3.list-manage.com/unsubscribe?u=4c0e7fa66594378a44ccd614e&id…> update subscription preferences <https://iscb.us3.list-manage.com/profile?u=4c0e7fa66594378a44ccd614e&id=044…> > International Society for Computational Biology · 9650 Rockville Pike · Bethesda, MD 20814 · USA > >

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Tenure-track position in bioinformatics at UCLouvain
by Jean Baptiste Demoulin 11 Dec '17

11 Dec '17

Dear colleagues, The University of Louvain (UCL) invites applications for a professor position in bioinformatics, located on its Medical campus in Brussels (Woluwé-Saint-Lambert), Belgium. Thank you for forwarding this message to potential candidates. Best regards, Prof. Jean-Baptiste Demoulin De Duve Institute & Faculty of Pharmacy and Biomedical Sciences University of Louvain - UCL Avenue Hippocrate 75, box B1.74.05 BE-1200 Brussels, Belgium Phone : +32 2 764 6529 Mobile : +32 485 589321 Web : www.deduveinstitute.be/research

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Postdoc position at Institute for Systems Biology - Shmulevich Lab - Computational Cancer Biology
by Theo Knijnenburg 08 Dec '17

08 Dec '17

Please feel free to distribute this ad among potential candidates. ___ *Institute for Systems Biology* *Postdoctoral Fellow* *Computational Cancer Biology* The Shmulevich group is seeking a computationally-oriented Postdoctoral Fellow. The successful applicant will work with an interdisciplinary team of computational biologists, bioinformaticians, basic scientists and clinical researchers to: 1) Integrate and analyze genomic data from The Cancer Genome Atlas (TCGA) and the Genomic Data Analysis Network (GDAN) with a focus on miRNA expression and regulation, and/or 2) Leverage heterogeneous cancer genomics data for drug sensitivity prediction and development of human cancer therapeutics as part of the Cancer Target Discovery And Development (CTD2) consortium. See attached PDF for details. https://www.systemsbiology.org/about/careers/

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Submit your abstract for Applied Bioinformatics in Life Sciences (2nd) 8-9 March 2018
by Alexander Botzki 08 Dec '17

08 Dec '17

Your invitation for #ABLS18 No Images? Click here http://email.vibconferences.be/t/r-e-jrtrirlk-kdnlrgz-u/ Deadline for abstract submission is 11 January 2018 Dear colleague, The second edition of the two day event ‘Applied Bioinformatics in Life Sciences’ organized by the Flanders Institute for Biotechnology (VIB), will take place on 8-9 March, 2018 in Leuven, Belgium. After a sold-out first edition in March 2016, this second edition will feature recent developments in bioinformatics research, and highlight the power of computational biology in the fields of medical, agricultural, and biotechnology research. With this email we would like to invite you to submit your own research for presentation and to join us and our speakers at #ABLS18. Register early [http://vibconferences.be/event/applied-bioinformatics-in-life-sciences-2nd-…] Special rate for PhD students + poster award To support junior researchers, VIB offers PhD students a special rate when registering before 11 January 2018. Showcase your own research to the international research community during the poster sessions at the conference. The best abstracts will be selected for a presentation and the best poster will receive a poster prize! Submit your abstract [http://vibconferences.be/event/applied-bioinformatics-in-life-sciences-2nd-…] Final program available The full line-up is as follows: Stein Aerts - VIB-KU Leuven Center for Brain & Disease Research, BENaama Barkai - Weizmann Institute of Science, ILStephan Beck - UCL, UKYana Bromberg - Rutgers University, USAlbert Heck - Utrecht University, NLMichael MacCoss - University of Washington, USSteven Maere - VIB-UGent Center for Plant Systems biology, BEChristine Orengo - University College London, UKMarkus Ralser - The Francis Crick Institute, UKSeung Yon (Sue) Rhee - Carnegie Institution for Science, USFrederic Rousseau - VIB-KU Leuven Center for Brain & Disease Research, BERon Shamir - Tel Aviv University, ILOliver Stegle - EMBL-EBI, UKHenk Stunnenberg - Radboud Institute for Molecular Life Science, NLInes Thiele - University of Luxembourg, LUJanet Thornton - EMBL-EBI, UKMichele Vendruscolo - University of Cambridge, UKVicki Wysocki - Ohio State University, US Grab this opportunity to meet experts in the field and to network with hundreds of scientists coming from all around the globe. Visit the website [http://vibconferences.be/event/applied-bioinformatics-in-life-sciences-2nd-…] for more info Explore the historical university city of Leuven Leuven households the KU Leuven. One of the oldest universities of Western Europe. The city is also home to the Anheuser-Busch InBev company, one of the world's largest brewing groups producing the Leuven-based Stella-Artois beer as one of their flagship brands. We hope to have triggered your interest in our conference. In case you have questions or remarks, please feel free to contact us. We look forward to welcoming you in Leuven in March 2018! With kind regards, Alexander Botzki Organizing Committee: Alexander Botzki, VIB Bioinformatics Core Brigida Gallone, VIB-KU Leuven Center for Microbiology Diether Lambrechts, VIB-KU Leuven Center for Cancer Biology Joost Schymkowitz, VIB-KU Leuven Center for Brain & Disease Research Vanezza Vermeirssen, VIB-UGent Center for Plant Systems biology Paola Masuzzo, VIB-UGent Center for Medical Biotechnology Evy Vierstraete, VIB Science Events manager To stop receiveiving our invitations please click below. Tweet http://email.vibconferences.be/t/r-tw-jrtrirlk-kdnlrgz-o/ Share [http://email.vibconferences.be/t/r-li-jrtrirlk-kdnlrgz-a/] Unsubscribe http://email.vibconferences.be/t/r-u-jrtrirlk-kdnlrgz-p/

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Postdoc position VIB-Janssen collaboration single cell transcriptomics
by Joke Reumers 06 Dec '17

06 Dec '17

Dear all, Please find at this link the job description for a postdoc position at Janssen Belgium in collaboration with the VIB Center for Inflammation Research, focused on single cell RNA sequencing in Alzheimer disease animal models. https://jobs.jnj.com/jobs/1700214162W/Post-Doctoral+Scientist%2C+Single+Cel… <https://jobs.jnj.com/jobs/1700214162W/Post-Doctoral+Scientist,+Single+Cell+…> For more information, you can contact me at jreumers(a)its.jnj.com <mailto:jreumers@its.jnj.com> +32 14 60 3324 Please forward to other channels where possible, Thanks, Joke Reumers

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