- BBClist - maillist.psb.ugent.be

PhD position "Analysis of genomic and epigenomic patterns in developmental disorders" (IB2, ULB, Brussels)
by Matthieu Defrance 08 Mar '17

08 Mar '17

Ph.D position "Analysis of genomic and epigenomic patterns in developmental disorders" (IB2, ULB, Brussels) A PhD position on the "Analysis of genomic and epigenomic patterns in developmental disorders" is available at the Interuniversity Institute of Bioinformatics in Brussels (IB2, Université Libre de Bruxelles, Belgium). The research goal is to contribute to the development of new bioinformatic methodologies in order to analyze both genetic and epigenetic alterations (e.g. genetic mutations, DNA methylation alterations) that are involved in developmental pathologies. Both fundamental and clinical aspects of alterations will be addressed by mixing high-throughput data generated locally with already available external data. The position will be funded for 4 years. Screening of applications begins immediately and will continue until an outstanding candidate has been selected. The deadline for the application is set to the 30th of April 2017. PhD is expected to start in October 2017. The candidate should hold a master degree in bioinformatics, engineering, statistics, or in computer sciences and demonstrate proficiency in algorithmics, statistics or machine learning and in software development (R, python). Experience with sequencing data, genome-wide data sets (e.g. ChIP-Seq, RNA-Seq) or massive datasets analysis would be a plus. The applicant should demonstrate interest for biology and interdisciplinary research. Applications should include a detailed CV, a motivation letter, and names of two referees and should be sent to Dr. Matthieu Defrance (matthieu.dc.defrance(a)ulb.ac.be) and Dr. Guillaume Smits (guillaume.smits(a)huderf.be)

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ELIXIR-EXCELERATE HPC Train-the-Researcher Course - 6-7 April 2017, Malaga, Spain
by Celia van Gelder 08 Mar '17

08 Mar '17

Dear all, ELIXIR-Spain is organizing a HPC Train-the-researcher Course, intended for bioinformatics users and developers that aim at using HPC resources to extend their activity beyond the limitations of sequential applications on commodity hardware (Note that this course will not suit participants that are looking for entry-level concepts in HPC). The course is organised as a two-day mini-symposium, and aims at introducing the participants in the complexities of parallel programming with emphasis on genome-scale comparison algorithms. · The theoretical aspects of this course cover (a) the parallel programing background, with a quick overview in the architectures and programming models; and (b) the basis for genome-scale sequence comparison algorithms. · The practical aspects are organised to master the concepts of data distribution and balancing using a Map-Reduce strategy and internal coding with MPI. The information about the course is here: https://chirimoyo.ac.uma.es/bitlab/portfolio/hpc-excelerate/ . ELIXIR Spain will be able to host a few people from each of the ELIXIR countries, there will not be a fee for the actual participation. Please spread this information in your organization as you see fit, Thank you! Best Celia Dr. Celia W.G. van Gelder Programme Manager Learning DTL/ELIXIR-NL Training Education Manager BioSB tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl websites: <http://www.dtls.nl/> www.dtls.nl, <http://www.biosb.nl/> www.biosb.nl skype: celia.van.gelder Postal address: DTL PO Box 19245 3501 DE Utrecht

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Galaxy Community Conference (GCC2017), Montpellier, France, 26-30 June
by Dave Clements 08 Mar '17

08 Mar '17

*2017 Galaxy Community Conference (GCC2017)* 26-30 June 2017 Montpellier, France https://gcc2017.sciencesconf.org/ -- The 2017 Galaxy Community Conference <https://gcc2017.sciencesconf.org/> will bring together several hundred researchers working in and supporting data intensive life science research. There is no better place to share your work and learn from others that are addressing diverse questions and facing common challenges in data intensive biology. GCC participants work across the tree of life, come from around the world, and represent universities, research organizations, industry, medical schools and research hospitals. GCC2017 will be in Montpellier, France, 26-30 June and will feature two days of presentations, discussions, poster sessions, lightning talks, computer demos, keynotes, and birds-of-a-feather meetups, all about data-intensive biology and the tools that support it. GCC2017 also includes data and coding hackathons <https://gcc2017.sciencesconf.org/page/hackathon>, and two days of training <https://gcc2017.sched.com/overview/type/Training> covering 16 different topics. GCC2017 will be held at Le Corum Conference Centre <http://www.montpellier-events.com/en/The-Corum/Presentation> in the heart of Montpellier <https://gcc2017.sciencesconf.org/page/location>, just 10km from the Mediterranean. Abstract submission <https://gcc2017.sciencesconf.org/page/submit> is now open. If you work in or support data intensive life science research then GCC2017 is an ideal opportunity to present your work. The deadline for oral presentations is Apr 15 (23:59 Paris local time), and posters and computer demonstration submission closes on May 27 (23:59 Paris local time). The Lightning talk submission deadline is June 23 (23:59 Paris time). Early registration <https://gcc2017.sciencesconf.org/page/registration> is also open and starts at less than 55€ / day for post-docs and students. You can also book low cost conference housing <https://gcc2017.sciencesconf.org/page/lodging> when you register. Travel fellowships <https://new.galaxyproject.org/news/2017-03-gcc2017-fellowships/> are being offered by the Galaxy Community Fund for early career researchers that are travelling from afar. About Galaxy Galaxy <https://galaxyproject.org/> is an open, web-based platform for data-intensive biomedical analysis used by tens of thousands of researchers around the world. It supports ad hoc exploration and analysis through scalable and repeatable data analysis pipelines for large research studies. Galaxy is available in over 90 free and publicly accessible web servers, on public and national cloud infrastructures, and is locally installed at hundreds, if not thousands, of research organisations around the world. We hope to see you this summer in Montpellier! Au revoir, The GCC2017 Organising Committee PS: Please redistribute this announcement to any interested groups. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Summer school on ecological network inference and analysis
by Karoline Faust 07 Mar '17

07 Mar '17

Dear all, We are pleased to announce our summer school on ecological network inference and analysis, which will take place in Leuven from the 11-13th of September 2017. The school will focus on ecological network theory and its practical application to sequencing data. Lectures and practicals will be given by a number of experts, including Stefanie Widder, Tim Poisot, Katharine Coyte, Elisa Beninca, Didier Gonze, Gipsi Lima-Mendez, Sebastian Schmidt, Hugo Roume, Vasilis Dakos, Miguel Fortuna and Jing Tang. For more information and registration, please visit: http://tinyurl.com/econetschool Kind regards, Karoline Faust, on behalf of the organizers -- Karoline Faust --------------------------------------------------- Email: karoline.faust(a)kuleuven.be Web: http://tinyurl.com/MicrobialSysBio --------------------------------------------------- Room 7.A130, Rega Institute Laboratory of Molecular Bacteriology Department of Microbiology and Immunology KU Leuven, Campus Gasthuisberg Herestraat 49, postbus 1028 3000 Leuven Belgium ---------------------------------------------------

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FW: [bioinfo] Conference 'Understanding Protein Interactions: from Molecules to Organisms', Lyon 24-26 April 2017
by Alexander Botzki 06 Mar '17

06 Mar '17

From: Juliette Martin [mailto:juliette.martin@ibcp.fr] Sent: 06 March 2017 15:17 To: bioinfo(a)sfbi.fr Subject: [bioinfo] Conference 'Understanding Protein Interactions: from Molecules to Organisms', Lyon 24-26 April 2017 It is still time to register to the international meeting 'Understanding Protein Interactions: from Molecules to Organisms' that will take place in Lyon 24-26 April 2017: https://mapping2017.sciencesconf.org Registration is free but mandatory. Participants will have the opportunity to present their work via selected short talks or during the special ‘Laptop Session’, an interactive and lively alternative to the traditional poster session, where participants come with their laptop and present a short slide-show (2-3 slides) and eventually a linked demonstration of their work The preliminary program is now available: 24th of April Alexandre Bonvin, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands "High-resolution, integrative modelling of biomolecular complexes from fuzzy data" Ozlem Keskin, Koç University, Computational Systems Biology Lab, Turkey "Protein-protein interfaces: amino acid variations and hot spot residues" Yanay Ofran, Bar-Ian University, Systems Biology and Functional Genomics, Israel "All models are wrong, some are useful": Predicting and designing interactions based on multiple wrong models Contributed talk 1 25th of April Ilya Vakser, University of Kansas, Center for Computational Biology, USA "Comparative vs. Free Docking in Modeling of Interactome" Franca Fraternali, King's College London, Bioinformatics and Computational Biology, UK TBA Peter Uetz, Virginia Commonwealth University, Center for the Study of Biological Complexity, USA "Protein complexes and protein interaction networks in bacteria" Contributed talk 2 Contributed talk 3 ** Laptop Session ** Emmanuel Levy, Weizmann Institute of Science, Cell architecture lab, Israel "Proteins evolve on the edge of supramolecular self-assembly" Julia Shifman, Hebrew University of Jerusalem, Protein-Protein Interactions, Israel "Cold spots in Protein Binding" Elisa Fadda, Maynooth University, Computational Biophysics, Ireland "Are structure-less protein regions really so structure-less? An atomistic view of the architecture of disorder and its functions in protein-protein interactions" Rob Russel, University of Heidelberg, Protein Evolution Germany TBA Contributed talk 4 26th of April Raphael Guerois, Institute of Integrative Biology of the Cell, CEA, Unit of Bioenergetics, Structural Biology and Mechanisms, France "Structural modeling and design of protein interactions using evolution" Monika Fuxreiter, University of Debrecen, Laboratory of Protein Dynamics, Hungary "Dynamic interactions and fuzziness in protein complexes and higher-order assemblies" Patrick Aloy, Institute for Research in Biomedicine, Barcelona, Spain "A network biology approach to novel therapeutic strategies" Contributed talk 5

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Vacancies ELIXIR Belgium
by Kim De Ruyck 06 Mar '17

06 Mar '17

Dear all, Within ELIXIR Belgium, we are looking for a [ http://www.vib.be/en/jobs/Pages/Software-Developer-ELIXIR-Belgium.aspx | Software Developer ] and a [ http://www.vib.be/en/jobs/Pages/ELIXIR-Trainer.aspx | Bioinformatics and Data Science Trainer ] . Both positions are in Gent, all information can be found on the provided links. Kind regards, Kim De Ruyck Kim De Ruyck PhD Coordinator ELIXIR Belgium VIB, Technologiepark 927, 9052 GENT | +32 (0)9 33 13 694 [ http://www.elixir-belgium.org/ | www.elixir-belgium.org ] [ https://twitter.com/ELIXIRnodeBE | @ELIXIRnodeBE ] [ http://eepurl.com/cl-xOX | Subscribe to our mailing list ]

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3 PhD student vacancies @UAntwerpen on data mining, bioinformatics and epidemiology of Tuberculosis
by Laukens Kris 02 Mar '17

02 Mar '17

Dear colleagues, UAntwerpen has 3 vacancies for PhD students on bioinformatics, large scale data mining and epidemiology of Tuberculosis. Feel free to distribute this among potentially interested participants. PhD in Omics Bioinformatics and/or Systems Biology for Mycobacterium tuberculosis https://www.uantwerpen.be/nl/jobs/vacatures/ap/2017bapfggwef074/ PhD Student in large-scale molecular data mining https://www.uantwerpen.be/nl/jobs/vacatures/ap/2017bapfwetef076/ PhD Student in Epidemiology of Tuberculosis https://www.uantwerpen.be/nl/jobs/vacatures/ap/2017bapfggwef075/ Thank you in advance! warm regards, Kris -- Kris Laukens, PhD Associate professor bioinformatics - biodata mining Advanced Database Research and Modelling (ADReM) Biomedical Informatics Network Antwerpen (biomina) Department of Mathematics and Computer Science University of Antwerp Middelheimlaan 1, G.111 B-2020 Antwerpen, Belgium T +32 (0)3 265 33 10 E kris.laukens(a)uantwerpen.be<mailto:kris.laukens@uantwerpen.be> W www.uantwerpen.be/en/staff/kris-laukens/<http://www.uantwerpen.be/en/staff/kris-laukens/>

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PhD position UGent - UZGent: Analysis of circulating tumour DNA for early detection and selection of cancer patients for precision medicine
by Björn Menten 02 Mar '17

02 Mar '17

Analysis of circulating tumour DNA for early detection and selection of cancer patients for precision medicine Job description You will join a team that focuses on the study of circulating tumor DNA (and RNA) for the diagnosis of cancer and therapeutic stratification for precision medicine (“liquid” biopsy). The development of these liquid biopsies is based on Massively Parallel Sequencing (Next Generation Sequencing) of circulating tumor DNA (and RNA) present in plasma of cancer patients. We will use Shallow Whole Genome Sequencing (for the detection of Copy Number Alterations), as well as targeted sequencing (for the detection of point mutations in many oncogenes, tumor suppressor genes and DNA repair genes). Your task in the team focuses on the development of bioinformatic and statistical tools for the analysis of the Next Generation Sequencing data. Furthermore, you will be intensely involved in the selection of genes for large panels relevant for the development of liquid biopsies. The aim of the project is early diagnosis of cancer, therapeutic stratification for precision medicine, follow-up after therapy, and the detection of potential targets for therapy. The project focuses on lung cancer and lymphoma, but the approach is also promising for other tumor types. The project is a collaboration between the Department of Pathology (Laboratory for Cancer Diagnostics and Pathology), the Center for Medical Genetics, the Department of Thoracic Oncology, the Department of Hematology, and the Center for Molecular Diagnostics Ghent. All these clinical departments and laboratories are located at the campus of Ghent University Hospital. Profile of the candidate ● You hold a master degree in one of the following disciplines: Bioengineering, Biochemistry and Biotechnology, Bioinformatics or an equivalent field. ● You are interested in challenging scientific research. ● You are interested in cancer biology and molecular biological techniques. In close collaboration with the other team members you will try to gain insight in the genetic alterations in tumors, important for the development of diagnostic and prognostic molecular tests on circulating tumor DNA (and RNA). ● You aim is to obtain a PhD degree. ● You have knowledge of bioinformatic tools and in particular of genomics data analysis (e.g. Whole Exome Sequencing, Whole Genome Sequencing, …). ● You have knowledge of commonly used programming languages in bioinformatics, like R, Python and Perl. ● You can work independently, but are also a good team player. ● You are a creative mind and a problem solver. ● You are communicative. ● You hold, or expect to hold by June 2017, a master degree (the latest starting date is August 1, 2017). How to apply? Interested? We are looking forward to receiving your C.V., together with an overview of your study results, a motivation letter and two references. Send your application to katrien.vanbost(a)ugent.be<mailto:katrien.vanbost@ugent.be>. For more information, please contact: Prof. dr. Jo Van Dorpe Department of Pathology - Laboratory for Cancer Diagnostics and Pathology jo.vandorpe(a)uzgent.be<mailto:jo.vandorpe@uzgent.be> T +32 9 332 51 38 Prof. dr. ir. Björn Menten Center for Medical Genetics Ghent bjorn.menten(a)ugent.be<mailto:bjorn.menten@ugent.be> T +32 9 332 52 84 Prof. dr. ir. Kathleen Claes Center for Medical Genetics Ghent kathleen.claes(a)ugent.be<mailto:kathleen.claes@ugent.be> T +32 9 332 24 78

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Post-doctoral position: Analysis of multi-level molecular networks in cancer.
by Francisco Azuaje 02 Mar '17

02 Mar '17

Dear colleague, We are looking for candidates for this position at the Luxembourg Institute of Health (LIH) : https://www.lih.lu/jobs/detail/post-doctoral-researcher-fa0317-12574 (start-date: Before 1st July 2017) Sincerely, Francisco. _________________________________ Francisco Azuaje, PhD Principal Investigator NORLUX Neuro-Oncology Laboratory Department of Oncology Luxembourg Institute of Health 1A-B, rue Thomas Edison, L-1445 Strassen Luxembourg Tel: +352 26970-875 Fax: +352 26970-719 Email: francisco.azuaje(a)lih.lu<mailto:francisco.azuaje@lih.lu> Website: https://www.lih.lu/ [http://files.lih.lu/outlookSignature/lih.jpg] Join us on Facebook and follow our activities on Twitter: https://www.facebook.com/Luxembourg.Institute.of.Health http://twitter.com/LIH_Luxembourg http://www.norlux.lu This message (including any attachments) is intended for the addressee only and may contain confidential and/or privileged information and/or information protected by intellectual property rights. If you have received this message by mistake, please notify the sender by return e-mail and delete this message from your system. You should not use, alter, copy or distribute this message or disclose its contents to anyone. E-mail transmission can not be guaranteed to be secure or error free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. Luxembourg Institute of Health shall not be responsible nor liable for the proper and complete transmission of the information contained in this communication nor for any delay in its receipt or damage to your system.

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ELIXIR-IIB training course on "Computational approaches to the study of protein interactions and rational drug design" - Padova, 10-13 April, 2017
by Alexander Botzki 01 Mar '17

01 Mar '17

COURSE ANNOUNCEMENT Please circulate this email to those who might be interested ELIXIR-IIB, in collaboration with the University of Padova and RGS-Italy, is pleased to inform you that the applications for the upcoming training course on "Computational approaches to the study of protein interactions and rational drug design" are now open. IMPORTANT DATES for this Course: - Deadline for applications: 28th March 2017 - Course date: 10-13 April 2017 Venue: Campus di Biologia e Biomedicina "Fiore di Botta", University of Padova, Via del Pescarotto, 8, Padova, IT Speakers: Prof. Alexandre Bonvin - Faculty of Science, Utrecht University, the Netherlands Dr. Norman Davey - University College Dublin, Dublin, Ireland) Dr. Stefano Forli - Dept. Molecular Biology, The Scripps Research Institute, La Jolla, USA Prof. Stefano Moro - Dept. of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy A maximum of 30 candidates will be accepted in the course. Selection will start on March 10th, 2017 and those with an adequate profile will be accepted immediately, especially if they come from other cities and/or countries (to allow them to find reasonably cheap flight tickets). Course description: This workshop is aimed at students in master degree courses, PhD students and post-doctoral researchers who are working or planning to work in the field of protein interactions from a molecular and structural point of view. In this workshop, participants will familiarise with docking approaches to the study of protein-protein interactions (PPIs) and protein-small molecule interactions. Irreversible binders design using molecular docking and computational methods to rational drug design will be also described, as well as the functional role of the intrinsically disordered proteins. Should you have any question, do not hesitate to contact the ELIXIR-IIB training coordinator, Dr Allegra Via, at allegra.via(a)cnr.it<mailto:allegra.via@cnr.it> or elixir.ita.training(a)gmail.com<mailto:elixir.ita.training@gmail.com>. Full details at: https://elixir-iib-training.github.io/website/2017/04/10/protein-interactio… Best regards, The ELIXIR-IIB Training Team

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