- BBClist - maillist.psb.ugent.be

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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Honory Doctorate Peer Bork
by Breukelen, B. van (Bas) 28 Feb '17

28 Feb '17

Honory Doctorate Peer Bork Read online<http://faculteitbetawetenschap.m12.mailplus.nl/txt31464944/BCbLAWe8kxYuaKB> [Utrecht Bioinformatics Center] [http://images.m13.mailplus.nl/user2110345/283/header_ubc.jpg] Dear Sir/Madam, The Utrecht Bioinformatics Center is very proud to announce that Professor Peer Bork will be receiving an Honorary Doctorate on the occasion of Utrecht University’s Dies Natalis. [http://images.m12.mailplus.nl/mailing31464944/500_fotopeerborkliggendklein.… Bork is a pioneering bioinformatics researcher. He has developed widely used bioinformatic tools and databases. These tools and databases have allowed him to exploit massive DNA databases to make fundamental discoveries in evolution and protein biochemistry. Today, Peer Bork works on understanding microbial ecosystems like the human microbiome and the world’s oceans. He has co-authored over 500 research articles in the broad area of computational biology and biomedical systems analysis, of which more than 60 were published in Nature, Science, and Cell. He co-founded five biotech companies, two of which went public. Professor Peer Bork is Senior group leader and Strategic Head of Bioinformatics, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. The Utrecht Bioinformatics Center cordially invites you to join the Dies Natalis ceremony as well as the seminar by Peer Bork. Best wishes, Prof. Berend Snel Register to attend the Dies Natalis<http://faculteitbetawetenschap.m12.mailplus.nl/nct37196367/BCbLAWe8kxYuaKB> » UBC seminar Peer Bork What is the current vision of Peer Bork on bioinformatics? Come and learn about Peer’s most recent research in this unique UBC seminar, entitled ‘Microbiome analysis of the human gut and the ocean’. Read more and register<http://faculteitbetawetenschap.m12.mailplus.nl/nct37196368/BCbLAWe8kxYuaKB> » UBC Master class Peer Bork How to build a scientific career in bioinformatics? Ask Peer Bork about his experience on career opportunities, publishing and science in general to help you start your scientific career. Please submit your questions using the registration form. Read more and register<http://faculteitbetawetenschap.m12.mailplus.nl/nct37196369/BCbLAWe8kxYuaKB> » [http://images.m12.mailplus.nl/mailing31464944/ubcvierlogos.png] Contact Unsubscribe<mailto:c.j.nijenhuis@uu.nl?subject=Unsubcribe%20from%20newsletter&body=Dear%20sir%2Fmadam%2C%0A%0AI%20would%20like%20to%20unsubscribe%20from%20the%20UBC%20newsletter.> ubc.uu.nl<http://faculteitbetawetenschap.m12.mailplus.nl/nct37196370/BCbLAWe8kxYuaKB> Bas. van Breukelen, PhD Assistant Professor, Biomolecular Mass Spectrometry and Proteomics | http://www.hecklab.com | Utrecht University Coordinator Bioinformatics | Utrecht Bioinformatics Center (UBC) | http://ubc.uu.nl | Utrecht University Hugo R. Kruytbuilding | Room O605 | Padualaan 8 | 3584 CH Utrecht | T +31(0)30253 9761 | M +31(0)6 42222520 | b.vanbreukelen(a)uu.nl<mailto:b.vanbreukelen@uu.nl> [cid:38CC9422-3A73-459B-A49F-56F402CA1718@arnhem.chello.nl]

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[Gtpb] RNAseq hands-on training course announcement
by Pedro L. Fernandes 25 Feb '17

25 Feb '17

ANNOUNCEMENT ADER17 Analysis of Differential Expression with RNAseq with Daniel Sobral, Daniel Faria and Mauro Truglio The GTPB is proud to announce that the above referenced hands-on training course is open for applications Important dates IMPORTANT DATES for this Course Deadline for applications: April 10th 2017 Course dates: April 17th - April 20th 2017 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. High-throughput technologies allow us to detect transcripts present in a cell or tissue. This course covers practical aspects of the analysis of differential gene expression by RNAseq. Participants will be presented with real world examples and work with them in the training room, covering all the steps of RNAseq analysis, from planning the gathering of sequence data to the generation of tables of differentially expressed gene lists and visualization of results. We we will also cover some of the initial steps of secondary analysis, such as functional enrichment of the obtained gene lists. http://gtpb.igc.gulbenkian.pt/bicourses/ADER17/ Hoping that this course meets your interests, Pedro Fernandes -- Pedro Fernandes Bioinformatics Training Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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postdoc position in Liège
by Gilles Vandewalle 24 Feb '17

24 Feb '17

Dear all, The Sleep Research Group of the University of Liège opens a position for a postdoctoral scientist in bioinformatics. The postdoc will be involved in modeling large genomic data sets to predict cognitive phenotypes in aging that would be related to sleep-wake traits. More details here: http://www.nature.com/naturejobs/science/jobs/603467-postdoctoral-position-… Best regards, Gilles Vandewalle -- Gilles Vandewalle, PhD FNRS Research Associate Sleep Research Group GIGA-Research CRC-In Vivo Imaging Unit Bâtiment B30, Université de Liège 4000 Liege, Belgium gilles.vandewalle(a)ulg.ac.be +32-4366-2367 http://www.giga.ulg.ac.be/sleep

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Still seats available: BioSB Course Programming in Matlab (2nd edition), 13 March 2017, Wageningen
by Femke Francissen 24 Feb '17

24 Feb '17

You can still register for the 1-day BioSB Course: Programming in Matlab on March 13, in Wageningen. Find more information about the course in the announcement below! -------------------- ** *BioSB Course Programming in Matlab, 13 March 2017, Wageningen* *Website: *http://biosb.nl/education/course-portfolio-2/course-matlab/ *Coordinators: *Hans Stigter (WUR), Celia van Gelder (BioSB, celia.van.gelder(a)dtls.nl) *Registration: *http://biosb.nl/education/course-portfolio-2/c ourse-matlab/enrollment-course-matlab/ *Please note that if you are (or become) a member of BioSB <http://biosb.nl/about/members/biosb-membership-information/> this course is free of charge for PhD students and with reduced fee for other researchers!* *Goal* The main goal of this course is to get acquainted with Matlab software for use within Systems Biology. After this introductory course you will have gained the basic knowledge to pursue further use via self-study of Matlab in order to apply more advanced programming techniques within Matlab in your own research. In summary, the sub-goals are: 1. To learn the philosophy behind Matlab and its syntax 2. To program simple Systems Biology models in Matlab (in ordinary differential equation format) and to solve these differential equations with Matlab *Target audience* Primarily targeting researchers from academia, but participants from the private sector are also welcome. The course focusses on the use of Matlab for building dynamic Systems Biology Models in terms of ordinary differential equations. *Course Description* This is a one-day introduction to the possibilities of Matlab as a programming environment for simulation and analysis of biological models. We will start with a simple introduction of the basics of Matlab (matrices, vectors, manipulation of matrices and presentation of data). Having obtained some basic programming knowledge (writing of simple scripts and functions in Matlab), we will move on to more advanced topics. These include programming and solving ordinary differential equation models (ODEs) and the concept of “vectorized thinking” while writing Matlab-code. Finally, calibration of parameters in ODE type of models using measured data will be discussed and examples will be given. The course also includes the basics of presenting your results (graphing) in various types of plots that can easily be drawn in Matlab. Participants will, of course, get hands-on experience with Matlab and write code themselves in a practical. *Programme* 09:45 Coffee/Tea 10:00 Welcome 10:05 Introduction Matlab Basics (functions, variables, matrices, etc) 10:45 Advanced Programming (vectorised thinking, solving dynamic ordinary differential equation models in Matlab, parameter estimation for ODE-models) 12:00 Afternoon: Solving basic and advanced problems in Matlab – hands-on experience on a PC. Exercises will be provided, but you can also bring your own problems that you have encountered in your own research. 12:30 Lunch 15:00 Coffee/tea 16:30 End *BioSB Education Programme* This course is part of the Education Programme of BioSB, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl or via education(a)biosb.nl. ** **

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NEW advanced bachelor program bioinformatics in Bruges (Belgium) (60 ECTS)
by Demeyere Mieke 23 Feb '17

23 Feb '17

Dear Madam/Sir Just 10 years ago, we (the University of Applied Sciences, Howest in Bruges, Belgium) have introduced in our Biomedical Laboratory Sciences program the option (or a major) in bioinformatics. Still, we understand from our (international) partners of the working field that the need of laboratory workers with bioinformatics skills is still growing. Therefore we have transformed our major into an advanced bachelor program that has been certified by the Flemish (or Belgian) government. In this way, we educate graduates with experience in "wet lab" techniques to solve biological problems by means of computational techniques. As the interest from abroad in our education programme keeps growing, we have decided to teach our bioinformatics advanced bachelor's program in English, starting next year. As our program is open to students from all over the world, we would like to give you some more details about our advanced bachelor program in bioinformatics. To be able to work in a "dry lab", we focus on three main topics: informatics, bioinformatics and programming. Within the field of informatics, the student learns to work on a Unix system, to store biological data and to analyse large datasets using data mining techniques. Second, the "dry lab" technician becomes familiar with comparative genomics, structural bioinformatics, systems biology and the analysis of high-throughput experimental data. In the last important topic, programming skills are introduced to create web applications, to script bioinformatics pipelines and to perform statistical analysis in R. This short and intensive one year (!) program (60 ECTS) runs from the half of September to the end of June. It is open for every bachelor, master and PhD with a profound knowledge of molecular biology and an interest in (bio)informatics. To improve the studyability, the structure of the program is divided into three blocks of six weeks. All three main topics are covered during each block, with only three to four courses per block. The majority of the courses are taught by experts in the field and they all combine theory with practical exercises. After every block the courses are immediately assessed. The program includes an internship in a work placement during eight weeks, starting around the spring holidays (the middle of April). It can be performed in Belgium or abroad in the home country. An overview of the bioinformatics program can be found on our website: www.howest.be/bioinformatics<http://www.howest.be/bioinformatics>. We believe that with this extra bachelor degree, the graduate will be stronger and have more opportunities on the job market. Next to our program we will help the student around our city and country. Our student support services will help with the accommodation in the charming city of Bruges, also referred to as the "Venice of Belgium". Next to the many historical and architectural features, there is also for example a 'chocolate walk', a chocolate trail that goes past all of the finest chocolate shops in the city centre. [Bruges Belfry in the Evening as seen from the Dijver Canal] Students in Bruges enjoy preferred access to museums, classical and modern music concerts and sports facilities. Around the historical centre of the City of Bruges, students can enjoy a great social life. A broad range of restaurants with traditional and international cuisine, wine bars and pubs offers the students the opportunity to discover the city's multifaceted night life. Our student society AmiScientia will be happy to guide you. As for transportation, throughout all of the city centre, busses are available. But most of the students take a bike rental formula as the traffic is not that crowded. With easy train access in less than an hour travel time, other cool Belgian cities as Brussels, Ghent and Antwerp are to be discovered. But also Amsterdam, Paris and London are easy to get there. For more information, please do not hesitate to send an e-mail to blt(a)howest.be<mailto:blt@howest.be>. Kind regards Mieke Demeyere Opleidingscoördinator Biomedische Laboratoriumtechnologie Program Coordinator Advanced bachelor bio-informatics [howest international_transparant] Howest University of Applied Sciences Campus Rijselstraat Rijselstraat 5 - 8200 Brugge - Belgium Tel.: +32 50 38 12 77 Fax: +32 50 38 11 71 www.howest.be/blt<http://www.howest.be/blt> Denk aan het milieu vooraleer je dit bericht of de bijlagen uitprint!

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