February 2016 - BBClist - maillist.psb.ugent.be

Postdoctoral position in Data Science, Gene/Variant prioritization and Oligogenic diseases
by Tom Lenaerts 29 Feb '16

29 Feb '16

Postdoctoral position in Data Science, Gene/Variant prioritization and Oligogenic diseases Position description The Brussels Universities (Université Libre de Bruxelles (ULB) and Vrije Universiteit Brussel (VUB)), are seeking candidates for a postdoctoral positions in data science and gene variant ranking. The successful candidates will participate in the (IB)2 Interuniversity Institute of Bioinformatics in Brussels, an institute that brings together the science, engineering and medical faculties of VUB and ULB in a collaborative and open atmosphere. The focus of the (IB)2 is on interdisciplinary research, with expertise in machine learning, big data, rare diseases, oligenic disorders, network analysis, genome analysis, metagenomics and structural bioinformatics. Located in heart of Brussels, both universities are known for quality research through their prestigious affiliate research centers and world-renowned faculty. Brussels, the capital of Belgium and the European Union, is a cosmopolitan city famous for its picturesque squares and buildings, serene parks and gardens and a very vibrant cultural life spiced up by many international languages. *Postdoctoral position in Data Science and Oligogenic diseases: The vacancy available (to be filled asap) offers tenure of at least two years. The researcher is expected to carry out fundamental data science and bioinformatics research as well as service development, which is an essential part of the BRIGHTanalysis project that is funding the position. This project’s goal is to develop novel ICT tools for the analysis and identification of variant combinations in oligogenic diseases. Qualifications Applicants for the postdoctoral position should have a recent PhD on a subject related to data science, machine learning or computational statistics. In particular, any research experience on the analysis of exome data and the prediction/ranking of genes and variants as well as the development of web services will be an asset. Applicants are expected to have strong programming skills, the ability to work independently, strong interpersonal skills, good writing, oral communication and project management skills. Upon offer of a position in IB2, the candidates who are non-EU citizens are required to obtain an appropriate long-term Schengen visa; further information is available from their nearest Belgian embassy. Deadline Applicants are encouraged to apply as soon as possible as positions will remain open until filled by a suitable candidate. Contact Candidates are invited to send a motivation letter, the contact details for 2 references, CV + with the detailed list of publications and a research statement in .pdf format by email to tlenaert(a)ulb.ac.be. The subject field of your email must include IB2-JOB: BRIGHTanalysis position. Equal Opportunity Employer ULB is an equal opportunity employer and is committed to employing more handicapped individuals and especially encourages them to apply. ULB wishes to increase the proportion of women in areas in which they are underrepresented. Women are strongly encouraged to apply.

1 0

Introduction to Next Generation Sequencing; technologies, applications and data analysis, 12-15 April 2016
by Sari van Heel - Vauhkala 29 Feb '16

29 Feb '16

Dear Members of BBClist, We would like to remind you about the international course that the Research Group Analysis Techniques in Life Science (Avans University of Applied Sciences, Breda, the Netherlands) will be offering in April 2016: Introduction to Next Generation Sequencing; technologies, applications, and data analysis Course date: 12 – 15 April 2016 Registration fee: €1.100,- (we offer you a 10% discount on this fee if you register before Monday 7 March 2016!) Website : http://www.alsavans.nl/avans-training-2545.htm The digital registration form is available on the website. Should you have any questions, please do not hesitate to contact us by email at: si.vanheel-vauhkala(a)avans.nl<mailto:si.vanheel-vauhkala@avans.nl> Kind regards, Ms. Sari van Heel-Vauhkala Secretary Research Group Analysis Techniques in Life Science Disclaimer ( http://www.avans.nl/over-avans/e-mail-disclaimer )

1 0

Fwd: Faculty position in Computational Biology at Dana-Farber and Harvard in Boston
by Yves Moreau 27 Feb '16

27 Feb '16

> Begin forwarded message: > > From: Chris Sander <chris(a)jimmy.harvard.edu> > > > > As I have moved to Boston to start a new academic venture, we are opening a round of faculty recruitment for a new Center at DFCI, called cBio Center for Information Biology, focused on Computational and Systems Biology, with strong links to Harvard Medical School. > > We are also recruiting for postdocs and a software engineer in the Sander research team at DFCI and HMS. > > Please forward the faculty ad below to interested researchers and encourage your best postdocs to apply. > > With best wishes, > > Chris Sander > > —————————————— > Computational Biology > Assistant/Associate Professor > Dana-Farber Cancer Institute > > The Dana-Farber Cancer Institute (DFCI) seeks an accomplished and innovative research faculty member. Pursue basic and translational research with an emphasis on solving biological problems by computational and data science methods. Collaborate with cancer researchers to achieve impact on data-driven clinical trials and cancer care in the age of genomically informed personalized medicine. Join a new Center focused on computational biomedicine, headed by Chris Sander. Home will be in the Department of Biostatistics and Computational Biology at DFCI with an academic appointment in the Department of Biomedical Informatics at Harvard Medical School (HMS). Participate in the scientific events of the Dana-Farber, Harvard and Boston area research communities and train graduate students in a highly interactive, supportive, collaborative and dynamic research environment. > > You have a Ph.D. or M.D./Ph.D. degree, with a significant record of discoveries and peer-reviewed publications. Your academic rank will be determined according to your experience and productivity. Send a letter of application and a concise statement of current and future research interests, curriculum vitae, sample publications, and the names of four referees to chair(a)jimmy.harvard.edu <mailto:chair@jimmy.harvard.edu> (cc: dwana(a)jimmy.harvard.edu <mailto:dwana@jimmy.harvard.edu>) and ask referees to independently provide letters of recommendation to the same address. Consideration of candidates will begin after the application package is complete. Please apply before February 28, 2016 (strongly preferred), but later applications will also be considered. > > We are an equal opportunity employer and all qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability status, protected veteran status, or any other characteristic protected by law. > > —————————————— > > Sander group: As you may know, I have moved from MSKCC as of Jan 2016 to set up a new cBio Center at DFCI / Harvard in Boston, with initially four groups, including two junior faculty to be appointed in 2016 and 2017. I will continue as adjunct @ MSKCC until June 30, 2016. > > Email: Please change my email address to: <chris(a)sanderlab.org <mailto:chris@sanderlab.org>> from <sanderc(a)mskcc.org <mailto:sanderc@mskcc.org>> or <sander(a)cbio.mskcc.org <mailto:sander@cbio.mskcc.org>> > > New affiliation: Chris Sander, cBio Center, Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, or, more briefly: Chris Sander, DFCI & HMS, Boston > > Science: Perturbation biology experiments, theory and computation to develop combination therapy in cancer, with focus on the problem of resistance to targeted therapy. > Continued involvement in cancer genomics and proteomics as well as cancer systems biology (successor of TCGA). > Evolutionary couplings for protein and RNA structure and function with Debora Marks' group at HMS. > Active development of cBioPortal for cancer genomics with Niki Schultz at MSKCC and Ethan Cerami at DFCI. >

1 0

International Chemical Discovery & Design Course, 15-26 June 2015, Nijmegen, NL
by Celia.vanGelder＠radboudumc.nl 27 Feb '16

27 Feb '16

International Chemical Discovery & Design Course, 6-17 June 2016, Nijmegen. Course website: http://www2.cmbi.ru.nl/groups/computational-discovery-and-design/icdd2016/ We would like to draw your attention to the 12th annual International Chemical Discovery & Design Course which will be held from 6-17 June 2016 at the Radboud University Nijmegen. This course covers the recent advances in discovery informatics, with a focus on the application to real life problems. The course, combining practicals and lectures, will introduce and discuss different scientific concepts as well as providing an opportunity to gain practical experience using industry standard software. You can expect lectures and practicals on the following topics: * Introduction to Computational Discovery & Design * Comparative Protein Modelling * Sequence Retrieval, Analysis and Alignment Techniques * Computational Medicinal Chemistry; Molecular Descriptors & Library Design * The Application of Computational Drug Design to Real Life Problems * Molecular Docking and Virtual Screening * Advanced 3D Database Searches and Scaffold Hopping * QSAR * Structure Based Drug Design Techniques The course is targeted to MSc students, PhD students and post-docs. A basic background in bioinformatics or computational chemistry is a prerequisite for attendance. Registration via email to Barbara van Kampen<mailto:barbara.vankampen@radboudumc.nl>. Please, provide information about your background and your motivation to participate in the course. The course is free. You should however pay for travelling and lodging expenses yourself. Best regards Gijs Schaftenaar (CDD/CMBI/Radboudumc Nijmegen) Celia van Gelder (CMBI/Radboudumc & BioSB/DTL) Dr. Celia W.G. van Gelder Education Manager BioSB Coordinator Education CMBI Programme Manager Learning DTL/ELIXIR-NL tel. +31613375327 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:Celia.vanGelder@radboudumc.nl> websites: www.nbic.nl<http://www.nbic.nl/>, www.biosb.nl, www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.dtls.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre PO Box 9101 6500 HB Nijmegen The Netherlands Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

1 0

Three structural bioinformatics post-doc positions in Brussels
by Wim Vranken 26 Feb '16

26 Feb '16

Dear all, Please find attached a PDF detailing 3 job openings for structural bioinformatics post-docs associated with the (IB)2 Interuniversity Institute of Bioinformatics in Brussels. Best regards, Wim

1 0

[Gtpb] NDARC16 - NGS Data Analysis RNAseq and ChIPseq - Announcement
by Pedro Fernandes 26 Feb '16

26 Feb '16

Dear all, The Applications for the bioinformatics training course NDARC16 - NGS Data Analysis RNAseq and ChIPseq, are now OPEN. IMPORTANT DATES for this Course Deadline for applications: March 20th 2016 Course dates: March 29th - April 1st 2016 Details are available here: http://gtpb.igc.gulbenkian.pt/bicourses/NDARC16 Overview High-throughput technologies such as next generation sequencing (NGS) can routinely produce massive amounts of data. These technologies allow us to describe all variants in a genome or to detect the whole set of transcripts that are present in a cell or tissue. However, such datasets pose new challenges in the way the data have to be analyzed, annotated and interpreted which are not trivial and are daunting to the wet-lab biologist. This course covers state-of-the-art and best-practice tools for NGS RNA-seq and ChIP-seq data analysis, which are of major relevance in today's genomic and gene expression studies. Methods The course is comprised of practical exercises preceded by short lectures. Exercises will be conducted primarily in the R programming language. Target Audiences Enthusiastic and motivated wet-lab biologists who want to gain more of an understanding of NGS data and eventually progress to analysing their own data. Pre-requisites There is a lot of material to cover in the course, so we will assume that you are familiar with a few basics before you come. The tool that will we do most of the analysis in is R. There will be a short recap of the key concepts at the beginning of the course; however it will be beneficial if you are already familiar with how to read data into R, perform basic subset operations and produce simple plots. Some introductory statistics, such as summary statistics for continuous data (mean, variance etc) and interpreting the results of a t-test, will be also be assumed. See "Statistics at Square One"" Chapters 1, 2, 3 and 7 (Statistics at Square One - BMJ) for a good overview. Basic unix skills, such as being able to list the contents of a directory and copy files, would also be an advantage. See "Session 1" of the Software Carpentry training for a Unix introduction (Shell-novice material from the Software Carpentry Foundation). Best wishes Pedro Fernandes GTPB Coordinator -- Pedro Fernandes 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

1 0

RegGenSIG 2016 - Call for abstracts
by Stein Aerts 24 Feb '16

24 Feb '16

Regulatory Genomics Special Interest Group (RegGenSIG) <http://www.reggen.net/2016> RegGenSIG 2016 will take place in Orlando, Florida, on Saturday, July 9, as part of ISMB 2016 <https://www.iscb.org/ismb2016>. The RegGenSIG meeting focuses on bioinformatics for regulatory genomics, which involves the study of the genomic "control system", which determines how, when and where to activate the "blueprint" encoded in the genome. An important goal of the meeting is to foster a collaborative community wherein scientists convene to solve difficult research problems in all areas of computational regulatory genomics. Please check <http://www.reggen.net/2016> for more information. *Call for abstracts - Oral presentations and poster presentations* To make an oral presentation at RegGenSIG, a one-page abstract should be submitted by April 11, 2016, to Jason Ernst (jason.ernst(a)ucla.edu<mailto:jason.ernst@ucla.edu>), with Subject: "RegGenSIG 2016 - Abstract for oral presentation", using the template found on the RegGenSIG web page. Based on the submitted abstracts, selected authors will be invited for oral presentation. Authors will be notified by May 2, 2016. Abstracts submitted for oral presentation may also be considered for poster presentation. For poster presentations, authors should submit a one-page abstract no later than May 9, 2016, to Jason Ernst (jason.ernst(a)ucla.edu<mailto:jason.ernst@ucla.edu>), with Subject: "RegGenSIG 2016 - Abstract for poster presentation", using the same template as for oral presentations. Author notification will occur no later than May 23, 2016. Yours sincerely, Finn Drabløs -- Department of Cancer Research and Molecular Medicine, Faculty of Medicine, Norwegian University of Science and Technology (NTNU) POST : P.O. Box 8905, NO-7491 Trondheim, NORWAY VISIT: Laboratory Center, Erling Skjalgsons gt. 1 Web http://bigr.medisin.ntnu.no Phone +47 72573333

1 0

Python for Life Scientists, 13-14 May 2016, Amsterdam
by Nicola Bonzanni 23 Feb '16

23 Feb '16

Dear all, I'm writing to announce the course "Python for Life Scientists". Tailored for life scientists with little or no prior programming experience, the course is driven by real-life use cases. Participants will learn by doing, completing snippets of code that they will be able to reuse in their everyday tasks. Extensive use of IPython Notebook (Jupyter) will encourage to annotate and document the code, building the basis for sound and reproducible data analysis. The course will run on May 13-14 2016 in Amsterdam. More information and the registration form are available from the Web site: http://www.enpicom.com/training/python Feel free to spread this information to people that might be interested. Kind Regards, Nicola Bonzanni ENPICOM | Science Park 402 | 1098 XH Amsterdam http://www.enpicom.com +31 (0)20 895 0964

1 0

Fwd: Last chance to join 'Applied Bioinformatics in Life Sciences'
by Frederik Coppens 22 Feb '16

22 Feb '16

Email not displaying correctly? View it in your browser. <http://vib.cmail20.com/t/r-i-vuilyo-l-i/> Last chance to join 'Applied Bioinformatics in Life Sciences' Late registration deadline March 3, 2016! The conference is almost sold out. Dear colleague, We want to remind you that the final registration deadline for Applied Bioinformatics in Life Sciences approaches. Make use of this last chance to join over 180 colleagues & stay up to date on the latest developments in the field of Bioinformatics. Register here <http://vib.cmail20.com/t/r-i-vuilyo-l-d/>. 19 INTERNATIONALLY RENOWNED SPEAKERS The conference will bring together some of the most highly regarded academics in the world of bioinformatics in several sessions, with topics focused on: Data Integration and Modeling // Next Generation Sequencing // Protein Bioinformatics // Systems Biology. The speakers covering these topics include:Matthias Mann (MPI,DE), Peer Bork (EMBL,DE), Luis Serrano (CGR,ES), Nuria Lopez-Bigas (University of Pompeu Fabra, ES) Christine Orengo(UCL,UK), Eran Segal (Weizmann Institute, IL), and many more <http://vib.cmail20.com/t/r-i-vuilyo-l-h/>. OVER 70 POSTER PRESENTERS Junior researchers have sent in their research and will present it via posters and presentations during the conference. After the closing remarks on the second day, a poster prize will be awarded. MORE THAN JUST TALKS The first day we welcome all the attendees to network at our unique Begian beer reception. On day one you can also enjoy a relaxing dinner in The Faculty Club <http://vib.cmail20.com/t/r-i-vuilyo-l-k/> located in the ancient historical site of the Grand Beguinage which was included in the UNESCO World Heritage List. Aguided walk through the ancient city will get you there. Select the dinner when you register <http://vib.cmail20.com/t/r-i-vuilyo-l-u/> for the conference. <http://vib.cmail20.com/t/r-i-vuilyo-l-o/> We hope to have triggered your interest in our conference. In case you have questions or remarks, please feel free to contact us. With kind regards, Alexander Botzki VIB BioInformatics Training and Service facility, VIB HQ On behalf of the organizing committee <http://vib.cmail20.com/t/r-i-vuilyo-l-b/> You received this email based on your expertise in the field. In case this research area is not of your interests, we apologize for any inconvenience. Please unsubscribe here <http://vib.cmail20.com/t/r-u-vuilyo-l-r/> | subscription preferences <http://vib.updatemyprofile.com/r-l-2AD73FFF-l-y> ================================================================== Frederik Coppens, Ph.D. Project Leader Applied Bioinformatics & Biostatistics IT manager Tel: 32 (0)9 3313812 Fax:32 (0)9 3313809 VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY, UGent Technologiepark 927, 9052 Gent, BELGIUM frcop(a)psb.ugent.be http://www.psb.ugent.be/abb ==================================================================

1 0

Introduction to Python for Biologists 4-8 April 2016 - Few places left
by Bert Overduin 22 Feb '16

22 Feb '16

Dear all, This is to let you know that we have a few places left on our Introduction to Python for Biologists course from 4-8 April 2016. As Python is an ideal first language for beginning programmers, this course is extremely well suited for those working in biology / genomics without any previous programming experience. The course will be taught by Martin Jones, founder of Python for Biologists (http://pythonforbiologists.com) and a very experienced Python teacher, assisted by myself. Having two instructors for around 20 students will guarantee lots of one-on-one time. For more information and to register, please have a look at: https://genomics.ed.ac.uk/introduction-python-biologists-april-2016 Note that the course will be repeated from 11-15 July 2016: https://genomics.ed.ac.uk/introduction-python-biologists-july-2016 Finally, I don't want to withhold from you some of the feedback we received for last week's course: *"Brilliantly well-run. From the book; to the USB stick with all the files we need; to the topics covered; to the system of helping us one-on-one, I cannot fault the course."* *"It was a great workshop full of amazing content and great people. Thank you!"* *"#Drawing upon 15 years of teaching experience at a University, I find: Num_faults == 0"* With kind regards, Bert -- Bert Overduin, PhD TRAINING AND OUTREACH BIOINFORMATICIAN Bert.Overduin(a)ed.ac.uk EDINBURGH GENOMICS The University of Edinburgh Ashworth Laboratories The King's Buildings Charlotte Auerbach Road Edinburgh EH9 3FL Scotland, United Kingdom tel. +44(0)1316507403 http://genomics.ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

1 0