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BioSB Course: Algorithms for Biological Networks (4rd edition) - registration open!
by Femke Francissen 01 Mar '16

01 Mar '16

*BioSB Course: Algorithms for Biological Networks (4rd edition) * - *Date:* 23-27 May 2016 - *Course coordinators:* Dick de Ridder (WUR), Jeroen de Ridder (TUD) - *Location:* Delft University of Technology (TUD), Delft, the Netherlands - *Website:* http://biosb.nl/education/course-portfolio/course-algorithms-for-biological… - *Registration:* follow this link <http://bit.ly/1WT8ODe> - *More information:* education(a)biosb.nl *Target audience* PhD students with a background in bioinformatics, computer science or a related field; a working knowledge of basic statistics and linear algebra is assumed. *Course Description * In the fourth edition of this course, we will first give a brief overview of molecular biology, the advent of high-throughput measurement techniques and large databases containing biological knowledge, and the importance of networks to model all this. We will highlight a number of peculiar features of biological networks. Next, a number of basic network models (linear, Boolean, Bayesian) will be discussed, as well as methods of inferring networks from observed measurement data and of integrating various data sources and databases to refine networks. Once networks are derived they often serve as the cornerstone in the visualization, analysis and interpretation of high-throughput data; we will discuss a number of methods in this area. As an alternative to static networks, a number of alternative dynamic network models more suited for high-level simulation of cellular behaviour for will be introduced. Finally, we will give some examples of algorithms exploiting the networks found to learn about biology, specifically for inspecting protein interaction networks and for finding active sub networks. *Course programme* The course website, including full course programme, can be found at http://helix.ewi.tudelft.nl/nbic/abn/. *BioSB Course Programme* The Education Portfolio of BioSB can be found at http://biosb.nl/education/course-portfolio/. *More information* For more information about the course you can contact Celia van Gelder at education(a)biosb.nl. **

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Symposium: Genomics In Agriculture, Fisheries and Food, ILVO, 21 April 2016
by Katrijn Vannerum 01 Mar '16

01 Mar '16

[1456228629220_PastedImage] Dear colleague, The Institute for Agricultural and Fisheries Research (ILVO) is pleased to invite you to the Symposium: Genomics In Agriculture, Fisheries and Food<http://www.ilvogenomics.be/EN/Symposium/Home>, which will be held on 21st of April 2016, in Melle, Belgium. Scope Genomics has radically changed the way we study the genetic composition and functionality of plant and animal populations and microbial communities. In this symposium, we present you an overview of current applications of ILVO`s Genomics Platform in our research program geared towards agriculture, fisheries and the food sector. For example, monitoring the composition of organisms, populations and communities, allows to understand their interaction with the environment, to steer (meta)populations towards optimal agronomical or ecological properties, or to develop diagnostic tools and control measures for harmful (micro)organisms in water, soil, and food. Programme<http://www.ilvogenomics.be/EN/Symposium/Programme/Default.aspx> Four invited speakers will present current applications of genomics and computational biology tools in conservation biology, for development of healthy and tasty food, in livestock breeding and to decipher functions in genomes. In addition, 18 ILVO scientists will present current research in four areas: * Genome structure, function, and diversity * Environmental and population genomics * Genomics for food quality and gastrointestinal microbial communities of livestock * The first and second plant genome function During Meet&Greet sessions, there will be plenty of opportunity to discuss with the presenters about their experiences with applied genomics, and exchange ideas about future applications. We close the day with a networking reception. Deadlines and other practical information For up to date information on the symposium background, programme, venue, and registration<http://www.ilvogenomics.be/EN/Symposium/Registration/Registrationnon-ILVOem…>, please check our website<http://www.ilvogenomics.be/EN/Symposium/Home>. Registration fee: 50€ for non-ILVO employees, includes registration, lunch and reception. Maximum number of participants: 150 Deadline for registration: April 4st, 2016 With further questions, please do not hesitate to contact us at genomics_symposium(a)ilvo.vlaanderen.be<mailto:genomics_symposium@ilvo.vlaanderen.be> We are looking forward to meeting you in Melle. With kind regards, The Organizers

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BioSB 2016: extended abstract submission deadline - March 8
by Femke Francissen 01 Mar '16

01 Mar '16

*Dutch Bioinformatics & Systems Biology Conference 2016 (BioSB 2016)* Date: April 19 / 20, 2016 Venue: Congrescentrum De Werelt, Lunteren, Netherlands Conference website: http://www.aanmelder.nl/biosb2016 *Call for abstracts - Extended abstract submission deadline for oral presentations: March 8!* Abstract submission for the BioSB 2016 conference is now open. You can submit an abstract for the following topics/sessions: - Gene regulation - Genotype/phenotype & disease - Industrial applications & synthetic biology - Metabolomics - Modeling - Networks & data integration - NGS data analysis - Proteomics - Statistics - Systems medicine - Infrastructure (Technology track ELIXIR-NL) - Metagenomics - Structural bioinformatics (NSBM) You can submit an abstract for a lecture in one of the sessions, a poster presentation or a poster/demo. Find out here how to submit your abstract <https://www.aanmelder.nl/biosb2016/wiki/154972/abstract%20submission>. *Keydates* - *EXTENDED: *Abstract submission deadline for oral presentations: *March 8, 2016* - Notification date oral presentations: March 22, 2016 - Abstract submission deadline for posters: April 14, 2016 ** ** *Registration for the conference is open!* *Contact: * Femke Francissen, community manager BioSB, email: femke.francissen(a)biosb.nl **

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Invitation: BeMGI 2016-Brussels Annual Meeting
by marilou.ramospamplona＠ulg.ac.be 01 Mar '16

01 Mar '16

Dear BBC Colleagues, We cordially invite you to the 2016 Annual Meeting of the Belgian Medical Genomics Initiative (BeMGI) entitled "From predisposing germline and somatic variants to disease-driving mechanisms." The scientific program will take place on Wednesay, 13 April, 12h00-17h30 in the UCLouvain-Brussels campus. Keynote lectures will be given by Prof ALEXIS BRICE (Genetic basis and mechanisms of Parkinson’s disease.) and Prof CHRISTINE BELLANNÉ-CHANTELOT (Search for predisposing factors in myeloid malignancies.). The meeting will also feature a number of selected talks and poster presentations from the BeMGI partner institutes. This meeting is open to the public and will be eligible for Belgian RIZIV-INAMI medical accreditation. Registration & Abstract submission: http://bit.do/BeMGI2016register. Closing date: 31 March 2016. More info: http://bit.do/BeMGI2016facebook; BelgianMGI(a)gmail.com. The BeMGI network (www.bemgi.be) a PAI-Belspo project coordinated by Prof Michel Georges (University of Liège), works on collaborative activities (Research, Bioinformatics, Education, ELSI) to promote the clinical application of genomics research and technologies. Thank you. See you in Brussels in April! Regards, The BeMGI network

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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.

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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 )

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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. >

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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.

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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

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[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

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