- BBClist - maillist.psb.ugent.be

Just two weeks left until ICBO 2015 in Lisbon
by Francisco Couto 15 Jul '15

15 Jul '15

There are still places available to join your fellow ontologists in Lisbon for the International Conference on Biomedical Ontology. Lisbon is a historical and cultural city by the sea, with a mixed panorama of modern and medieval architecture. ICBO will be held at the Faculdade de Ciencias Campo Grande Campus, just a short metro ride from the city centre. Don’t miss out on the great weather, great discussions and great food! The schedule of the full event, including two days of workshops and two days of main conference sessions, is now available online at http://icbo2015.fc.ul.pt/program.html#schedule. Registration is open at http://icbo2015.fc.ul.pt/registration.html.

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PhD in Australia
by Stephane Rombauts 13 Jul '15

13 Jul '15

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PhD projects@JCU on shrimp aquaculture and evolutionary genomics: https://research.jcu.edu.au/itrh-apb/vacancies We are looking for students with skills in genomics, transcriptomics and evolutionary bioinformatics for the following projects: Project 5 - Functional transcriptomics of viral infection in the black tiger prawn (James Cook University and CSIRO) This project will examine whether the manner in which a black tiger prawn ( Penaeus monodon ) is challenged with Gill-associated virus (GAV) affects what defence response pathways can be activated to protect the prawn against infection/disease. Essential components of the project will be GAV challenge trials in P. monodon and the generation and interrogation of RNAseq data to identify/predict genes and gene pathways activated in response to GAV challenge via the various infection routes examined. Silencing of gene expression using RNA interference (RNAi) will also be employed to further explore the functioning of genes predicted to have pivotal roles in the prawn defence response. The desired candidate will preferably have a background in molecular genetics along with skills in next-generation sequencing approaches and computational analyses. ____________________________________________________________________________________________________________________ Project 6 - Comparative, evolutionary and functional genomics of the black tiger prawn (University of Sydney & James Cook University) This project will be a component of the full genome assembly of an inbred black tiger prawn ( Penaeus monodon ) based on a combination of short-read sequences and standard mate-pair end Illumina together with the use of long-read sequencing data based on PacBio, HiC, Nanopore platforms for improved hybrid assembly (scaffold/chromosome level). After the genome is annotated thoroughly, the project will aim to find syntenic blocks and reconstruct the evolutionary history of Decapods/crustaceans by comparing the P. monodon genome to the genomes of Daphnia , Artemia , Litopenaeus vannamei and potentially of other decapods/crustaceans. The desired candidate will preferably have a background in molecular genetics along with skills in next-generation sequencing approaches and computational analyses. -- Stephane Rombauts Senior staff scientist Tel:+32 (0)9 331 38 21 Department of Plant Systems Biology VIB, Ghent University Technologiepark 927 9052 Ghent, Belgium http://www.psb.ugent.be

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Registration is open for the Utrecht Bioinformatics Center Symposium, Monday sept 14th 2015
by Breukelen, B. van (Bas) 08 Jul '15

08 Jul '15

The UBC proudly announces the: Annual UBC Bioinformatics (Mini) Symposium Everyone who is interested in bioinformatics and would like to hear a few great talks is welcome to attend. There is no fee at all, we only ask you to register yourself to make sure that there are enough chairs to sit on, coffee at the start and drinks afterwards. You can register by clicking on the link below or via http://ubc.uu.nl : http://www.eventbrite.nl/e/ubc-annual-mini-symposium-registration-149561201… Programme: 13:00 Welcome with coffee and tea 13:15 Introduction * Berend Snel: Welcome and Utrecht Bioinformatics Center progress report 13:30 Wouter de Laat: Gene regulation in the 3D genome 14:00 Alexandre Bonvin: Structure, affinity and specificity riddles in biomolecular interactions 14:30 Coffee and tea break 15:00 Frank Holstege: Understanding regulatory circuitry through large-scale genetic perturbation analyses 15:30 Keynote: Søren Brunak: Creating Disease Trajectories from Big Biomedical Data covering Millions of Patients 16:15 Reception (till 18:00) The UBC symposium is an ideal way to meet and talk to other bioinformaticians in the field and perhaps start some interesting collaborations. Everyone is welcome, See you soon, Berend Snel, Patrick Kemmeren and Bas van Breukelen p.s. Please spread the word: You are welcome to forward this mail to anyone you think might be interested in this symposium. 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:2CDF3FE1-6FA1-40F3-A816-1D933B578100@science.uu.nl]

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PhD Position in Plant Bioinformatics (Ghent Belgium)
by Michiel Van Bel 08 Jul '15

08 Jul '15

Dear colleague, The department of Plant Systems Biology (VIB-UGent) is currently looking for an assistant computational scientist. More information available at: http://www.psb.ugent.be/jobs/412-assistant-computational-scientist kind regards -- Michiel Van Bel Postdoctoral fellow Tel:+32 (0)9 331 36 95 Department of Plant Systems Biology VIB, Ghent University Technologiepark 927 9052 Ghent, Belgium http://www.psb.ugent.be

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Vacancy PhD student at RIVM
by Annelies Kroneman 03 Jul '15

03 Jul '15

Dear Colleagues, The department of virology at the RIVM in Bilthoven, the Netherlands, has a job opportunity for a PhD in bioinformatics. Please find information on this position at: www.academictransfer.com/28690 Candidates can apply via the online form (in Dutch) or by sending their CV and motivation letter to vacature(a)rivm.nl. Kind regards, Annelies Kroneman RIVM Centre for Infectious Disease Control Virology department Proclaimer RIVM http://www.rivm.nl/Proclaimer

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Ph D fellowship environmental transcriptomics available at Ghent University
by Karel De Schamphelaere 03 Jul '15

03 Jul '15

Dear all, Our research group is currently looking for a highly motivated researcher with lots of scientific curiosity, high interest in 'big data analysis' and with a strong educational record in molecular biology, genome biology, biotechnology or bioinformatics. The selected candidate will be able to work for 4 years as a Ph D fellow on a project entitled: "Developing a mechanistic understanding of the combined impact of chemical pollution and climate change across different organisms and habitats". The project will predominantly make use of nextgen mRNAseq data. You can submit your application until August 3rd, 2015 via E-mail to Karel.Deschamphelaere[at]UGent.be and Jana.asselman[at]UGent.be. More details on the project and application procedure can be found in the attachment. Best regards, Karel Karel De Schamphelaere, Ph D Associate Professor www.ecotox.ugent.be Follow us on Twitter @GhEnToxLab Ghent University (UGent) Laboratory of Environmental Toxicology and Aquatic Ecology Environmental Toxicology Unit (GhEnToxLab) Jozef Plateaustraat 22 B9000 Gent Belgium Tel. +32 9 264 3764 Fax +32 9 264 3766 skype karel.de.schamphelaere Researcher ID: <http://www.researcherid.com/rid/A-1600-2008> http://www.researcherid.com/rid/A-1600-2008 Disclaimer: <http://helpdesk.ugent.be/e-maildisclaimer.php> http://helpdesk.ugent.be/e-maildisclaimer.php

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BioSB course RNA-seq data analysis course (5th edition), 7-9 September 2015
by Celia.vanGelder＠radboudumc.nl 30 Jun '15

30 Jun '15

BioSB RNA- seq data analysis course (5th edition) Date: 7-9 September, 2015 Location: Leiden, the Netherlands Course coordinators: Peter-Bram 't Hoen (LUMC), Jan Oosting (LUMC), Celia van Gelder (BioSB, education(a)biosb.nl<mailto:education@biosb.nl> ) Course website: http://biosb.nl/education/course-portfolio/rna-seq/ . Registration: http://biosb.nl/education/enrollment-rna-seq/ More information: education(a)biosb.nl<mailto:education@biosb.nl> Course description BioSB/and partner LUMC are organizing a 3-day course on RNA-seq. This is an expert course for people with experience in NGS and a follow-up course on the general NGS data analysis course (coordinator Jeroen Laros, LUMC). The course will consist of seminars and hands-on command line, Galaxy and R practicals and will focus on data preprocessing, quality control, alignment, visualization and statistics for differential transcript expression. Examples will be taken from human and mouse studies. The course does not cover prokaryotic RNA profiling nor plant- and metagenomics aspects. Course topics RNA-seq experimental approaches Alignment and de novo assembly Statistics for differential gene expression eQTL analysis and allele specific expression Variant calling and RNA editing Small RNA profiling Software for RNA-seq data analysis Programme The tentative programme can be found here: http://biosb.nl/wp-content/uploads/2015/06/Preliminary_RNAseq2015_program.p… Target audience Participants for the RNA-seq course should preferably have participated in the general NGS course or otherwise have demonstrated hands-on experience with NGS data analysis. The course is aimed at PhD students and post-docs, but scientific programmers and data analysts with a background in biology and bioinformatics may also attend. Registrations will be handled on a first-come-first-served basis but experience and motivation will be reviewed. Seats have been reserved for participants in the FP7-funded project RD-Connect and Marie Curie European Training Network TranCYST. BioSB Course Programme This course is part of the Course Portfolio<http://biosb.nl/education/course-portfolio-2/> of BioSB, 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>. More information For more information about the course you can contact Celia van Gelder at education(a)biosb.nl<mailto:education@biosb.nl>. Dr. Celia W.G. van Gelder Education Manager BioSB Coordinator Education CMBI Programme Manager Learning DTL/ELIXIR-NL tel. +31-(0)24-3666120 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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Job: Bioinformatician | NGS Diagnostic Testing @ Dept. Hum. Gen., Liege Univ. Hospital, BELGIUM
by Leonor Palmeira 30 Jun '15

30 Jun '15

Dear all, The department of Human Genetics of the University Hospital of Liège is looking for a bioinformatician who is interested in designing, developing, and managing data analysis solutions that have direct impact on Medical management of patients. Our department develops NGS diagnostics tests in the field of human genetics requiring robust data analysis, in order to implement these tests in a diagnostic medical context. *Job description* • Development and validation of NGS data analysis pipelines in diagnostics • Development of quality control and data management tools • Interacting/collaborating with internal and different national bioinfomatics teams • Writing and presenting reports • Organizing internal training sessions *Desired Skills and Experience* • Master Level Degree in either Engineering, Computational Biology, Computer Sciences or Physics with a complementary Master in Bioinformatics, • Experience in bioinformatics, • Knowledge in probabilities and statistics, • Background in data management and analysis, • Solid experience in NGS data handling, distributed computing, development and maintenance of NGS pipelines, • Excellent programming skills and experience in Perl/Python and R, • Fluent in English; knowledge of Dutch and French is an asset, • Candidates are expected to be autonomous and have personal initiative regarding their field of expertise as well as be able to work effectively as part of a team. *Our offer* • A fulltime contract • You will be based in Liège (Belgium) Review of applications starts on* August 24*. Please send your application letter, including your CV and the names of 2 referees, to vbours(a)ulg.ac.be

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[Gtpb] Bioinformatics Training course announcemet PDA15 Proteomics Data Analysis
by Pedro Fernandes 30 Jun '15

30 Jun '15

COURSE ANNOUNCEMENT We are pleased to inform you that the applications for the upcoming training course PDA15 - Proteomics Data Analysis with Lennart Martens, Harald Barsnes and Marc Vaudel are open. IMPORTANT DATES for this Course Deadline for applications: July 31st 2015 Latest notification of acceptance: August 1st 2015 Course date: September 7th - September 10th 2015 Full details at http://gtpb.igc.gulbenkian.pt/bicourses/PDA15/ Course description Mass spectrometry based proteomic experiments generate ever larger datasets and, as a consequence, complex data interpretation challenges. In this course, the concepts and methods required to tackle these challenges will be introduced, covering both protein identification and quantification. The course will rely exclusively on free and user friendly software, all of which can be directly applied in your lab upon your return from the course. An introduction to the available online resources and repositories will also be given. Here you will see how to link the results from proteomic experiments with external data to conduct pathway, gene ontology and interaction analyses. In the course, you will also learn how to submit data to the ProteomeXchange online repositories, and how to browse and reprocess publicly available data from these repositories. The course will provide a solid basis for beginners, but also new perspectives to those already familiar with standard data interpretation procedures in proteomics. Thank you for your interest, Pedro Fernandes -- Pedro Fernandes GTPB 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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[Gtpb] Fwd: GTPB PGDH15 Training Course NEW DEADLINE for applications July 1st
by Pedro Fernandes 29 Jun '15

29 Jun '15

NEW DEADLINE for APPLICATIONS Dear friend, Applications are still open for PGDH15 Population Genetics and Demographic History: model-based approaches with Mark Beaumont, Lounes Chikhi, Willy Rodriguez and Barbara Parreira IMPORTANT DATES for this Course Deadline for applications: July 1st 2015 <========== NEW! Latest notification of acceptance: July 1st 2015 Course date: July 6th - July 9th 2015 Details are available at: http://gtpb.igc.gulbenkian.pt/bicourses/PGDH15/ Course description Genetic data are increasingly used by ecologists and evolutionary biologists in general. It has thus become important for many biologists with different levels of experience to produce and analyse genetic (and genomic) data. In this course we will take a practical approach to the analysis of genetic data, but we will also provide some of the theoretical background required to understand the outputs of the software used. This course will be organised so as to mix lectures where important notions are introduced with practicals where freely available software will be used. While this will not be the focus of the course, we will also introduce and discuss genealogical (coalescent-based) simulation methods and those based on forward-in-time simulations. Altogether this will allow to discuss the potentialities and limitations of the tools available to the community. In this four-day course we will introduce the main concepts that underlie many of the models that are frequently used in population genetics. We will focus on the importance of demographic history (e.g. effective sizes and migration patterns) in shaping genetic data. We will go through the basic notions that are central to population genetics, insisting particularly on the statistics used to measure genetic diversity and population differentiation. The course will also cover a short introduction to coalescent theory, Bayesian inference in population genetics and data simulation, as they are connected to what makes landscape genetics today on the basis of multilocus data. We will also introduce two methods that have been recently developed to analyse genomic data. The PSMC of Li and Durbin reconstructs the demographic history of a species or population with the genome of a single individual. The Rehh package is an R implementation of the Extended Haplotype Homozygosity (EHH) test for selective sweeps and looks for signals of selection based on the analysis of genomic regions. Most theory will be put into practice in practical sessions, analyzing real and/or simulated datasets. In these sessions, we will look at measures of genetic diversity and differentiation and use methods to detect population structure as implemented in the program STRUCTURE and discuss related programs such as FastSTRUCTURE. We will learn how to perform coalescent simulations of genetic data (using SPAms and ms). Some exercises will make use of R scripts (R being a freely available statistical program). Basic R knowledge is a pre-requisite but we will provide a short introduction to R. The R statistical package is a very powerful tool to analyse data outputs from many population genetics software, and can also be used to simulate genetic data under simple demographic scenarios. Thanks for your interest, Pedro -- Pedro Fernandes GTPB 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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