- BBClist - maillist.psb.ugent.be

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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Fwd: RCAM2015 - Announcement and call for abstracts
by Magali Michaut 28 Jun '15

28 Jun '15

> > > > > > ------------------------------------------------------------------ > 2nd Edition of the Workshop > > Recent computational advances in metagenomics (RCAM'15) > ------------------------------------------------------------------ > > 6th October, 2015 > Institut Pasteur, 28 rue du Dr, Roux, Paris, France > Satellite Workshop of GdR BiM 2015 > > IMPORTANT DATES > --------------- > Submission Deadline (abstract) 6th September, 2015 > Notification 14th September, 2015 > Registration Deadline: 1st Octobre, 2015 > Workshop Date 6th October, 2015 > > > OBJECTIVES > ---------- > > This workshop aims at promoting discussions and collaborations between > biologists (modelers), computer scientists and applied-mathematicians > involved in metagenomics and/or metatranscriptomics studies, either in > the bioinformatics or statistical aspects of such analysis. > > Metagenomics studies refer to analyses based on high-throughput > sequencing of environmental samples and microbial ecosystems. Both > marker-gene (16S, 18S, ITS, ...) and whole-genome strategies will be > adressed to cover a wide array of question ranging from quantifying > the microbial diversity in order to find structuring factors to > assessing the functional role of microbial communities. > > The workshop will provide an overview of the state-of-the-art methods > currently used in metaomics including comparative metagenomics and > metatranscriptomics. At the other end of the spectrum, case-studies > will illustrate how these methods produce insightful biological > knowledge. > > > SCOPE > ----- > > The program of this workshop will consist mainly of presentations of > refereed papers (30 minutes) and invited talks (50 minutes). Contributions are > welcomed on all aspects about bioinformatics and statistical analyses > of metaomics datasets, including, but not limited to: > * new methods, tools or pipelines involved in the characterisation of microbial diversity, > * original methods for taxonomical assignment, > * data reduction, > * comparative metaomics, > * models for community assembly, > * challenges for tackling the complexity of metaomics datasets. > > CONFIRMED SPEAKER > ----- > > Christopher Quince, University of Glasgow > > SUBMISSION > ---------- > > Please send the abstract to rcam(a)jouy.inra.fr > > All submitted abstracts will be peer-reviewed by the program committee. > Submitted abstracts should not exceed 2 pages including bibliography, > > Abstracts must be written and presented in English. They may describe > work that has already been published or that is simultaneously > submitted to a journal, conference, or workshop with refereed > proceedings. > > REGISTRATION > --------------- > The worskhop is free of registration fees but registration still mandatory > though the registration form (to come) available at > http://maiage.jouy.inra.fr/?q=fr/rcam2015 > Registration will close on October 1st. > > IMPORTANT DATES > ----------------------------- > Submission Deadline (abstract): September 6th 2015 > Notification: September 14th 2015 > Registration deadline : October 1st 2015 > Workshop Date: October 6th 2015 > > ORGANIZERS > ---------- > Anne-Laure Abraham, INRA/MICALIS, Jouy-en-Josas, France > Valentin Loux, INRA/MaIAGE, Jouy-en-Josas, France > Mahendra Mariadassou, INRA/MaIAGE, Jouy-en-Josas, France > Eduardo Rocha, Institut Pasteur, Paris, France > Sophie Schbath, INRA/MaIAGE, Jouy-en-Josas, France > > SPONSOR > ------------------ > The workshop is supported by the metaprogramme "Metaomics of Microbial Ecosystems (M2E)" from the French National Institute for Agricultural Research (INRA) and the Institut Pasteur. > > > >

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group leader Bioinformatics
by Vera van Noort 25 Jun '15

25 Jun '15

Please forward to possible candidates: Group Leader position with start-up package in Bioinformatics NCMM is seeking new outstanding international candidates for the position of group leader with a start-up package in bioinformatics. We expect to hire one new principal investigator through this call and particularly encourage international applicants. The successful candidate is expected to initiate a new independent research program integrating bioinformatics and experimental science with a clear relevance to molecular medicine and disease mechanisms. The bioinformatics research should be closely linked to biological research in the same disease areas. NCMM provides attractive sustainable support packages for new group leaders of more than 2.0 million EUR over the first five-year period. This includes salaries of the group leader, a postdoctoral fellow, a doctoral student as well as a programmer / technician, consumables and modern laboratory facilities.The candidate is expected to complement this budget through other national or international grants and/or through industrial collaborations. Application deadline: July 2, 2015 See: http://www.ncmm.uio.no/open-positions/group-leader-position-with-start-up-pa ckage-in-bio.html and link to full add and web-based application portal, here: http://uio.easycruit.com/vacancy/1388168/70932?iso=no Best regards, Kjetil Kjetil Taskén, Professor of Medicine, M.D., Ph.D.; Director, Centre for Molecular Medicine Norway, Nordic EMBL Partnership; Director, The Biotechnology Centre of Oslo; University of Oslo P.O. Box 1125, Blindern N-0317 Oslo NORWAY Phone: +47-22840505 Fax: +47-22840506 Cellular phone: +47-90860759 email: kjetil.tasken(a)ncmm.uio.no or kjetil.tasken(a)biotek.uio.no Web: www.ncmm.uio.no <http://www.ncmm.uio.no/> or www.biotek.uio.no <http://www.biotek.uio.no/> -- Vera van Noort Professor Computational Systems Biology KU Leuven - Faculty of Bioscience Engineering Kasteelpark Arenberg 22 box 2460 3001 Leuven Belgium URL: www.biw.kuleuven.be/m2s/cmpg/research/CSB

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[Gtpb] GTPB PGDH15 Training Course REMINDER deadline June 28th
by Pedro Fernandes 24 Jun '15

24 Jun '15

REMINDER 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: June 28th 2015 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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Job announcement: Postdoc position in Cancer Bioinformatics
by Can Kesmir 24 Jun '15

24 Jun '15

Dear all We have an exciting postdoc position available in cancer bioinformatics, that should be filled in as soon as possible. *Job description* The postdoc will be part of a joint international effort to implement personalized immunotherapy, targeting unique tumor associated mutations in patients. This is an exciting position at the crossroad of the blooming field of cancer genomics, and immunological bioinformatics. The postdoc will be working on two main projects: 1) evaluation and further development of existing models to predict the likelihood that a presented tumor mutation (in the form of a peptide-MHC complex) is recognized by the patient’s immune system, and 2) based on the primary sequence information of T cell receptors, predict their most likely ligands (e.g., mutations found in the individual patients). These innovative and ambitious projects will be performed in close collaboration with Prof. Ton Schumacher from Dutch Cancer Institute (NKI). The position is part of the EU Horizon2020 project called "APERIM: Advanced bioinformatics platform for PERsonalised cancer Immunotherapy” (H2020-PHC-2014), consisting of eight academic partners and three companies. *Qualifications* We are looking for a bioinformatician at the postdoc level with a keen interest in immunology and/or cancer. The position can be converted into a PhD student in case we have an excellent candidate. Applications from cancer immunologists with some computational experience are highly welcome. * Offer* The candidate is offered a full-time position for three years.The salary is supplemented with a holiday bonus of 8% and an end-of-year bonus of 8,3% per year. In addition we offer: a pension scheme, a partially paid parental leave, flexible employment conditions <http://www.uu.nl/EN/informationfor/jobseekers/Working-for-Utrecht-Universit…>. Conditions are based on the Collective Labour Agreement Dutch Universities. The research group will provide the candidate with necessary support on all aspects of the project. *About the organisation* Utrecht University <http://www.uu.nl/en> has great ambitions for its teaching quality and study success rates. This also applies to its clear research profiles which are centred around four themes: Dynamics of Youth, Institutions, Life Sciences and Sustainability. Utrecht University plays a prominent role in our society and contributes to finding the answers to topical and future societal issues. The Faculty of Science <http://www.uu.nl/en/organisation/faculty-of-science> consists of six departments: Biology, Pharmaceutical Sciences, Information and Computing Sciences, Physics and Astronomy, Chemistry and Mathematics. The Faculty is home to 3500 students and nearly 2000 staff and is internationally renowned for the quality of its research. The Faculty's academic programmes reflect developments in today's society. The theoretical biology and bioinformatics <http://tbb.bio.uu.nl/> (TBB) group at the Biology department of Utrecht University employs computational and mathematical models and bioinformatics to perform fundamental biological research in a variety of biological disciplines, and part of the group is specialized in immunology (Prof. Rob de Boer and Dr. Can Kesmir). We have long a standing expertise in modeling the immune system and in applying bioinformatics (mainly data-driven methods) to predict the specificity of the immune responses. The group is part of the Institute of Biodynamics and Biocomplexity <http://www.ibb-uu.nl/> (IBB <http://www.ibb-uu.nl/>), embedded in one of the largest Biology departments in the Netherlands (>200 new students per year). We are part of the Utrecht Center for Quantitative Immunology <http://tbb.bio.uu.nl/ucqi>(UCQI <http://tbb.bio.uu.nl/ucqi>), which brings together an experienced collaborative team of immunologists, bioinformaticians, and mathematical modelers. This unique position allows daily collaboration with wet lab immunologists and biologists. The group teaches modeling and bioinformatics to biology students at the bachelor and master level. PhD students in the group have diverse backgrounds ranging from biology, physics to mathematics, and typically half of them are from abroad. The IBB focuses on molecular life sciences, and is collaborating with other departments of the Faculty of Science, the Faculty of Medicine, and the Hubrecht Institute in Utrecht. UCQI is a joint effort between Utrecht University and the Utrecht Medical Center. *How to apply?* Application deadline is 1st of July. Please use the following link to apply: https://lnkd.in/dPDXR_7

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