- BBClist - maillist.psb.ugent.be

Junior PI meeting @ECCB: still time to register!
by Magali Michaut 26 Jul '14

26 Jul '14

** Registration deadline: August 1 ** Date of the meeting: 7 September 2014 http://www.eccb14.org/program/satellite-meetings/jpi Transitioning from Post-doc to (junior) PI is a major step in the scientific career ladder bringing new challenges to the scientist. Key among these challenges is moving from a single project-based responsibility to being responsible for the projects of students, technicians, and postdocs. On top of this, the researcher is expected to be a successful grant writer, a human resources manager, an engaging speaker, etc. In this meeting we aim to bring together scientists who have recently started or wish to start their own research group. This meeting will serve as a platform for building a community of junior PIs within the broader field of Computational Biology. The meeting will consist of (scientific!) speed-dating, short presentations and round-table discussions. Speakers: Sampsa Hautaniemi, University of Helsinki Lennart Martens, Ghent University, VIB Oliver Kohlbacher, University of Tübingen Sebastian Schultheiss, Computomics Alice C. McHardy, University Duesseldorf (ECCB keynote) Organizers: Virginie Bernard, Curie Institute, Paris, France Magali Michaut, Netherlands Cancer Institute, Amsterdam, the Netherlands Lennart Martens, Ghent University and VIB, Belgium Theodore Alexandrov, University of Bremen, Germany; University of California San Diego, USA Sponsor: F1000 Research We hope to see you in France in September! COSI JPI: http://cosi.iscb.org/wiki/JPI:Home contact: jpicontact(a)iscb.org ISCB COSIs: http://www.iscb.org/iscb-cosis

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Environmental Metagenomics Course & Symposium, 15-19 September 2014, Wageningen, the Netherlands
by Celia.vanGelder＠radboudumc.nl 26 Jul '14

26 Jul '14

Dear colleague, Metagenomics has quickly become one of the most important discovery tools in microbial ecology. Metagenomics is a powerful tool to study the organisms in microbial communities, that has numerous applications in many areas of biomedical science. By bypassing the need for laboratory culturing, this technology can unlock the massive uncultured microbial diversity, enabling the microbial component of specific environments to be surveyed, discover new organisms, and explore the dynamic ecology of microbial populations under changing conditions. The high throughput nature of metagenomics means that huge datasets are generated, and in order to extract biological information from these data, advanced bioinformatics and statistical tools are indispensable. >From 15-19 September 2014 we organize a five-day course at NIOO-KNAW in Wageningen. Participants will get hands on experience in the analysis and treatment of metagenomic data, including preprocessing and quality filtering, data handling and submission to public archives, annotation, multivariate statistical analyses, and metagenome assembly. Course website: http://nioo.knaw.nl/en/metagenomics-course . Course fee: 350 euro, including hotel accommodation. On the last day of the course, 19 September 2014, we are organizing an Environmental Metagenomics Symposium which will bring together renowned scientists in microbial ecology and bioinformatics, who will present their recent explorations of the microbiota of different environments. Moreover, we will welcome the presentations of several students of the metagenomics course held in the week leading up to this symposium. Together, this will be an exciting opportunity to see the latest advances in environmental metagenomics from young talents as well as established leaders in the field. The symposium is open for everyone interested in environmental metagenomics. Symposium website: http://nioo.knaw.nl/en/metagenomics-symposium Symposium fee: Attending the symposium is free of charge, but you have to register via the symposium website A pdf with the programme of both course and symposium is attached to this mail. The organization of course and symposium has been made possible with the generous support of AllBio.<http://www.allbioinformatics.eu/doku.php> Best regards, Bas Dutilh (Utrecht University & Radboudumc) Eiko Kuramae (NIOO-KNAW) Celia van Gelder (Radboudumc) Dr. Celia W.G. van Gelder Projectleader Education NBIC/BioSB Coordinator Education CMBI Programme Manager Learning DTL tel. +31-(0)24-3666120 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:C.vanGelder@umcn.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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Disease Comorbidities, Workshop ECCB'14 - Time to register!
by BAUDOT Anaïs 24 Jul '14

24 Jul '14

Dear all, We are pleased to announce the ECCB'14 satellite workshop dedicated to Disease Comorbidities that will take place Sunday, 7th September, 2014, in Strasbourg, France. The workshop is organised around 3 sessions scoping the discovery, the interpretation and the exploitation of disease comorbidities. Program and registration: http://www.eccb14.org/program/workshops/csbdc Sunday, 7th of September 9:00 - 17:00 Forum Building Strasbourg Faculty of Medicine Deadline for early registration: August, 1st !! Looking forward seeing you in Strasbourg, Anaïs Baudot and Alfonso Valencia

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Postodoctoral position (29 months) in bioinformatics at ULB, Brussels, Belgium
by chermans 23 Jul '14

23 Jul '14

Postodoctoral position (29 months) in bioinformatics Lab. of Plant Physiology and Molecular Genetics, Universite Libre de Bruxelles, Brussels, Belgium ********************** Genetic and nutritional influences on the root architecture of Brassicaceae species Nitrogen (N) is the quantitatively most important nutrient required by crops, however a considerable fraction of N fertilizer gets lost as runoffs with detrimental consequences to the environment and greenhouse gas emission. Faced with those pressing societal costs, innovation has to make a step change to improve Nitrogen Use Efficiency (NUE) of plants. While the root organ is largely out of sight, the proposal aims at modifying root architecture (more branched system) to take up N sources more efficiently and thereby provides a sustainable and bio-economical solution to maintain crop productivity whilst reducing N input. The goal of this research is to first identify the genetic determinism that regulate N-related root morphology in the model species Arabidopsis, then to use that information in parented Brassica crops for redesigning their root architecture and ultimately improve NUE. One post-doc fellowship for non-Belgian resident (29 months) - as early as August 2014 Bioinformatics analyses of genomic data (Arabidopsis thaliana and Brassica napus) Relevant experience: gene network regulation, data mining, comparative genomics, next-generation sequencing, RNAseq, genome wide association, ShoreMap Conditions: < 5 y after PhD, < 3 y residency in Belgium Enthusiastic bioinformatician researchers meeting these criteria are kindly invited to contact Christian HERMANS (chermans(a)ulb.ac.be) Include your CV, qualifications, publications list and the names of two academic referees whom I can approach prior to appointment. Applications must be received by August 15th 2014.

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Call for participation and posters - MLSB14, Machine Learning in Systems Biology
by Pierre Geurts 23 Jul '14

23 Jul '14

[Apologies for cross-postings] Call for Participation and Poster Presentation MLSB14, the eighth International Workshop on Machine Learning in Systems Biology http://www.mlsb.cc Organized in conjunction with ECCB 2014 Strasbourg, France, September 6-7, 2014. --- We invite you to join us for the eighth installment of Machine Learning in Systems Biology (MLSB) 2014, which will be held as a 2-day ECCB workshop on September 6 and 7 in Strasbourg, France The full program of MLSB 2014 can be found online at http://mlsb.cc The highlights of MLSB 2014 include five invited talks by * Pierre Baldi, UCI University, California, USA Carbon-Based Computing Vs Silicon-Based Computing: A New Theory of Circadian Rhythms Abstract * Anne-Laure Boulesteix, Department of Computational Molecular Medecine, IBE, Ludwig-Maximilians Universität München, Germany Title to be announced * Karsten Borgwardt, Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich Machine Learning for Personalized Medicine Abstract * Jean-Loup Faulon, IBSS, CNRS, Genopole, University of Evry, France Using Machine Learning in Synthetic Biology: The Design-Build-Test and Learn cycle Abstract * Nicola Segata, Centre for Integrative Biology, University of Trento, Italy Machine learning challenges in computational meta'omics One page abstract can still be submitted through the easychair submission system until August, 15 for poster presentation at the workshop: http://www.easychair.org/conferences/?conf=mlsb2014 Please note that the early registration deadline for MLSB/ECCB is August 1, 2014 (for registration visit http://www.eccb14.org/registration) We are looking forward to meeting you in Strasbourg! Best regards, Florence d'Alché-Buc and Pierre Geurts

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Workshop on “Exploiting and understanding Solanaceous genomes”
by Warris, Sven 21 Jul '14

21 Jul '14

Dear all, We have an announcement for a workshop on Solanaceous genomes. The workshop is free of charge. See attached documents for more information. Best, Sven Warris Workshop on “Exploiting and understanding Solanaceous genomes” Organised by the transPLANT Consortium[1], October 13-14, 2014 Wageningen, the Netherlands We are pleased to announce the 3rd transPLANT user Training Workshop in Wageningen, the Netherlands (Wageningen University & Research Centre) on October 13-14, 2014. transPLANT is a vibrant consortium of 11 European partners gathered to address the challenges of complex plant genome data integration and analysis. It aims to develop a trans-national infrastructure for plant genomic science. For details, please visit http://transplantdb.eu/. This third workshop (see detailed program below) focuses on current developments in plant data resources at transPLANT partner sites, with a special reference to Solanaceae and its genomes, especially tomato and potato. The workshop is targeted at (experimental) biologists and breeders who have needs to use these resources in everyday work to interpret own observations and plan new research objectives. No particular prior (informatics) knowledge or skills are required. In the different sessions, the workshop will introduce partner resources and tools, with emphasis on hands-on training how to obtain, search and use this data. The local organizer is Wageningen University & Research Centre (WUR), Applied Bioinformatics, Plant Research International. ________________________________ [1] The transPLANT project is funded by the European Commission since September 2011 within its 7th Framework Programme under the thematic area "Infrastructures", contract number 283496.

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Research Associate in Bioinformatics (Imperial College, London).
by Nicos Angelopoulos (Imperial College London) 21 Jul '14

21 Jul '14

Research Associate in Bioinformatics. Imperial College London - Department of Surgery and Cancer Applications are invited for a Research Associate (Bioinformatician) based within the Parturition Research Group at the IRDB Hammersmith Campus. This is a key post to join an exciting and expanding team implementing NMR and MS based metabonomics and next generation DNA sequencing (NGS) to the understanding and prediction of preterm labour. There will also be opportunities to work in a range of other women’s health problems including miscarriage, cervical cancer and urinary incontinence. The post is funded by SPARKS, the wider research team has funding from MRC, Action Medical Research, Genesis Research Trust and the National Institute for Health Research. The successful candidate will hold a PhD or equivalent qualification, ideally in Bioinformatics or Computer Sciences with good knowledge of metabonomics, metagenetics and transcriptomics Applicants should be motivated, well organised, with an ability to work effectively in collaborative research projects and cross disciplinary teams and to direct the work of a small research team and motivate others to produce a high standard of work. This post is full time and fixed term for 30 months and will be based at the Hammersmith Campus, located in East Acton. See on-line advert for contact information and further details: http://www.jobs.ac.uk/job/AJC906/research-associate/

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FW: Experienced bioinformatician
by Claesson, Marcus 16 Jul '14

16 Jul '14

Please see add below for a managerial bioinformatics position in Cork, Ireland. Subject: Experienced bioinformatician Hi there, NSilico is currently looking to recruit an experienced bioinformatician as part of a European funded research project. There is an excellent annual remuneration package of >€100k. There's also a possibility of a long term job after the project. Details of the position can be found at: http://www.cloudxi.eu/jobs.html Best, Nora

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PhD position in bioinformatics (Brussels, Belgium)
by Patrick 16 Jul '14

16 Jul '14

PhD position in “Whole-genome sequencing and genotyping of non-model Eukaryotes for evolutionary biology” * Project description New generation sequencing technologies offer exciting new prospects for studying evolution, but also create great challenges related to the large amount of sequence data to be analysed in a single project. We seek a PhD candidate that will work on developing software pipelines for whole genome sequencing and analyse genomic variation for non model organisms, for several evolutionary biology projects. The projects involved concern (1) investigating adaptation of an herbivorous insect to its host plant at the genomic level, (2) inferring demographic history of various plant species from genomic variation, and (3) identification of candidate sex pheromones from transcriptome sequencing. * Student skills The ideal candidate has a Masters Degree with a strong background in bioinformatics, with good programming and statistical skills, and a good understanding of the processes that govern biological evolution. Because the PhD candidate is expected to contribute to several projects, his ability to communicate and collaborate with others is essential. In general, the (IB)2 is a highly collaborative environment, and good interpersonal skills and an open attitude are expected. The candidate should also be fluent in English, the main language of the institute. Note that some language requirements (related to knowledge of english or dutch) have to be fulfilled for enrolment at the VUB (http://www.vub.ac.be/english/infofor/prospectivestudents/languagetest.html) * Promotor information The student will work at the Interuniversity Institute of Bioinformatics in Brussels (IB)2 (http://ibsquare.be) located on the campus of the Université Libre de Bruxelles (ULB), and will enrol at both ULB, with promotor Patrick Mardulyn (http://ebe.ulb.ac.be/) and Vrije Universiteit Brussel (VUB), with promotor Tom Lenaerts (http://www.ulb.ac.be/di/map/tlenaert) Other co-promotors will supervise specific aspects of the research: Olivier Hardy (ULB, http://ebe.ulb.ac.be/) Ludwig Triest (VUB, http://www.vub.ac.be/APNA/staff/Triest/) Guillaume Smits (ULB, http://ibsquare.be) and Franky Bossuyt (VUB, http://www.amphibia.be) * Important note We can only guarantee one year of funding; prospects exist for full 4 years funding, but this will depend on the success of project grant applications and/or on personal grant applications by the candidate. Full support will be provided by the promotors to succeed with personal grant applications. * Interested? Please send a CV, letter of motivation, and contact information of two references to Patrick Mardulyn (pmarduly(a)ulb.ac.be) Further enquiries about the position can be directed to the same address. The candidate is expected to start 1st October 2014 and the position will be filled as soon as a suitable candidate is found. —————————— Patrick Mardulyn Evolutionary Biology and ecology, CP 160/12 Free University of Brussels (ULB) av. FD Roosevelt 50 1050 Brussels Belgium Phone: (32)(2)6502649 Fax: (32)(2)6502445 e-mail: pmarduly(a)ulb.ac.be homepage: homepages.ulb.ac.be/~pmarduly/ lab website: http://ebe.ulb.ac.be/ebe/ebe-Welcome.html

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PHD candidate position - Bioinformatics of microRNA regulation in Alzheimer’s disease
by Mark Fiers 14 Jul '14

14 Jul '14

Dear all, we're looking for a motivated PhD candidate to work on the bioinformatics of miRNA regulation in Alzheimer's. See here for more details: http://www.vib.be/en/jobs/Pages/PHD-candidate---Bioinformatics-of-microRNA-… thanks Mark

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