January 2014 - BBClist - maillist.psb.ugent.be

BBC 2013 abstract submission through EasyChair
by BBC2013 01 Apr '14

01 Apr '14

BBC2013 – BeNeLux Bioinformatics Conference 2013 Date: December 9 & 10, 2013 Venue: Salle Dupréel (Université Libre de Bruxelles), Brussels, Belgium Website: http://bbc2013.ibsquare.be Abstract submission deadline: October 1, 2013 Early registration deadline: November 1, 2013 Dear Colleagues, The 8th edition of the BeNeLux Bioinformatics Conference will take place in Brussels on the 9th and 10th of December 2013. The theme of this year's conference is: "Bioinformatics at all scales of life". Since 2005, the BeNeLux Bioinformatics Conference gives bioinformaticians, from the BeNeLux and beyond, the opportunity to discuss their results and build new collaborations, in a relaxed and friendly atmosphere. This year's edition will be enhanced by the presence of three distinguished keynote speakers: Alfonso Valencia (Spanish National Cancer Research Center, http://bit.ly/14SAITQ) Anna Tramontano (University of Rome "La Sapienza", http://www.biocomputing.it) and Jim Haseloff (Plant Synthetic Biology, University of Cambridge, http://www.haseloff-lab.org) Call for abstracts We invite you to submit an abstract for an oral presentation (20 available slots: 6 long, 14 short) and/or a poster presentation. Contributions from all fields of bioinformatics are welcome and encouraged. We have provided a template to use for submission through the EasyChair system: https://www.easychair.org/conferences/?conf=bbc2013 . Details on the submission procedure can be found at http://bbc2013.ibsquare.be/content/call-abstracts . We hope to see you all in Brussels! -- The BBC 2013 organising committee BeNeLux Bioinformatics Conference 2013 December 9-10, 2013 (Brussels)

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Open industrial position: Computational scientist immunology at Janssen, Beerse
by Ceulemans, Hugo [JRDBE] 31 Jan '14

31 Jan '14

Computational Scientist position Date: 30-Jan-2014, for updates on position availability and application, kindly visit http://bit.ly/1eiF2Ee Company: Janssen, Johnson & Johnson Location Beerse, BE Description Janssen Discovery Sciences is supporting transformational research harnessing state-of-the-art multi-parametric platforms and systems analysis of the immune response in preclinical models and clinical studies to identify and evaluate innovative interventions in oncology, pathogenic infections and auto-immune diseases and guide prophylactic and therapeutic vaccine development. This commitment aims to bridge the gap between the single molecule/single regimen pharmacology and the orchestration of host response in animal models and in the clinic, taking into consideration the cooperative and cross-talking, non-linear processes of immune cells transitioning in a continuum of states and leading to emergent deleterious or disease resolving behaviors. Internal investments in mass cytometry, high-content imaging, single cell sequencing and access to new emerging platforms that allow the systematic evaluation of single cell behaviors with a buildup of a network of key strategic academic partners in the evolving scientific field are key components of our systems immunology strategy. SCOPE A major scope is the integration of high dimensional data from preclinical and clinical compound profiling studies and disease models, often from different biological levels single cell, tissue and patient level. Contribution to the design and the selection of new experiments and studies is an integral part of the role. The transition to tractable molecular determinants and experimental model systems will demand close coordination with the experimental scientists to identify relevant and testable hypotheses as well as assayable readout combinations. Collaborations with game-changing scientific teams in the field should provide a choice of optimal analysis and modeling approaches, also driven by incentives to publish the non-proprietary new science. Qualifications - PhD in Computational Biology or a related multidisciplinary field with at least three years of post-doctoral experience in an academic or industrial setting in the field of host response or related fields, focusing on the analysis and modeling of control mechanisms of heterogeneous multicellular processes. - Demonstrated experience with high-dimensional data integration and biological interpretation that led to hypothesis driven simulation and experimental testing. - Demonstrated experience in handling high-dimensional single cell data, e.g. mass cytometry, high-content imaging derived features, single cell transcriptomics, and their integration at the population level. Strong programming and scripting skills that enable the development of functional prototypes. Experience in the analysis of genomics, proteomics, image analysis and/or flow cytometry data using R/Bioconductor or similar software. Experience with graph based probabilistic modeling, ODE/PDE based modeling or related predictive approaches would be an asset - Excellent communication, reporting and team working skills, yet able to work independently Primary Location:Europe/Middle East/Africa-Belgium-Antwerp-Beerse Organization: Janssen Pharmaceutica N.V. Job Function: R&D

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NSBM Spring meeting 2014 April 8th - NBIC Conference
by Barbara.vanKampen＠radboudumc.nl 31 Jan '14

31 Jan '14

[logo.png]NSBM Spring meeting April 8th 2014 In conjunction with the Netherlands Bioinformatics Conference 2014 Venue: Congrescentrum De Werelt, Lunteren The Netherlands Society on Biomolecular Modelling (NSBM) cordially invites you to visit its spring meeting, a topical track of the Netherlands Bioinformatics Conference 2014 (NBIC2014) on April 8th 2014. During several parallel sessions, the floor will be given to PhD students and postdocs who study protein structure and/or structural bioinformatics or related topics (see a list below). Speakers and attendees will have the opportunity to join the NBIC2014 activities and visit keynote lectures of a.o. Yves van de Peer (VIB UGent, Belgium). Programme April 8th Invited speaker: Christian Ottmann<https://www.aanmelder.nl/nbic2014/wiki/christian%20ottmann>, Eindhoven University of Technology, the Netherlands Abstract submission All abstracts should be submitted via the NBIC2014 abstract submission system<https://www.aanmelder.nl/nbic2014/wiki/abstract%20submission>. Please indicate in the form that you are submitting for the NSBM Spring meeting. Starting PhD students are particularly encouraged to present their research! For questions regarding the abstract or meeting please contact Gert Vriend, gerrit.vriend(a)radboudumc.nl<mailto:gerrit.vriend@radboudumc.nl> Topics for presentations may include, but are not limited to: * Computational Biology and Bioinformatics * Computer-aided drug design * Drug design and drug discovery * Grid computing * Homology modelling * Molecular and supramolecular dynamics * Molecular modeling and simulation * Mutational analysis * Protein crystallography * Protein NMR * Protein structure analysis * Protein structure prediction * Protein-protein interactions * Protein-small molecules interaction * Protein software design * Proteomics * Structural bioinformatics * Structure-function analysis * Text mining & information extraction * Virtual screening Registration Registration should be done via the NBIC2014 registration form<https://www.aanmelder.nl/nbic2014/wiki/registration>. Registration for the conference (for one day/April 8th) includes: participation to conference and evening poster session on April 8th, lunch, coffee/tea during breaks, internet access and conference dinner. Should a lack of funding be a hurdle for visiting the NSBM Spring meeting, please contact prof. Gert Vriend at gerrit.vriend(a)radboudumc.nl<mailto:gerrit.vriend@radboudumc.nl> so that an arrangement can be made. Key dates * Abstract submission deadline for oral presentations: February 23, 2014 * Notification date selection oral presentations: March 4, 2014 * Abstact submission deadline for posters & demos: April 4, 2014 Sponsored by: [DSM]<http://www.dsm.com/> [Genalice] <http://www.genalice.com/> [Keygene NV]<http://www.keygene.com/> [Bio-prodict] <http://www.bio-prodict.nl/> NSBM Mailing list --- NEW EMAIL: barbara.vankampen(a)radboudumc.nl Barbara van Kampen [Radboudumckleine.png] CMBI 260 Radboud University Medical Centre / RIMLS CMBI Office / Room 0.02 PO Box 9101 Geert-Grooteplein 26-28 6500 HB Nijmegen 6525 GA Nijmegen Phone: +31(0)24 36 19390 Fax: +31 (0)24 36 19395 www.cmbi.ru.nl<http://www.cmbi.ru.nl/> 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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Allbio Metagenomics meeting @ NBIC Conference
by Bas E. Dutilh 29 Jan '14

29 Jan '14

Dear colleagues, Like last year, we are filling one day at the Netherlands Bioinformatics Conference with Metagenomics: the Allbio Metagenomics meeting on April 9, 2014 in Lunteren! Our keynote speaker will be Marcus Claesson from the University College Cork, who will be speaking about his work on inflammatory bowel disease. The remainder of the presentations will be selected from submissions, so please upload your abstracts for consideration for a talk and/or poster through the conference web site. Registration is now open: https://www.aanmelder.nl/nbic2014/wiki/metagenomics%20topical%20track. The poster is attached, please spread it among any interested colleagues. We are looking forward to an interesting day! Best regards, the organizing commitee, Sacha and Bas -- Dr. Bas E. Dutilh CMBI | NCMLS | Radboud University Medical Centre http://www.cmbi.ru.nl/~dutilh

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Introduction & Employment Opportunity
by Ricardo Savedra 28 Jan '14

28 Jan '14

Hello - My name is Ricardo and I am employed by a US-based CSO. We are currently looking to recruit a PhD-level BioComputational Biologist to one of our Client Teams (located in Beerse). I would like to make the following URL (which contains all of the job requirements) available to your members: http://www.linkedin.com/jobs2/view/11219974?trk=job_nov I can be contacted at rsavedra(a)labconnectllc.com for those who are interested or require additional information. Thank you! Best, Ricardo [Description: Description: LCLogoSmall]Ricardo Savedra, PhD, MBA | Associate Director, Scientific Operations | o: 314.632.6215 | c: 314.853.7425 | rsavedra(a)labconnectllc.com<mailto:rsavedra@labconnectllc.com> LabConnect, LLC ● 605 1st Avenue, Suite 300 ● Seattle, WA 98104 ● www.labconnectllc.com<http://www.labconnectllc.com/>

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Post-doctoral position in bioimage and bioinformatics for microRNA therapeutics in heart failure
by Pierre Geurts 28 Jan '14

28 Jan '14

Job Advertisement: Position at the post-doctoral level for 1 year at the Systems and Modeling research unit at the GIGA Biomedical Research Center and at the Montefiore Institute of Electrical Engineering and Computer Science, at the University of Liège, Belgium. Within European FP7 Marie Curie Work Programme coordinated by Prof. dr. S. Heymans (Maastricht University), we are looking for an excellent, highly competitive researcher at the post-doctoral level. He/she should have worked for at least 3 years outside Belgium during the past years. Topic : Development & application of machine learning, image analysis, and bioinformatics techniques for high-throughput and high-content analysis for microRNA-medicines for Cardiac Metabolic Diseases. Keywords: Machine Learning – Image Analysis – Bioimage Informatics - Bioinformatics Environment: The GIGA Research Center with excellent research groups in biology, bioinformatics, and machine learning fields grouped together. Project: The researcher will be working closely with a team of software developers, researchers in machine learning & bioinformatics, and biologists, to advance high-throughput automated analysis of bioimaging & microRNA data. The applicant will be involved in the application of existing algorithms and the design of novel algorithms and their large-scale evaluation for cellular image recognition and phenotype quantification to discover novel microRNAs implicated in heart failure. She/He will have access to a high-performance computing environment and various bioinformatics tools including the inhouse developed Cytomine platform able to process terabytes of imaging data. Capacities & Experiences: Applicants should hold a PhD and have strong knowledge in machine learning, bioinformatics and/or computer vision. Programming and data analysis skills are also highly desirable. The candidates should be highly motivated, with a strong interest in large-scale biomedical applications. A working knowledge of English language is mandatory This project is a collaborative project (exchange of people) between Maastricht University (Netherlands), Cenix Biosciences (Dresden, Germany) and SystMod (GIGA, Liège, Belgium). Interested candidates should send a CV, a brief statement of research and development interests, three relevant publications, and the names and contact details of two references by e-mail (with subject “Postdoc CardiomiR”) to: raphael.maree(a)ulg.ac.be; pierre.geurts(a)ulg.ac.be Related links: http://www.montefiore.ulg.ac.be/systmod http://www.giga.ulg.ac.be http://ec.europa.eu/research/participants/portal/page/people?callIdentifier… http://www.cenix.com http://www.cytomine.be/ http://www.montefiore.ulg.ac.be/~maree http://www.montefiore.ulg.ac.be/~geurts

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PhD position bioinformatics for COMREC
by Peters, Sander 27 Jan '14

27 Jan '14

We are looking for Bioinformatics PhD student on "Bioinformatic analyses of meiotic recombination in tomato hybrids and related species". COMREC is built on the hypothesis that the control of meiotic crossover (CO) frequency and distribution is dependent on the interplay between the biochemical processes of the recombination machinery, the programmed reorganisation of the chromosomes during meiotic progression and the organisation of the chromatin "landscape". The PhD project "Bioinformatic analyses of meiotic recombination in tomato hybrids and related species" specifically focuses on a multidisciplinary approach to analyze (i) the genetic variation in recombination, (ii) CO sequence features and types, (iii) the frequency of recombination, and (iv) the synteny and structural homology involved in recombination cold and hot spots. The various types of sequence- and genome-topology data will be integrated to predict recombination "cold spots" and "hot spots". The PhD will work in close cooperation with the other PhDs appointed in the COMREC programme. The position requires a researcher holding at least a Bachelor degree in Bioinformatics or a related discipline in computer science or the life sciences with proven affinity with the topic of the PhD project. More information can be found at www.birmingham.ac.uk/comrec<http://www.birmingham.ac.uk/comrec> Dr. ir. Sander Peters, Applied Bioinformatics, Department of Bioscience, Plant Research International<http://www.pri.wur.nl/UK/>, Wageningen University Research Centre<http://www.wur.nl/UK/>. Address: Building 107, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands. Tel: +31-317-481123 (office) E-mail: sander.peters(a)wur.nl<mailto:sander.peters@wur.nl> [LinkedIn]<http://www.linkedin.com/pub/sander-peters/b/660/837>

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Postdoctoral research associate: Bioinformatics
by stephane Rombauts 27 Jan '14

27 Jan '14

-------- Original Message -------- Subject: job ad, please distribute in your group Date: Fri, 24 Jan 2014 12:48:49 -0600 From: Susan Brown <sjbrown(a)ksu.edu> To: Monica Poelchau <mpoelchau(a)gmail.com>, Stephen Richards <stephenr(a)BCM.edu>, Jay Evans <Jay.Evans(a)ARS.USDA.GOV>, Michael Pfrender <Michael.Pfrender.1(a)nd.edu>, Daniel Lawson <lawson(a)ebi.ac.uk>, "Daniel A. Hahn" <dahahn(a)ufl.edu>, Chris Elsik <elsikc(a)missouri.edu>, Stephane Rombauts <stephane.rombauts(a)psb.vib-ugent.be> Postdoctoral research associate: Bioinformatics USDA-ARS in Manhattan, Kansas Description: We are looking for a bioinformatician to work with two large sequence databases. The first project involves population genetics and phylogeography of disease vector mosquito species. The mosquitoes were collected throughout their known geographic distribution and sequenced using a barcoding approach to identify SNPs throughout the genome. As a team member, the incumbent will use bioinformatic techniques to construct a full genome mosquito SNP database, which can be used for phylogenetic, population genetic, and associating mutations to characteristics that impact animal health. The second project involves transcriptomes of biting midges (Culicoides) and gene regulation based on various feeding states. The incumbent will work on /Culicoides/ projects including a /de novo/ transcriptome assembly which will need annotation when the /Culcoides/genome is sequenced. Therefore, methods and skills needed for both projects will include bioinformatics analysis, landscape genetics, and gene expression studies including high-throughput sequencing analysis. The Arthropod-Borne Animal Disease Research Unit is seeking an independent researcher who is a good writer and wants to publish. More information can be found here: https://www.usajobs.gov/GetJob/ViewDetails/357973800 The position is open until a candidate is found. Start date is negotiable. Please follow the instructions at the USAjobs link for application instructions or contact Lee Cohnstaedt (Lee.Cohnstaedt(a)ars.usda.gov <mailto:Lee.Cohnstaedt@ars.usda.gov>). _______________________________________________________________ -- ================================================================== Stephane Rombauts Principal Scientific staff Bioinformatics & Systems Biology Division Tel:+32 (0)9 331 38 21 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM strom(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be/ ==================================================================

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Metagenomics Approaches and Data Analysis (2nd edition), 31 March - April 2, Nijmegen, the Netherlands
by Celia.vanGelder＠radboudumc.nl 24 Jan '14

24 Jan '14

Metagenomics Approaches and Data Analysis (2nd edition) Date: March 31 - April 2, 2014 Location: Nijmegen, the Netherlands Course coordinators: Sacha van Hijum (Radboudumc/NIZO food research), Bas Dutilh (Radboudumc/CMBI), Celia van Gelder (Radboudumc/NBIC/BioSB) Website & registration: http://biosb.nl/education/course-portfolio/course-metagenomics-approaches-a… Course description The Metagenomics course covers Metagenomics and metatranscriptomics of prokaryotes, eukaryotes and viruses. Topics are Metagenomics-specific issues like calling taxa, functional annotation, metagenome assembly and comparative Metagenomics. Target audience The course is aimed at PhD students and post-docs or researchers with a similar level, but scientific programmers and data analysts with a background in biology and bioinformatics may also attend. Participants will be invited to introduce their own research questions. Towards the end of the course remaining questions specific to your research will be discussed with the group. Course programme The programme for the course can be found at http://biosb.nl/wp-content/uploads/2014/01/Program_Metagenomics_2014_v2.pdf BioSB Course Programme The course portfolios of NBIC (bioinformatics) and NCSB (systems biology) will be integrated and continued in the Netherlands Bioinformatics and Systems Biology Research School (BioSB). 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)nbic.nl<mailto:education@nbic.nl>. Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:C.vanGelder@umcn.nl> websites: www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.nbic.nl<http://www.nbic.nl/> Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS 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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NBIC2014 - Call for abstracts - Netherlands Bioinformatics Conference 2014 - April 8-9
by Femke Francissen 24 Jan '14

24 Jan '14

Invitation & Call for abstracts for NBIC2014 Netherlands Bioinformatics Conference 2014 (NBIC2014) April 8 & 9, 2014 Conference Center De Werelt, Lunteren Conference website: http://www.aanmelder.nl/nbic2014 ============================================================ On April 8 and 9, 2014 the Dutch bioinformatics community will meet for the 9th time in conference centre De Werelt in Lunteren. A lively programme will provide for presentations about the latest developments in bioinformatics but also for the highly appreciated social networking opportunities during breaks and evening programme. Registration is open!: https://www.aanmelder.nl/nbic2014/wiki/registration Science & applications NBIC2014 discusses the latest developments in bioinformatics and computational biology and interrelated disciplines, and their wide-ranging applications in life sciences & health, agriculture, food & nutrition and industrial biotechnology. NBIC2014 offers a cross-disciplinary scientific program of (poster) presentations, application demonstrations and workshops. Keynote speakers - Marcus Claesson, University College, Cork, Ireland - Ilya Shmulevich, Institute for Systems Biology, Seattle USA - Jelle Goeman, Radboudumc Nijmegen, the Netherlands - Christian Ottmann, Eindhoven University of Technology, the Netherlands - Yves van de Peer, VIB, Ghent University, Belgium Programme - Topical tracks: Allbio Metagenomics meeting & Spring meeting of the Netherlands Society on Biomolecular Modelling (NSBM) - Industry meeting organised by the Bioinformatics Users Platform (BIUP) - Parallel sessions of contributed lectures - A poster session during the conference dinner on April 8th - Presentation of the Young Investigator Award 2014 - Birds of a Feather sessions - A PhD retreat by the Regional Student Group on April 7th - Plenty of networking possibilities Read more: https://www.aanmelder.nl/nbic2014/part_program Abstract submission You can submit an abstract for a lecture, a poster or a demo. Abstracts for the NBIC2014 general conference programme may cover any bioinformatics related subject. Based on the abstract submissions, the NBIC2014 programme will be filled with several thematic sessions and abstracts will be distributed over these sessions. Abstracts can also be submitted for the Allbio Metagenomics meeting and the NSBM Spring meeting. More information: https://www.aanmelder.nl/nbic2014/wiki/abstract%20submission Key dates - Abstract submission deadline for oral presentations: February 23, 2014 - Notification date: March 4, 2014 - Abstract submission deadline for posters and demos: April 4, 2014

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