- BBClist - maillist.psb.ugent.be

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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ASSISTANT or ASSOCIATE PROFESSOR OF BIOINFORMATICS FOR MICROBIOLOGY, DELFT UNIVERSITY OF TECHNOLOGY
by Marcel Reinders - EWI 23 Jan '14

23 Jan '14

ASSISTANT or ASSOCIATE PROFESSOR OF BIOINFORMATICS FOR MICROBIOLOGY The Delft University of Technology is seeking a new staff member for its bioinformatics ambitions in microbiology. THE ORGANISATION: DELFT UNIVERSITY OF TECHNOLOGY, ELECTRICAL ENGINEERING, MATHEMATICS AND COMPUTER SCIENCE The Faculty of Electrical Engineering, Mathematics and Computer Science (EEMCS) is known worldwide for its high academic quality and the social relevance of its research programmes. The faculty’s excellent facilities accentuate its international position in teaching and research. The faculty offers an interdisciplinary setting for its 500 employees, 350 PhD students and 1700 undergraduates. Together they work on a broad range of technical innovations in the fields of sustainable energy, telecommunications, microelectronics, embedded systems, computer and software engineering, interactive multimedia and applied mathematics. EEMCS: Your Connection to the Future. The Department of Intelligent Systems conducts research on processing and interpretation of data to enable man and machine to deal with the increasing volume and complexity of data and communication. We have a strong focus on medical and health sciences. One of our research labs is the Delft Bioinformatics Lab (bioinformatics.tudelft.nl). THE GROUP: THE DELFT BIOINFORMATICS LAB The Delft Bioinformatics Lab performs research and educates students in the fields of bioinformatics for ‘health and disease’ and for ‘microbiology’. We stand out in designing novel data-driven algorithms that are based on the latest developments in the field of Pattern Recognition. We are inspired by a variety of applications but also want to further these scientific application domains with our solutions. Therefore, we actively collaborate with scientists that are at the forefront of their fields and participate in their research questions. THE JOB Within the Delft Bioinformatics Lab, the candidate heads the Bioinformatics for microbiology research theme and educational activities. This theme aims to improve understanding of microorganisms to either increase production yields or to produce new compounds or proteins. At the heart of this research is basic understanding of microorganisms under a variety of growth conditions as well as protein sequence properties that favour secretion. For this, the candidate designs pioneering bioinformatics methodologies emphasising on high-throughput (gen)omic data analysis. Impact in microbiology is realised by intense collaborations with eminent Dutch microbiologists in Delft, Utrecht and Leiden. The candidate expands these collaborations and launches novel research directions that firmly establish a position at the forefront of the international field of computational microbiology. You will: * Provide leadership in bioinformatics for microbiology research. * Act as principal investigator, leading day-to-day research activities. * Contribute to education at the BSc, MSc and PhD levels. * Identify promising avenues with existing partners in microbiology and establish collaborations with internationally leading labs. * Foster creativity and scientific excellence. * Be active in relevant (computer science and biology) communities. CANDIDATE REQUIREMENTS The candidate has a PhD in computer science or a related discipline with a proven track record in bioinformatics. An affinity for pattern recognition and microbiology are considered an advantage. He/she must be able to work effectively in a multidisciplinary team and have the ambition to build partnerships with leading institutions worldwide. The candidate shares our view that communication skills are important, as is the ability to interact with peers, students and technical staff. Teaching experience is important; teaching certificates are considered to be an advantage. CONDITIONS OF EMPLOYMENT TU Delft offers an attractive benefits package, including a flexible work week, free high-speed Internet access from home (with a contract of two years or longer), and the option of assembling a customised compensation and benefits package (the 'IKA'). Salary and benefits are in accordance with the Collective Labour Agreement for Dutch Universities. The position offered is a tenure-track position for a period of five years. Based on performance indicators agreed upon at the start of the appointment, a decision will be made in the final year whether to offer you a permanent faculty position. TU Delft sets specific standards for the English competency of the teaching staff. TU Delft offers training to improve English competency. Inspiring, excellent education is our central aim. If you have less than five years of experience and have not yet obtained your teaching certificate, we allow you up to three years to complete this. TENURE TRACK A Tenure Track, a process leading up to a permanent appointment with the prospect of becoming an Associate or full Professor, offers young, talented academics a clear and attractive career path. During the Tenure Track, you will have the opportunity to develop into an internationally acknowledged and recognised academic. We offer a structured career and personal development programme designed to offer individual academics as much support as possible. For more information about the Tenure Track and the personal development programme, please visit www.tudelft.nl/tenuretrack. INFORMATION AND APPLICATION For more information about this position, please contact Prof. M.J.T. Reinders, phone: +31 (0)15-2786424, e-mail: m.j.t.reinders(a)tudelft.nl. To apply, please e-mail a detailed CV, a research and an education statement, at least three references and at most five key publications along with a letter of application by 14 March 2014 to Mrs. C.J.C. Kohlmann-van Noord, Hr-eemcs(a)tudelft.nl. When applying for this position, please refer to vacancy number EWI2014-01.

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A relevant petition
by Vincent Detours 22 Jan '14

22 Jan '14

Hello, Patient privacy is key when it comes to get patient consent for participation in research. Edward Snowden's revelations about mass surveillance may impact trust and affect in the long run our ability to obtain data or work with them. Those of working with patients data, including genomic data, may find this petition relevant: http://www.avaaz.org/en/send_snowden_home_loc/?copy. All the best, Vincent Detours, Ph. D. http://homepages.ulb.ac.be/~vdetours/ IRIBHM Bldg C, room C.4.116 ULB, Campus Erasme, CP602 808 route de Lennik B-1070 Brussels Belgium Phone: +32-2-555 4220 Fax: +32-2-555 4655 Skype: vdetours E-mail: vdetours at ulb.ac.be

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NGS
by Jeanie van Driel - Blom 20 Jan '14

20 Jan '14

Dear reader, We, Avans University of Applied Sciences, Research Group Analysis Techniques in Life Science, organize an international shortcourse on next generation sequencing in Breda from 1 untill 4 April 2014. Aim of the course: DNA sequencing technologies are currently developing at an incredible speed and new applications are presented monthly, incl. DNA/RNA profiling, ChIP-seq, re-sequencing, de novo genome sequencing and metagenomics. The aim of this course is to introduce next generation sequencing technologies, highlight different applications of these new technologies, and show ways to analyse data. Please visit the course website for detailed information: http://www.alsavans.nl/avans-training-2542.htm Looking forward to meeting you in Breda Best regards Jeanie van Driel-Blom Avans university of applied science p.o. box 90116 Disclaimer ( http://www.avans.nl/over-avans/e-mail-disclaimer )

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