September 2013 - BBClist - maillist.psb.ugent.be

postdocs wanted to work in Pretoria, South Africa
by Yves Van de Peer 14 Sep '13

14 Sep '13

The Van de Peer lab (http://bioinformatics.psb.ugent.be/beg/) is setting up a joint lab in Bioinformatics and Systems Biology at the University of Pretoria (http://web.up.ac.za) Recently, the University of Pretoria founded a new Genomics Research Center, focusing on five major themes, namely Microbial and Environmental Genomics, Plant Genomics, Fungal Genomics, Animal and protozoon genomics, and Human Genomics. To support research in these respective fields, we are setting up a new Bioinformatics and Systems Biology research group at the University of Pretoria, which will be closely interconnected with the Bioinformatics group at Ghent University. In this respect, we are currently looking for 3 Postdoctoral Fellows (to be working in Pretoria). We seek creative, skilled and highly motivated candidates with a PhD in bioinformatics or computational biology. We do require strong analytical, computational skills proven by an excellent publication record. Experience with next generation sequence and whole genome sequence data is also required. Applicants should be proficient in programming (Perl, Python, C++ or Java) and knowledge in statistics and/or mathematical modeling would be an asset. Good communication skills are essential and applicants should be proficient in English, both speaking and writing. Funding is secured for at least three years, and may be extended. Contact Yves Van de Peer (yves.vandepeer(a)psb.ugent.be) for more information and/or to apply. To apply, please send a single PDF file that contains a cover letter describing your research interests and experience, full C.V., and contact information for three references. Review of applications will begin on October 1st and continue until the positions are filled. Start: As soon as possible. -- Check out http://www.plantgenomeevolution.com/ Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Systems Biology, Department of Plant Systems Biology Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be/

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NBIC PhD course Protein Structures: production, prowess, power, promises, and problems
by C.vanGelder＠umcn.nl 13 Sep '13

13 Sep '13

NBIC PhD course Protein Structures: production, prowess, power, promises, and problems Date: 4 - 8 Nov 2013 Course coordinator: Gert Vriend Location: Center for Molecular and Biomolecular Informatics (CMBI), UMC Radboud, Nijmegen, the Netherlands Website: http://www.nbic.nl/education/nbic-phd-school/course-schedule/protein-struct… Registration: http://www.nbic.nl/education/nbic-phd-school/enrolment/ Target audience The course is suitable for both PhD students working in structural bioinformatics as well as for PhD students in the life sciences who want to learn more about using structural informatioin in their research. The course schedule accommodates both groups, parallel sessions for both groups will be scheduled when necessary. Course Description In the right hands, protein structures are a 'power'ful tool to answer bio-molecular questions. Knowledge of the structure is a pre-requisite for rational drug design, for biotechnology, for chemical biology, and for answering a whole series of biomedical questions. In this course we will discuss the 'production' of protein structures by NMR, X-ray, and homology modelling. These methods all have their pro's and cons so a certain 'prowess' is needed to follow all 'promises' and start attacking bio-medical 'problems' using protein structures. The course will be split in three parts. Part 1) Looking and seeing things in protein structures, learning to operate the software, understanding some of the algorithms. Part 2) Protein structure determination (prediction) with NMR, X-ray, and homology modelling, and the possibilities and problems that come with each of these three techniques. Part 3) Applying all that was learned in real-life example studies. Course topics Day 1: Homology modelling Day 2: Protein structure determination and validation Day 3: Electrostatics and molecular dynamics Day 4: Protein structure comparison Day 5: Own project executed with help from CMBI staff. Examples of questions you will be able to answer after following the course: * Why is a person with this mutation sick? Or in other words, how does the molecular phenotype cause a disease state? * This enzyme converts mannose. Can I make is specificity broader? * This enzyme doesn't function in my in vitro assay. Should I add some ions? * I want to add a tag to my enzyme, should I put it on the N-terminus, the C-terminus, or is something different needed? * This receptor binds a ligand, but if I look at the structure, that ligand doesn't fit at all. Can I predict motions that take place upon ligand binding? NBIC PhD School This course is part of the Education Programme of the NBIC PhD School. The NBIC PhD School offers training and education for PhD students in bioinformatics. More information about the NBIC PhD School can also be found on http://www.nbic.nl => Education => NBIC PhD School. More information For more information about the course you can contact Celia van Gelder (NBIC Education) at celia.van.gelder(a)nbic.nl<mailto:celia.van.gelder@nbic.nl>. -- Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: C.vanGelder(a)umcn.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 UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud University Nijmegen Medical Centre is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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Symposium - New Genomics toward personalized medicine - 10/10/2013 Lille
by Olivier Sand 13 Sep '13

13 Sep '13

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10th Network Biology Symposium and Cytoscape Workshop 2013 in Paris, France, October 9-10
by P. Molenaar 09 Sep '13

09 Sep '13

The 10th annual Network Biology Symposium and Cytoscape Workshop brings together an international Network Biology community, including Cytoscape users and developers, for an update to the field of Network Biology, and Cytoscape tutorials and workshops. PROGRAM The meeting will kick off with the public symposium (Wednesday Oct. 9th) and poster session on the latest developments in Network Biology on the campus of the Pasteur Institute. Confirmed speakers include: - Patrick Aloy (IRB Barcelona) - Andreas Beyer (Univ. Cologne) - Nils Blüthgen (Charité Berlin) - Trey Ideker (UC San Diego) - Julio Saez-Rodriguez (Cambridge) - Esti Yeger-Lotem (Ben-Gurion University, Negev) Thursday, October 10th: Cytoscape User and Developer Workshop REGISTER NOW DEADLINE: September 23, 2013 http://nrnb.org/cyretreat2013 Reduced student rate available! REGISTER FOR A POSTER AND/OR A FLASH TALK Posters will be available all day 5-minute flash talks Cytoscape is a free, open-source software platform for visualizing and analyzing complex networks and associated data. Find out more at http://cytoscape.org<http://cytoscape.org/> For any questions, e-mail cyretreat2013(a)gmail.com<mailto:cyretreat2013@gmail.com> Piet Molenaar piet.amc(a)gmail.com<mailto:piet.amc@gmail.com> Department of Oncogenomics, M1-131 Academic Medical Center University of Amsterdam Meibergdreef 9 1105 AZ Amsterdam the Netherlands tel (+31) 20-5666592 fax (+31) 20-6918626 ________________________________ AMC Disclaimer : http://www.amc.nl/disclaimer ________________________________

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TPNC 2013: call for posters
by GRLMC 07 Sep '13

07 Sep '13

The 2nd International Conference on the Theory and Practice of Natural Computing (TPNC 2013) invites authors to submit poster presentations. TPNC 2013 will be held in Cáceres (Spain) on 3-5 December, 2013. See http://grammars.grlmc.com/tpnc2013/ Poster presentations are intended to enhance informal interactions with the conference participants, at the same time permitting in-depth discussion. TOPICS Authors are encouraged to submit presentations that discuss novel work in progress on: - nature-inspired models of computation, - synthesis of nature by means of computation, - nature-inspired materials, - information processing in nature, - applications of natural computing. Posters do not need to present final research results. Work that may lead to new interesting developments is welcome. KEY DATES Submission deadline: October 20, 2013 Notification of poster acceptance or rejection: October 27, 2013 SUBMISSION Please submit a .pdf abstract through: https://www.easychair.org/conferences/?conf=tpnc2013 It should contain the title, author(s) and affiliation, and should not exceed 500 words. PRESENTATION Posters will be allocated 8 minutes each in the programme for oral presentation. Moreover, they will remain hanging during the whole conference for discussion. PUBLICATION Posters will not appear in the LNCS proceedings volume of TPNC 2013. However, they will be eligible for submission to the post-conference Soft Computing journal special issue. REGISTRATION Authors of accepted posters have to register to the conference. Their registration fare is reduced: 150 Euro (appr. one third of the fare for PhD students).

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BBC 2013 abstract submission deadline is approaching
by BBC2013 06 Sep '13

06 Sep '13

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, We are happy to announce the 8th edition of the BeNeLux Bioinformatics Conference, which 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. 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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Fwd: opening for bioinformatics post-doc in mycobacteriology
by Laukens Kris 06 Sep '13

06 Sep '13

Dear colleagues, please find attached the details for a job opening for a post-doc bioinformatics in mycobacteriology, in Antwerpen. Best regards, Kris Laukens Dear colleagues, friends, We are advertising for a bioinformatics specialist. Please pass the attached job description on to those you think might be interested. Kind regards, Bouke de Jong, MD PhD Head, Mycobacteriology Unit Institute of Tropical Medicine Nationalestraat 155 2000 Antwerp Belgium Phone: 00-32-3 247 6590 P Please consider the environment before printing this e-mail Disclaimer<http://www.itg.be/disclaimer> Directions to our location(s)<http://g.co/maps/ua89b>

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Phd vacancy in systems biology in Brussels
by Didier Gonze 05 Sep '13

05 Sep '13

Here is an announcement for a PhD position in systems biology (modeling) in Brussels (ULB/VUB). Didier Gonze Unité de Chronobiologie Théorique Service de Chimie Physique CP 231 Université Libre de Bruxelles Bvd du Triomphe 1050 Bruxelles Belgium

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Vacancy analysis genetic variants in Brussel
by Tom Lenaerts 04 Sep '13

04 Sep '13

We are looking for a doctoral student to work on a project wherein statistical and machine learning techniques will be used to decipher the genetic architecture of oligo- and polygenic disorders. This work will be performed in the context of the new Interuniversity Institute for Bioinformatics in Brussels (http://www.ibsquare.be/ ), called (IB)2. The project Recent advances in genome-wide sequencing technologies and data analysis have proven to be very successful in the delineation of the genetic basis of hitherto poorly understood, fully penetrant, monogenic disorders. In practice, disease-causing genetic variants are identified through a set of filtering steps, which potentially reduce the large collection of exonic variants, typically around 20000, to one or a few variants (or genes). These filtering steps eliminate variants by assuming that the causative variants alter the RNA splicing or protein sequence, that they are rare in the normal healthy population, show complete penetrance and detectance. Although significant successes have been achieved with this approach, additional tools are still required when the outcome of the variant filtering does not provide a simple answer. The task of filtering out the causative variants/genes becomes even more challenging when dealing with congenital conditions with complex inheritance patterns, distributed along an oligo- to polygenic continuum. In this context, the assumption is that a combination of rare variants spread over coding and non-coding genes is causative for the observed phenotype. Since these variants are rare in the population, it makes them hard to detect using standard single variant association tests and therefore more aggregative techniques are required. In this project we aim to develop methods that can distill, from the large collection of rare variants, those that have any relevance to the phenotype under investigation. The project is a collaboration between the Genetics Center of the Université Libre de Beuxelles (Hôpital Erasme and Hôpital Universitaire des Enfants Reine Fabiola), Center for Medical Genetics of the Vrije Universiteit Brussel (Universitair Ziekenhuis Brussel) and the Machine Learning group and Artificial Intelligence lab of the Computer Science Departments of the Université Libre de Bruxelles and the Vrije Universiteit Brussel respectively. Equal opportunity employer (IB)2 and the connected universities, ULB and VUB, is an equal opportunity employer and is committed to employing more handicapped individuals and especially encourages them to apply. (IB)2 wishes to increase the proportion of women in areas in which they are underrepresented. Women are strongly encouraged to apply. Responsibilities · Performing bioinformatics research in biomedical sciences with a focus on human genetics. · Development of machine learning techniques to filter and analyze variant data. · Development of bioinformatics pipelines for omics data assembly, analysis and annotation. · Assisting and enabling investigators in analyzing their data using developed and existing analysis tools and pipelines. · Presenting developments and results at international scientific meetings and in peer-reviewed international scientific journals. Qualifications · Master in bioinformatics, computational biology, biostatistics, computer sciences, bioengineer, life sciences or a related discipline · Research-oriented person for the primary analysis of omics data in the field of human genetics · Experience or a clear interest in computational biology and genomics and in particular in machine learning · Knowledge in bioinformatics and/or biostatistics · Experience or a clear interest in statistical computing (e.g. R ,..) · Software and database development skills (e.g. Perl, SQL , Python, C++,… on different OS) · Well organized working style · Team player · High motivation to succeed in scientific and translational research · Strong oral and written communication skills (English and Dutch and/or French) How to Apply We need a letter of motivation, a CV, a copy of your PhD, Master and Bachelor diploma’s, PhD diploma (if applicable) and the contact information of two people who can provide references. In addition, we require a list of the grades obtained for the different courses during your master and bachelor education. You can send these in PDF format to Tom Lenaerts (tlenaert(a)ulb.ac.be) mentioning “IBsquare SNP position” in the subject. For inquiries you can send a message to this same address. ================================== Benelux Bioinformatics Conference 2013 ; http://bbc2013.ibsquare.be ================================== ULB: http://www.ulb.ac.be/di/map/tlenaert/ http://mlg.ulb.ac.be/ VUB: http://ai.vub.ac.be/

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11th RECOMB satellite meeting on Comparative Genomics
by Macha Nikolski 02 Sep '13

02 Sep '13

Dear colleagues, Registration is now open to attend the 11th Recomb satellite meeting on Comparative Genomics that will be held in Lyon-Villeurbanne (France) from Thursday 17 to Saturday 19 October 2013. http://rcg2013.sciencesconf.org/ We invite you to attend this meeting and send an abstract for a poster presentation. During this meeting, best posters will be awarded! Please pay attention that our early bird registration fees are ending September 6th. Keynote speakers are - Tal Dagan (Christian-Albrechts-Universität zu Kiel, Germany) - Kay Pruefer (Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany) - Ludovic Orlando (University of Copenhagen, Denmark) - France Denoeud (Genoscope, Evry, France) - Nicolas Galtier (Institut des Sciences de l'Evolution, Montpellier, France) - Laurent Duret (Laboratoire de Biométrie et Biologie Evolutive, Lyon, France) In addition, 19 short presentations have been selected upon the acceptance of their article through a peer review process chaired by Macha Nikolski and Yves van de Peer, that will be published in BMC bioinformatics. We will be happy to host you in Lyon-Villeurbanne Please visit: 11th RECOMB - Comparative Genomics 2013 in Lyon (France) http://rcg2013.sciencesconf.org/ Macha Nikolski on behalf of the local organizing, program and steering committees. -- Head of Bordeaux Bioinformatics Center Research Scientist LaBRI / CNRS CBiB - Université Bordeaux 146, rue Léo Saignat, 33076 Bordeaux www : http://dept-info.labri.fr/~macha/ tel : 05 57 57 12 47

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