- BBClist - maillist.psb.ugent.be

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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[Gtpb] Reminder: WESRDA13 Bioinformatics Training Course - open for applications
by Pedro Fernandes 01 Sep '13

01 Sep '13

GTPB - The Gulbenkian Training Programme in Bioinformatics Applications for the Bioinformatics Training Course WESRDA13 - Whole Exome Sequencing and RNA-seq data analysis with Ignacio Medina and Javier Santoyo-Lopez are now OPEN! IMPORTANT DATES for this Course Deadline for applications: *September 27th 2013* Notification of acceptance within 72 hours of application (working days count) Course date: *October 8th to October 11th 2013* Details about the course including instructions on how to apply can be found in the appropriate page of the GTPB website http://gtpb.igc.gulbenkian.pt/bicourses/WESRDA13/ We hope that you enjoy it. Best regards Pedro Fernandes GTPB organiser Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt Course description High-throughput technologies such as next generation sequencing (NGS) are characterized for producing massive a mounts of data. These technologies for example can allow to describe all variants in a genome or to detect the whole set of transcripts that are present in a cell or tissue. However, at the same time, posses new challenges in the way the data has to be analyzed, annotated and interpreted which are not trivial. Whole Exome Sequencing produces sequence data using NGS assays and allows the study of genetic variations in the exonic regions of all genes that can be transformed in biological information at an unprecedented level of detail. Traditionally transcriptomic analysis has been used to find genes that are differentially expressed among distinct experimental conditions, or correlated to diverse parameters. Currently, NGS technologies such as RNA-seq can also allow to digitally quantify all, known and unknown, transcripts or to discover new isoforms and splice sites for all the genes. However, NGS data analysis can be a major bottleneck for many researchers which are still applying inefficient tools for the processing of the data and inadequate methods for the interpretation of their results in order to have meaningful results. This course covers state-of-the-art tools and methods for NGS RNA-seq and exome variant data analysis, which are of major relevance in today's genomic and gene expression studies. The aim of this course is to familiarise course participants with the latest analysis methodologies and to provide hands-on training on the analytical approaches implemented for RNA-seq data and whole exome variant analysis. _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb ----- End forwarded message ----- ----- End forwarded message ----- _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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BOFZAP position KULeuven
by Stein Aerts 29 Aug '13

29 Aug '13

An interesting position for an independent group leader and Tenure Track professorship (BOFZAP) in any field of bioinformatics, computational biology, or systems biology at the University of Leuven. Best regards, Stein Aerts Stein Aerts, PhD Assistant Professor Laboratory of Computational Biology Center for Human Genetics University of Leuven Herestraat 49, P.O. Box 602 3000 Leuven, Belgium Office +32 16 330710 Lab + 32 16 330142 Mobile +32 486 659003 http://med.kuleuven.be/lcb/

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Fwd: Post-doctoral candidate wanted CNRS Lille
by Marc Lensink 28 Aug '13

28 Aug '13

Dear colleagues, please be advised that this call is still open and will remain so until the third week of September. Please make suitable candidates aware of this excellent opportunity! Thanks, Marc Lensink ----- Forwarded message ----- Subject: post-doctoral candidate wanted dear Friends and Colleagues, I would appreciate if you could make suitable candidates aware of the following call. We are looking for an excellence-level post-doctoral candidate with at least 18 months of post-doctoral experience coming October. many thanks in advance! Marc CALL FOR POST-DOCTORAL CANDIDATE We are looking for a post-doctoral candidate to work on a computational project in cancer research. The successful candidate will participate in a regional grant proposal of which the deadline is October 22nd, 2013. The targeted starting date is March/April 2014, at which date the candidate must be no older than 35 years and have at least two years of post-doctoral experience, preferably outside of France. Scientific excellence is sought and the successful candidate will be offered a 18- or 24-month contract with a highly competitive salary. The project evolves around the Ets-1 oncoprotein, a transciption factor that regulates many genes involved in cancer progression and tumor invastion. We identified and purified novel interaction partners, including two DNA repair enzymes. Our work highlights that the interaction between Ets-1 and both DNA repair enzymes is important for the cancer cell. The three-dimensional structures of the interacting partner domains are known and we aim at using protein docking and molecular modeling to sketch a molecular picture in order to increase our understanding of these important biological interactions and design mutagenesis experiments. If granted, the candidate will join my team of Computational and Theoretical Molecular Biology at the French CNRS Interdisciplinary Research Institute in the Lille area (north of France), and work in close collaboration with the experimental team of Marc Aumercier. Lille is a vibrant and dynamic region, with 35% of the population under 25, and the heart of the Eurometropole Lille-Kortrijk-Tournai, counting close to 2 million inhabitants. It features high-speed train connections to Brussels, Paris and London. The call will remain open until end of August, 2013, or when a suitable candidate has been identified. Informal questions may be directed to dr. Marc Aumercier (marc.aumercier(a)iri.univ-lille1.fr) or dr. Marc Lensink (marc.lensink(a)iri.univ-lille1.fr) ----- End forwarded message ----- -- Marc F. Lensink, CR1, PhD Interdisciplinary Research Institute (IRI) - USR3078 CNRS Computational Biology marc.lensink(a)iri.univ-lille1.fr Parc de la Haute Borne, 50 Avenue de Halley, BP 70478 F-59658 Villeneuve d'Ascq, France tel: +33 3 62 53 17 28 fax: +33 3 62 53 17 01

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Job opening: postdoc/ bioinformatician on integrative analysis of epigenomic data (Leiden, The Netherlands)
by B.T.Heijmans＠lumc.nl 28 Aug '13

28 Aug '13

Dear colleagues, I'd like to draw your attention to two positions in my group at the Leiden University Medical Center: 1. Postdoc/bioinformatician on integrative analysis of epigenomic data - https://www.academictransfer.com/employer/LUMC/vacancy/19671/lang/en/ 2. PhD student: Epigenetic mechanisms in cardiovascular disease -https://www.academictransfer.com/employer/LUMC/vacancy/19677/lang/en/ Thanks for your attention, Bas Heijmans www.lumc.nl/basheijmans<http://www.lumc.nl/basheijmans>

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[Gtpb] WESRDA13 Bioinformatics Training Course, Announcement
by Pedro Fernandes 27 Aug '13

27 Aug '13

GTPB - The Gulbenkian Training Programme in Bioinformatics Applications for the Bioinformatics Training Course WESRDA13 - Whole Exome Sequencing and RNA-seq data analysis with Ignacio Medina and Javier Santoyo-Lopez are now OPEN! IMPORTANT DATES for this Course Deadline for applications: *September 27th 2013* Notification of acceptance within 72 hours of application (working days count) Course date: *October 8th to October 11th 2013* Details about the course including instructions on how to apply can be found in the appropriate page of the GTPB website http://gtpb.igc.gulbenkian.pt/bicourses/WESRDA13/ We hope that you enjoy it. Best regards Pedro Fernandes GTPB organiser Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt Course description High-throughput technologies such as next generation sequencing (NGS) are characterized for producing massive a mounts of data. These technologies for example can allow to describe all variants in a genome or to detect the whole set of transcripts that are present in a cell or tissue. However, at the same time, posses new challenges in the way the data has to be analyzed, annotated and interpreted which are not trivial. Whole Exome Sequencing produces sequence data using NGS assays and allows the study of genetic variations in the exonic regions of all genes that can be transformed in biological information at an unprecedented level of detail. Traditionally transcriptomic analysis has been used to find genes that are differentially expressed among distinct experimental conditions, or correlated to diverse parameters. Currently, NGS technologies such as RNA-seq can also allow to digitally quantify all, known and unknown, transcripts or to discover new isoforms and splice sites for all the genes. However, NGS data analysis can be a major bottleneck for many researchers which are still applying inefficient tools for the processing of the data and inadequate methods for the interpretation of their results in order to have meaningful results. This course covers state-of-the-art tools and methods for NGS RNA-seq and exome variant data analysis, which are of major relevance in today's genomic and gene expression studies. The aim of this course is to familiarise course participants with the latest analysis methodologies and to provide hands-on training on the analytical approaches implemented for RNA-seq data and whole exome variant analysis. _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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Bioinformatics positions at Keygene
by Antoine Janssen 22 Aug '13

22 Aug '13

Dear all, Please forward the following vacancies to potential candidates: * Mathematician / Computer scientist * Quantitative / Statistical Geneticist Additional information can be obtained from Dr. Jaap Buntjer, Program Scientist Breeding Strategies, telephone +31 317 466866, email jaap.buntjer(a)keygene.com, or Dr. Roeland van Ham, VP Bioinformatics, telephone +31317 466866, email roeland.van-ham(a)keygene.com<mailto:roeland.van-ham@keygene.com>. Thanks Antoine Janssen Team Leader Bioinformatics [http://www.keygene.com/images/maillogo.jpg]<http://www.keygene.com/> Keygene N.V. P.O. Box 216 6700 AE Wageningen The Netherlands Tel. (+31) 317 46 68 66 Fax. (+31) 317 42 49 39 Web: http://www.keygene.com<http://www.keygene.com/> [http://www.keygene.com/images/phenodays20131.jpg]<http://www.phenodays.com/> The information contained in this message, and attachments if any, may be privileged and/or confidential and is intended to be received only by persons entitled to receive such information. Use of any part of this message and/or its attachments if any, in any other way than as explicitly stated by the sender is strictly prohibited. Should you receive this message unintentionally please notify the sender immediately, and delete it together with all attachments, if any. Thank you. The transmission of messages and/or information via the Internet is not secured and may be intercepted by third parties. KeyGene assumes no liability for any damage caused by any unintentional disclosure and/or use of the content of this message and attachments if any.

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(no subject)
by Nicolaes G (BIOCH) 22 Aug '13

22 Aug '13

LS, Would you be so kind as to disperse the following Call for Abstracts? best regards, Gerry Nicolaes Call for Abstracts The NSBM cordially invites you to visit its fall meeting, 2013. During the meeting, the floor will be given to PhD students and post-docs who study protein structure and/or structural bioinformatics or related topics (see a list below). The title of the meeting will be: "First Euregional Meeting on Structural Bioinformatics and Modeling of Biomolecules in Belgium, Germany and Netherlands" As guest speakers, Prof. Joost Schymkowitz of the VIB Switch Laboratory, KULeuven, Belgium will give a seminar titled: "Protein aggregation in disease and design" and Dr. Christian Ottman of the Biomedical Technology department, TUe will give a seminar titled: "Small-molecule stabilization of Protein-Protein Interactions". Abstract Format Abstracts should be limited to a maximum of 10 lines, with 12-pt font and single-spaced text, giving a short description of the research done. Please include a title in bold. The name(s) and affiliation(s) of the author(s) should follow the title. The opportunity will be given to present a limited number of posters, though this is not mandatory. If you wish to present a poster, please indicate so. Abstract Submission All abstracts, should be submitted electronically in MSWord via e-mail attachment to g.nicolaes(a)maastrichtuniversity.nl<mailto:g.nicolaes@maastrichtuniversity.nl> with as subject line "NSBM Fall meeting 2013". The deadline for receipt of all abstracts is October 10th 2013. Selected candidates will be notified no later than October 15th 2013. Presentations will be 20 min, including a 5 min discussion. Starting PhD students are particularly encouraged to present their research. For questions regarding the abstract or meeting please contact Gerry Nicolaes, +31-(0)43 3881688, g.nicolaes(a)maastrichtuniversity.nl<mailto:g.nicolaes@maastrichtuniversity.nl> Registration Registration can be made free of charge via e-mail to g.nicolaes(a)maastrichtuniversity.nl<mailto:g.nicolaes@maastrichtuniversity.nl> with as subject line "NSBM Fall meeting 2013". A lunch and coffee/tea breaks will be provided for. In consideration of traveling time, the registration will take place from 10:00-10:30, the program ends at 17:00h. Further details on the specific program and location will be announced. Should a lack of funding be a hurdle for visiting the NSBM Spring Meeting, please contact prof. Gert Vriend at vriend(a)cmbi.ru.nl<mailto:vriend@cmbi.ru.nl> so that an arrangement can be made. 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 [cid:image002.png@01CE9F1C.1E7A1120]Conference Chairs: Prof. Dr. Gert Vriend, professor of Bioinformatics, CMBI and Dr. Gerry Nicolaes, 3D structure-function unit, Cardiovascular Research Institute Maastricht [cid:image003.jpg@01CE9F1C.1E7A1120] Gerry Nicolaes, PhD Senior Researcher Cardiovascular Research Institute Maastricht Biochemistry Department g.nicolaes(a)maastrichtuniversity.nl<mailto:g.nicolaes@maastrichtuniversity.nl> www.maastrichtuniversity.nl <http://www.maastrichtuniversity.nl/> Universiteitssingel 50, 6229 ER Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 3881688 F +31 43 3884159 http://www.unimaas.nl/3dstructure-function [cid:image004.jpg@01CE9F1C.1E7A1120]Please consider your environmental responsibility before printing this e-mail. [cid:image003.jpg@01CE9F1C.1E7A1120] Gerry Nicolaes, PhD Senior Researcher Cardiovascular Research Institute Maastricht Biochemistry Department g.nicolaes(a)maastrichtuniversity.nl<mailto:g.nicolaes@maastrichtuniversity.nl> www.maastrichtuniversity.nl <http://www.maastrichtuniversity.nl/> Universiteitssingel 50, 6229 ER Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 3881688 F +31 43 3884159 http://www.unimaas.nl/3dstructure-function [cid:image004.jpg@01CE9F1C.1E7A1120]Please consider your environmental responsibility before printing this e-mail.

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