- BBClist - maillist.psb.ugent.be

Position for PhD/PostDoc bioinformatics @ Utrecht University, Biomolecular Mass Spectrometry and Proteomics Group
by Breukelen, B. van (Bas) 11 Oct '12

11 Oct '12

The Biomolecular Mass Spectreometry and Proteomics Group at Utrecht University the Netherlands is looking for a PhD student or PostDoc in Bioinformatics for the following; In this project we will develop novel proteomics technology to address proteome complexity in melanoma, which shows a rapid increase in incidence and is known for its aggressive nature in development of malignant metastasis and therapeutic resistance. The oncogenic BRAFV600E protein kinase, which leads to activation of the RAS–RAF–MEK–ERK signaling pathway, is frequently mutated in human cancer, including approximately 70% of malignant melanomas. In on-going collaborative efforts with the NKI we target the BRAFV600E proteome using high throughput proteomics, focusing on a variety of posttranslational modifications (PTMs). Currently we are looking for a Bioinformatician to support these efforts. He/she will develop novel software tools that allow mining of the data for biological relevant PTM-expression changes and potential ‘crosstalk’ between the different PTMs and the signaling networks involved. For questions and/or application please mail, m.altelaar(a)uu.nl<mailto:m.altelaar@uu.nl> =========================== Maarten Altelaar Assistant Professor Biomolecular Mass Spectrometry and Proteomics Group Utrecht University Padualaan 8, 3584 CH, Utrecht The Netherlands ----------------------------------------------- E: m.altelaar(a)uu.nl<mailto:m.altelaar@uu.nl> W: http://www.hecklab.com ===========================

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NSBM Fall Meeting November 26 2012
by Barbara van Kampen 11 Oct '12

11 Oct '12

The NSBM cordially invites you to visit its fall meeting November 26 2012. During the meeting, 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). The main topic for this year’s meeting will be: */“Dissecting and designing interactions”/* As guest speaker, *Dr. Carlos Camacho*of Pittsburgh University, USA, will give a lecture on an "Interactive and efficient discovery tool of small molecule protein-protein interaction antagonists". ** * * *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 poster, 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 science.secr.nmr(a)uu.nl <mailto:science.secr.nmr@uu.nl>with as subject line /“NSBMmeeting 2012”/. The deadline for receipt of all abstracts is November 5^th 2012. Selected candidates will be notified no later than November 13^th 2012. 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 science.secr.nmr(a)uu.nl <mailto:science.secr.nmr@uu.nl>with as subject line /“NSBMmeeting 2012”/. A lunch and coffee/tea breaks will be provided for. 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 Conference Chairs: *Prof. Dr. Alexandre Bonvin*, professor of Computational Structural Biology and *Dr. Gerry Nicolaes*, Cardiovascular Research Institute Maastricht -- Barbara van Kampen CMBI 260 Radboud University Nijmegen-Medical Centre / NCMLS 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

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vacancies for 3 postdocs & 4 PhD students
by Kris Laukens 04 Oct '12

04 Oct '12

Dear colleagues, we have job openings in Belgium for three post-doctoral researchers four PhD students in data mining, machine learning, bioinformatics, and computational proteomics These positions are available at: • Ghent University and VIB, Computational Omics and Systems Biology Group • KU Leuven, Machine Learning Group • University of Antwerp, Biomina / Department of Mathematics and Computer Science • The Flemish Institute for Technological Research (VITO). The job openings have been created in the context of the IWT-SBO project ‘inspector: an integrated informatics platform for mass spectrometry-based protein assays’. The goal of this project is to increase the efficiency of targeted proteomics methods such as selected reaction monitoring (SRM), enable high-throughput and semi-automatic quality control of proteomics experiments, and provide more sensitive detection of peptides carrying complex or unexpected post-translational modifications. Please see the individual job adverts of the respective groups below for full function descriptions, profiles, and application details: http://genesis.ugent.be/files/costore/inspector/inspector_vacancy.pdf Feel free to distribute these vacancies towards potential candidates! Thanks. Kris -- Kris Laukens Advanced Database Research and Modelling (ADReM - adrem.ua.ac.be) Biomedical Informatics research center Antwerpen (biomina - www.biomina.be) University of Antwerp, Belgium

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Belgian RSG talk by Prof. Yves Van de Peer
by Evangelia Dougali 01 Oct '12

01 Oct '12

Dear researcher, We are pleased to announce a talk by Prof. Yves Van de Peer organized by RSG Belgium aimed at young researchers in the field of Computational Biology and Bio-informatics, titled 'Journey through the past: 200 million years of plant evolution'. This is a unique opportunity to meet and interact with one of the leading bio-informatic experts in Belgium. This seminar will be held in the LEAF room at the UGent-VIB research building (FVSM) in Ghent on the 5th of October. The talk will be proceeded by an evening social event in the city center of Ghent with plenty of networking opportunities. Schedule 15h30: Gathering at the reception of the UGent-VIB research building 15h45: Introduction 16h00: Talk by Prof. Yves Van de Peer 17h30: Start social event How to get there General travel information can be found on the UGhent website: http://www.psb.ugent.be/contacts/how-to-reach-us More information on this event can be found on our website: http://www.iscbsc.org/rsg/rsg-belgium See you on the 5th! The RSG Belgium committee [We apologize for any cross-posting that may have occurred] -- ================================================================== Evangelia Dougali Tel:+32 (0)9 331 38 23 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM evdou(a)psb.vib-ugent.be http://www.psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================

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BeNeLux Bioinformatics Conference 2012 (BBC12): call for abstracts
by Femke Francissen 27 Sep '12

27 Sep '12

BeNeLux Bioinformatics Conference 2012 (BBC12): call for abstracts The 7th edition of the BBC12 will be organized in Nijmegen, the Netherlands on 10-11 December 2012. Key theme: "Bioinformatics at the interface". Confirmed keynote speakers: - Franca Fraternali, Molecular Structure group at King's College, London - Christine Orengo, University College London Call for abstracts: Abstracts can report research results in any area of bioinformatics, computational biology or related disciplines. Abstracts submission: http://www.nbic.nl/about-nbic/events/bbc2012/abstract-submission/ Submission deadline: 22 October 2012. Conference website: http://www.nbic.nl/bbc2012 Click here<http://www.nbic.nl/about-nbic/events/bbc2012/registration/> to register! Organizers: Barbara van Kampen<mailto:b.vankampen@cmbi.ru.nl> (Centre for Molecular and Biomolecular Informatics) Femke Francissen<mailto:femke.francissen@nbic.nl> (Netherlands Bioinformatics Centre)

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[Gtpb] Fwd: ANNOUNCEMENT: HPND12 - "Hunting for Promoters" Bioinformatics Training Course
by Pedro Fernandes 20 Sep '12

20 Sep '12

ANNOUNCEMENT HPND12 - Hunting for Promoters with NGS data with Alexander Kel, Martin Enge and Chritian Zinser Course description: This course is set-up to review the basic principles of gene regulation, first of all, by prediction of promoters and distant enhancers and silencers and by analysis of structure of the gene regulatory regions and identification of binding sites for transcription factors. The most intriguing parts of genomes, still hiding from clear understanding, are the gene regulatory regions -- promoters and enhancers. Analysis and prediction of the regulatory sites in the genome, which is now a hot topic as a result of the growth of the number of newly sequenced genomes, and the result of high throughput sequencing methodologies becoming commonplace. Also, the introduction of high throughput-sequencing based techniques for genome-wide epigenetic analysis such as ChIP-seq has revolutionized our ways for studying the gene regulatory mechanisms. of First of all, effective and robust methods for annotation of new genomes are urgently needed now.But also, recognition and analysis of these areas in the new and existing genomes becomes one of the most important parts of understanding the mechanisms of genome functioning. In this course, the attendees will learn several techniques of finding promoters and enhancers and the principles on which these methods are based. Through "hands on" exercises, several analytical tools will be displayed and the results citicized in the light of assessing their reliability and the possibilities that they open of assigning gene function based on automatic prediction. Also, the course will include an overview of the state of the art in lab techniques for studying gene regulation as well as a detailed account of data analysis for the more commonly used techniques such as ChIP-seq. Objectives The course will consist of lectures that lay out the conceptual framework as needed and and "hands on" exercises will provide the practical insight on the use of the methods, gradually, in order to produce skills that can be used with a relatively high degree of independence. Participants will know how to set-up some of the programs, and use publicly available servers for more complex analytical jobs, in an informed fashion, so that they fully understand the output generated and how its quality can be assessed. Participants will also learn the novel principles of organization of gene regulatory regions, which will help them to interpret their results of genomics and transcriptomics studies. Target Audience: The course is directed to researchers in biology, bioinformatics, biochemistry and medicine. Background knowledge in elementary bioinformatics is not absolutely necessary, but can be very useful. Please note that the PathProt brainstorming event takes place on the week just before this course. You will need to register in PathProt separately, though. Please use its specific PathProt website Course Pre-requisites: Basic biochemistry. Elementary computing skills Futher details, including application instructions available at http://gtpb.igc.gulbenkian.pt/bicourses/HPND12 thank you for your interest Pedro Fernandes -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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NBIC advanced NGS course: RNA-seq data analysis course on October 15-17th
by Patrick Koks 05 Sep '12

05 Sep '12

RNA-seq data analysis course On October 15-17th, NBIC, LUMC and AMC will organise the 2nd edition of the NBIC advanced NGS course: RNA-seq data analysis. The course is open for application. Course description The course is focussed on data pre-processing, quality control, and statistical methods for detection of differential gene expression. This is an expert course for people with experience in NGS and a follow-up course on the NBIC/LUMC NGS data analysis course (September 2012 in Rotterdam.) The course will consist of seminars and hands-on Galaxy and R practicals and will focus on data pre-processing, quality control, and statistical methods for detection of differential gene expression. * RNA-seq experimental approaches * Alignment and de novo assembly * Statistics for differential gene expression * eQTL analysis and allele specific expression * Software for RNA-seq data analysis Participants of the RNA-seq course should preferably have participated in the NGS data analysis course or have demonstrated hands-on experience with NGS data analysis. Dates: October 15-17th, 2012 Venue: AMC, Amsterdam, The Netherlands Coordinator: Peter-Bram 't Hoen (LUMC) For more information and registration see our website: www.nbic.nl/?id=NGSRNAseq www.nbic.nl/?id=rnaseqappform2012 Or send e-mail to Patrick Koks (education(a)nbic.nl) The NBIC BioWise Life Sciences (BioWise-LS; www.nbic.nl/education) programme currently offers five bioinformatics courses focussing on application and data-analysis of Next-generation sequencing (NGS). All NBIC NGS courses are co-developed and co-organised by experts in the field and in close collaboration with leading research groups throughout the Netherlands. All NBIC courses are taught in English and are open to PhD students and researchers worldwide. Patrick Koks, NBIC BioWise - Education phone: #31-(0)24-3615210 e-mail: Patrick.koks(a)nbic.nl web: www.nbic.nl, www.ebiomics.org Postal Address: CMBI 260 Radboud University / UMC / NCMLS PO Box 9101, 6500 HB Nijmegen, The Netherlands __________ Information from ESET NOD32 Antivirus, version of virus signature database 7448 (20120905) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com

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BeNeLux Bioinformatics Conference 2012: register now!
by Femke Francissen 31 Aug '12

31 Aug '12

BeNeLux Bioinformatics Conference 2012: register now! The 7th edition of the BeNeLux conference (BBC12) will be organised by the Centre for Molecular and Biomolecular Informatics (CMBI) and the Netherlands Bioinformatics Centre (NBIC). This year's key theme will be "Bioinformatics at the interface". Both registration and abstract submission for the BBC12 are now open. Dates: 10 & 11 December 2012 Venue: UMC St Radboud, Nijmegen, the Netherlands Website: http://www.nbic.nl/bbc2012 Click here<http://www.nbic.nl/about-nbic/events/bbc2012/registration/> to register! We look forward to welcoming you in Nijmegen. CMBI & NBIC Barbara van Kampen (CMBI) Femke Francissen (NBIC)

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final program invited lectures symposium Radboud University Nijmegen 6 september
by elenam＠cs.ru.nl 29 Aug '12

29 Aug '12

Dear Colleague, Please find below the final program of the invited lectures of the one-day symposium on the integrative analysis of brain diseases to be held at the Radboud University Nijmegen, The Netherlands (see http://macbrain2012.cs.ru.nl/program) A pdf version of the program with abstracts of talks can be downloaded at http://macbrain2012.cs.ru.nl/files/program-with-abstracts.pdf Registration at http://macbrain2012.cs.ru.nl/registration Could you please distribute this information to your colleagues? Thanks in advance. Kind regards, Elena Marchiori --------------- Program Thursday 6 September 2012 Opening: Elena Marchiori and Inge Huitinga 9:00 9:30 Registration, coffee and opening Session 1: Brain Banks Chair: James Ironside 9:30 10:20 Jean-Paul Vonsattel Director of the New York Brain Bank at Columbia University The NYBB at Columbia University and donor data 10:20 11:10 Maree Webster Director SMRI Brain Collection and Research Laboratory The Stanley Medical Research Institute (SMRI) Brain Collection and Database 11:10 11:30 Coffee break Session 2: Data Mining and Machine Learning Chair: Pedro Larranaga 11:30 12:20 Sophia Ananiadou Director of the National Centre for Text Mining (NaCTeM) Extracting Events of Biological Relevance from Text 12:20 13:10 Yves Moreau KU Leuven ESAT-SCD & SymBioSys Center for Computational Systems Biology Candidate Gene Prioritization by Genomic Data Fusion 13:10 14:00 Lunch break Session 3: Clinical and Pathological Studies Chair: Peter Lucas 14:00 14:50 Amanda Kiliaan Department of Anatomy/Cognitive Neurosciences, Radboud University Nijmegen On Diet and the Brain: from mice to men 14:50 15:40 Harro Seelaar Erasmus MC Genetic background of frontotemporal dementia and its relation with the neuropathology 15:40 16:00 Coffee break 16:00 16:40 Tineke van Veen Dept. of Psychiatry, Leiden University Medical Centre, The Netherlands Cross-linking pathological and clinical observations in depression and anxiety: building a genetic bridge 16:40 17:10 Inge Huitinga and Elena Marchiori Netherlands Brain Bank & Radboud University Machine Learning in Action: Mining the Netherlands Brain Bank 17:10 18:00 Closure and Drinks

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vacancies at Galapagos
by Véronique Deiteren 21 Aug '12

21 Aug '12

Dear Sir, Dear Madam, Please find below 3 vacancies in BioInformatics/BioIT for Galapagos for our Mechelen (Belgium) and Leiden (Netherlands) sites. More information can be found in attachment [Description: blocks.png] Senior Scientist Bioinformatics, MEC-115 As member of the Discovery Informatics team you will give day to day support to the research teams using dedicated BioIT/research software and perform daily bioinformatics tasks supporting the different research projects of Galapagos. Where needed you will adapt or develop new BioIT/BioInformatics applications. You will maintain the different sequence annotation pipelines and further develop new bioinformatics annotation pipelines where needed. You will configure dedicated research software in order to optimally support the research teams. You will continuously guard data consistency and data integrity over the different applications and databases. You will closely collaborate with the multidisciplinary disease biology and drug discovery teams. This position offers an exciting opportunity to develop and provide information-based services to the science and business at Galapagos. [Description: blocks.png] Scientist Bioinformatics, MEC-115b As member of the Discovery Informatics team you will give day to day support to the research teams using dedicated BioIT/research software and perform daily bioinformatics tasks supporting the different research projects of Galapagos. Where needed you will adapt or develop new BioIT/BioInformatics applications. You will maintain the different sequence annotation pipelines and further develop new bioinformatics annotation pipelines where needed. You will configure dedicated research software in order to optimally support the research teams. You will continuously guard data consistency and data integrity over the different applications and databases. You will closely collaborate with the multidisciplinary disease biology and drug discovery teams and this position offers an exciting opportunity to develop and provide information-based services to the science and business at Galapagos. [Description: blocks.png] Bioinformatician, LEI-032 This position offers a unique experience to work in an exciting and dynamic environment of a well-known international biotech company. You will give day to day support to the research teams by performing bioinformatics tasks such as data collection and analysis and by configuring dedicated research software for data management and analysis. You will continuously guard data consistency and data integrity over the different applications and databases. Where needed, you will adapt or develop new BioIT/bioInformatics applications supporting the research teams. Best regards Veronique Deiteren HR Manager Galapagos NV Generaal De wittelaan L11 A3 2800 Mechelen Belgium Tel 015 342 900 Fax 015 342 910 -- This e-mail and its attachment(s) (if any) may contain confidential and/or proprietary information and is intended for its addressee(s) only. Any unauthorized use of the information contained herein (including, but not limited to, alteration, reproduction, communication, distribution or any other form of dissemination) is strictly prohibited. If you are not the intended addressee, please notify the originator promptly and delete this e-mail and its attachment(s) (if any) subsequently. Neither Galapagos nor any of its affiliates shall be liable for direct, special, indirect or consequential damages arising from alteration of the contents of this message (by a third party) or as a result of a virus being passed on.

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