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

N2N seminar series program 2014-2015
by Katrijn Vannerum 31 Oct '14

31 Oct '14

Dear, The N2N seminar series on bioinformatics program 2014-2015 is available. Please save the dates. Up to date information can always be found at www.nucleotides2networks.be/events<http://www.nucleotides2networks.be/events> www.nucleotides2networks.be/node/232<http://www.nucleotides2networks.be/node/232> Hoping to meet at the seminars, With best regards, Katrijn Vannerum Project manager N2N (From Nucleotides to Networks) Multidisciplinary Research Partnership Bioinformatics and Systems Biology Ghent University http://www.nucleotides2networks.be/ twitter: @N2N_UGent Katrijn.Vannerum(a)UGent.be<mailto:Katrijn.Vannerum@UGent.be> Technologiepark 927 9052 Gent, Belgium +32 (0)9 331 36 85 [cid:image001.png@01CFF449.F01C9A30]

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MSc. Research Project Opportunity in Integrative Bioinformatics
by Francisco Azuaje 30 Oct '14

30 Oct '14

MSc. Research Project Opportunity in Integrative Bioinformatics We are seeking a student to develop new computing models and applications for an international research cooperation project: infused-project.eu Required essential skills and experience: We are looking for a student currently enrolled on an MSc course in computer science, bioinformatics or systems biology, who meets the following requirements: 1. Good understanding of machine learning techniques. 2. Solid skills and enthusiasm to code software in any of the following languages: Java, C, Python or R. 3. Skills in statistical analysis or data mining. 4. Good communication skills in English. What we offer: 1. The opportunity to complete a MSc. research dissertation in a dynamic and truly inter-disciplinary research environment. 2. To be part of a larger research effort relevant to improving human health. 3. You will expand your knowledge and skills on: machine learning, translational bioinformatics, biological network models, and the integration of in silico with in vivo biological research. Where and when: The successful applicant will be affiliated with the NorLux Neuro-Oncology Laboratory at CRP-Santé in Luxembourg (www.crp-sante.lu<http://www.crp-sante.lu>). This full-time position will begin as early as 5 January 2014, and will have a total duration of 6 months. The successful candidate will receive a monthly allowance. If you wish to apply for this position, submit your CV together with a short letter explaining your interest in this opportunity through: http://www.crp-sante.lu/Jobs2/Jobs-opportunities/Selection (Department of Oncology section) Deadline for receiving applications: 1 December 2014. _________________________________ Francisco Azuaje, PhD Senior Researcher NORLUX Neuro-Oncology Laboratory Centre de Recherche Public de la Santé (CRP-Santé) 1A-B, rue Thomas Edison, L-1445 Strassen Luxembourg Tel: +352 26970-875 Fax: +352 26970-396 Email: francisco.azuaje(a)crp-sante.lu<mailto:francisco.azuaje@crp-sante.lu> Website: http://www.crp-sante.lu<http://www.crp-sante.lu/> Join us on Facebook and follow our activities on Twitter: http://www.facebook.com/crpsante http://twitter.com/crpsante http://www.norlux.lu This message (including any attachments) is intended for the addressee only and may contain confidential and/or privileged information and/or information protected by intellectual property rights. If you have received this message by mistake, please notify the sender by return e-mail and delete this message from your system. You should not use, alter, copy or distribute this message or disclose its contents to anyone. E-mail transmission can not be guaranteed to be secure or error free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. CRP-Santé shall not be responsible nor liable for the proper and complete transmission of the information contained in this communication nor for any delay in its receipt or damage to your system.

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Reminder: Register now for Multiscale Modeling of Biomolecular Systems symposium - 28 November 2014
by Sanne Abeln 29 Oct '14

29 Oct '14

The deadline for registration for the Multiscale Modeling of Biomolecular Systems (MMBS) symposium is approaching. This meeting is jointly organized by the Amsterdam Center for Multiscale Modeling (ACMM) and the Netherlands Society for Biomolecular Modeling (NSBM), please find the programme below. *Deadline for registration: *5 November 2014 *Registration & posters: *https://www.aanmelder.nl/79914/subscribe Programme Multiscale Modelling of Biomolecular Systems (combined ACMM/NSBM symposium) Date and location: Friday 28 November 2014, VU University, Amsterdam 10.30 - 11.00 Welcome and coffee 11.00 - 11.05 Opening 11.05 - 12.00 Ursula Roethlisberger (EPFL, Lausanne, Switzerland Keynote: TBA 12.00 - 12.20 João Rodrigues (Utrecht University) Co-evolution as a powerful resource for predicting the structure of protein-protein complexes 12.20 - 13.30 Lunch and poster session 13.30 - 13.50 Manuel Melo (University of Groningen) Adaptive resolution simulations with Martini 13.50 - 14.10 Csaba Daday (University of Twente) Excited states in complex environments: You can't always get what you want 14.10 - 14.30 Behrouz Eslami-Mossalam (Leiden University) Multiplexing nucleosome positioning signals and genetic information 14.30 - 14.50 René de Jong (DSM) Engineering nature’s enzyme repertoire for food and pharma 14.50 - 15.50 Tea break and poster session 15.50 - 16.10 Xianlong Wang (UESTC, Chengdu, China and VU University) Full system quantum mechanical calculation of protein-ligand interaction energy with subsystem density functional theory approach 16.10 - 16.30 Matteo Giani (University of Twente) Coarse-grained simulations of clathrin assembly initiated by adaptor proteins 16.30 - 17.25 David Jones (University College London, UK) Keynote: Progress and challenges in predicting protein structure from amino acid sequence covariation 17.25 - 17.30 Closure 17.30 - 19.00 Drinks and poster session Program Committee: Jocelyne Vreede (UvA), Paola Gori-Giorgi (VU) Daan Geerke (VU), Sanne Abeln (VU) Advisory Board (NSBM+ACMM): Gerry Nicolaes (UM), Gert Vriend (UMCN) Peter Bolhuis (UvA), Evert Jan Meijer (UvA) Matthias Bickelhaupt (VU), Luuk Visscher (VU) -- Sanne Abeln s.abeln(a)few.vu.nl Assistant Professor - VU University Amsterdam www.few.vu.nl/~abeln Treasurer - Prelude Foundation www.preludefund.org

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PhD Position in Bioinformatic Analysis of Astrocyte Function
by Mark Fiers 28 Oct '14

28 Oct '14

Dear all. We have an exciting PhD position open on the analysis of single cell transcriptomics on astroctyes. with best regards Mark Fiers

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PhD position: Haplotyping in polyploid crops
by Ridder, Dick de 28 Oct '14

28 Oct '14

We have an exciting opportunity for an enthusiastic PhD student to develop new methodology for haplotyping genomes of polyploid crops, using novel genotyping-by-sequencing approaches. We are looking for an ambitious PhD student with an MSc degree in bioinformatics, computer sciences, statistics, biotechnology, biology or plant sciences. The PhD project 'Haplotyping in polyploid crops using genetics, genomics and bioinformatics' aims at solving important questions in crops like potato, leek, rose, chrysanthemum, that have four or six copies of a genome: what is the composition (haplotype) of each of the underlying genomes, both locally (gene level) and over larger distances (chromosome level)? Can we distinguish different dosages of haplotypes? Can we characterize plants in terms of haplotype composition? Can we relate observed haplotypes to variation in phenotypic traits? In this project, the goal is to develop statistical, genetics and bioinformatics tools for novel genotyping-by-sequencing (GBS) approaches for polyploid crops. The project will deliver effective strategies for haplotyping in polyploid crops, faster discovery of candidate genes and of their allelic variants for traits of interest to plant breeders. It is a collaborative initiative of the Bioinformatics and Plant Breeding chair groups at Wageningen University. You will work in close cooperation with other PhD students and researchers involved in related projects on the development of a genetic analysis pipeline for polyploid crops and novel sequencing strategies for polyploid genomes. More information about the position, the research groups involved, and a possibility to apply for this position can be found at: http://www.wageningenur.nl/en/Education-Programmes/PhD-Programme/PhD-Vacanc… Interested candidates can apply up to September 15, 2014 through the above-mentioned website. Dr. Chris Maliepaard (Quantitative aspects of Plant Breeding) Prof. Dick de Ridder (Bioinformatics) Wageningen University The Netherlands

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Highly motivated Bio-informatician/PhD student position offered University of Antwerp
by Vandamme Timon 27 Oct '14

27 Oct '14

Dear all, The Center for Oncological Research (CORE) and the Center for Medical Genetics from the University Hospital Antwerp (UZA) and the University of Antwerp (UA) is looking for a PhD-student/bio-informatician for a research project on integrated next-generation sequencing data analysis. Further information can be found after following link: * Highly motivated Bio-informatician/PhD student<https://www.uantwerpen.be/nl/jobs/vacatures/ap/2014bapfggwef251/> Please distribute this position offer to anyone who could be interested. With kind regards, Timon. --- Timon Vandamme, MD PhD fellow - Medical Oncology resident [cid:F6644A61-F5A0-4860-A92E-D045AA7837C2] Human Molecular Genetics Prins Boudewijnlaan 43, 2nd floor B2650 Edegem, Belgium Department of Oncology Antwerp University Hospital Wilrijkstraat 10 B2650 Edegem, Belgium e-mail | timon.vandamme(a)uantwerpen.be<mailto:timon.vandamme@uantwerpen.be> e-mail | timon.vandamme(a)uza.be<mailto:timon.vandamme@uza.be> Please consider the environment before printing this message.

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Job opportunity: Bioinformatics group leader in Heidelberg
by J.J.B. Koster 23 Oct '14

23 Oct '14

Dear Colleagues, The department of Pediatric Neurooncology at the DKFZ in Heidelberg, Germany, has a job opportunity for a 'Bioinformatics Group Leader' Please find information (in English) on this position and how to apply at: http://www.dkfz.de/en/stellenangebote/index.php?id=169/2014 All the best, Jan Koster ________________________________ AMC Disclaimer : http://www.amc.nl/disclaimer ________________________________

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[Gtpb] CSDM14 - Chromosome structure determination using modelling and Hi-C data - Bioinformatics Training Course - Announcement/Reminder
by Pedro Fernandes 21 Oct '14

21 Oct '14

TRAINING COURSE ANNOUNCEMNT/REMINDER The training course CSDM14 is open for applications. IMPORTANT DATES for this Course Deadline for applications: November 15th 2014 Notification of acceptance within 72 hours of application Course date: November 25th to November 28th 2014 http://gtpb.igc.gulbenkian.pt/bicourses/CSDM14/ CSDM14 - Chromosome structure determination using modelling and Hi-C data with Marc Marti-Renom, Davide Baù and François Serra Welcome to the world of using Hi-C data - http://www.ncbi.nlm.nih.gov/pubmed/22652625 - in the context of discovering genome organization. Course description The sequence of a genome alone does not carry enough information to fully understand how genomic processes are carried out in the cell nucleus; to achieve this, the knowledge of the three-dimensional (3D) architecture of a genome is necessary. Advances in genomic technologies and the development of new analytical methods, such as 3C-based methods, have allowed getting insights at unprecedented resolution into how the genome is organized. Recently, it has been shown that chromatin is organized in Topologically Associating Domains (TADs), large interaction domains that appear to be conserved among different cell types. In this course, participants will learn to use TADbit, a software for the analysis and modeling of Hi-C data. The course will cover all the aspects of modeling with Hi-C data: Generation of Hi-C contact matrices from raw data (that is, iterative mapping of the fastq reads to the reference genome, cleaning and normalization) Analysis of Hi-C matrices (Hi-C map visualization, TAD identification, experiment comparison, and TAD selection) 3D modeling and analysis of TADs The 3D module of TADbit is based on a computational module of the Integrative Modeling Platform (IMP, http://www.integrativemodeling.org) that uses chromosome conformation capture data to determine the 3D architecture of genomic domains and entire genomes at unprecedented resolutions. Participants can bring-in specific biological questions and/or their on data to work on during the course. At the end of the course, participants will be familiar with the TADbit software, enabling them to fully analyze and model Hi-C data. Target Audience The course is oriented to experimental researchers and bioinformaticians at the graduate and post-graduate levels. The last edition of this course was attended by people with different backgrounds and interested in the genome organization. Moreover, Hi-C data have recently been used in metagenomics studies to accurately cluster metagenome assembly contigs into groups that contain nearly complete genomes of each species. It is likely that the participants to this course aim at getting involved in generating Hi-C data for chromosome structure determination or that they just want to be able to correctly interpret and analyze publicly available data. The Linux and Programming skills are really only recommended, not essential. Thank you for your interest Pedro Fernandes -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt ----- 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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[Gtpb] Training course announcement/reminder BPB14 Bioinformatics using Python for Biologists
by Pedro Fernandes 20 Oct '14

20 Oct '14

TRAINING COURSE ANNOUNCEMNT/REMINDER The training course BPB14 is now open for applications. IMPORTANT DATES for this Course Deadline for applications: October 28th 2014 Latest notification of acceptance date: October 29th 2014 Course date: November 3rd to November 7th 2014 http://gtpb.igc.gulbenkian.pt/bicourses/BPB14/ This course is specifically designed to provide a jump start into programming for life science researchers. Participants will learn to use programming approaches to solve problems using the Python programming language. This is one of the most popular training courses. Feedback from last year's edition shows a high degree of satisfaction. From the questionnaires here is a couple of anonymous testimonials "I am very happy that I took this course" "BPB has introduced me to a new world of possibilities and I hope that it is going to make my work/life even more interesting" "A clear and thorough introduction to Python that can make one want to learn more" "Fantastic" Please make sure that you have a look at the course description. http://gtpb.igc.gulbenkian.pt/bicourses/BPB14 Each course participant will receive a copy of the NEW book Managing your biological data with Python" to take home. The book includes texts and exercises that will be used in the course, naturally, because there is a strong connection with the course content and origin. http://www.clbme.bas.bg/bioautomation/2014/vol_18.2/files/newbooks_1.pdf Thank you for your interest Pedro Fernandes -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt ----- End forwarded message ----- _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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Job: Bioinformatician (cancer research)
by Irrthum Alexandre 20 Oct '14

20 Oct '14

Dear colleagues, My organisation is hiring a bioinformatician to work in the field of cancer research. Please find the details here: http://www.bigagainstbreastcancer.org/career-opportunities Best regards, Alexandre ________________________________ Alexandre Irrthum, PhD Bioinformatician / Cancer Geneticist Breast International Group (BIG)-aisbl c/o Jules Bordet Institute Blvd de Waterloo 121, 7th fl 1000 Brussels, Belgium Tel: +32 2 541 7243 www.breastinternationalgroup.org<http://www.breastinternationalgroup.org/>

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