- BBClist - maillist.psb.ugent.be

symposium: "from big data to bedside"
by Katleen De Preter 14 Nov '14

14 Nov '14

Dear Colleague, We are pleased to announce a symposium on translational bioinformatics that will take place in Ghent, 2nd of April 2015: "From big data to bedside: translational bioinformatics in cancer research". Several international and national top-speakers will present their data (see attached poster and website). On the 1st of April a workshop will be organised for PhD students and young post-docs (program under construction). Registration will start on the 1st of December 2014 (seats are limited: 180 for symposium (small registration fee), 40 for workshop (free)). Further info on http://bigdata.cmgg.be. Please, feel free to spread this announcement! Hope to meet you at the symposium! Kind regards, organiser: Katleen De Preter co-organisers: Frank Speleman, Jo Vandesompele, Pieter Van Vlierberghe, Pieter Mestdagh

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[Gtpb] CSDM14 - Chromosome structure determination using modelling and Hi-C data - Bioinformatics Training Course - Announcement/Reminder
by Pedro Fernandes 13 Nov '14

13 Nov '14

Dear GTPB members, Last 3 seats available for the CSDM14 Bioinformatics training course: "Chromosome structure determination using modelling and Hi-C data". Nov. 25th-28th Deadline: November 15th 2014. http://gtpb.igc.gulbenkian.pt/bicourses/CSDM14/ Best wishes Pedro -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL 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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JOBS: several PhD-candidate and postdoc positions in systems biology
by Arts Ilja (EPID) 10 Nov '14

10 Nov '14

The Maastricht Centre for Systems Biology (MaCSBio) is now hiring!!! The 6 PhD-candidate and 6 postdoc positions are online at http://macsbio.maastrichtuniversity.nl/current-vacancies-0 and on Academic Transfer. Maastricht University, The Netherlands, is looking for several PhD candidates and postdocs who will work on the integration of biological data coming from different empirical domains using mathematical multi-scale modelling approaches. This research will occur within two highly integrated research lines in the new Maastricht Centre for Systems Biology (MaCSBio). The centre, which is a joint activity of three Faculties, will offer a dynamic, challenging environment with high profile multidisciplinary research. We are looking for candidates who are specialists in the approaches needed and who have the ambition and the competences to think and work outside the usual disciplinary boxes. Description research lines: Research line 1: SYStems biology approach TOwards targeted Personalised Prevention of chronic diseases in the 'obese system' (SYSTOPP) By studying the 'obese system', we aim to improve our mechanistic insight into the development of chronic diseases, and to identify new strategies for prevention and treatment based on personalised risk profiles for obese people. We will focus on data- and knowledge-driven approaches to integrate and mathematically model multi-omics data with phenotypic continuous traits and disease states, in the context of interacting environmental factors. We will use the large body of human data and samples available in Maastricht. Research line 2: A systems biology approach to model experience and disease-induced modifications in NEUral and GENetic NETworks (NeuGenNet) This multidisciplinary research programme has the overall goal of achieving new insights into the processes of normal and abnormal experience-induced modifications in brain and genetic networks, using mathematical tools and modelling approaches to bridge research domains and spatial scales of inquiry. The start-up of the programme will focus on advancing dynamic systems theories for modelling complex biological networks and applying these models to study: 1) the neural mechanisms of experience-induced changes in healthy brain networks and cognitive processes and 2) the genomic mechanisms underlying disease-induced changes in these networks and processes. [cid:image001.jpg@01CFE4A8.DE3297D0] Ilja C.W. Arts, PhD Professor of Molecular Epidemiology of Chronic Diseases Dept. of Epidemiology ilja.arts(a)maastrichtuniversity.nl <mailto:ilja.arts@maastrichtuniversity.nl> www.maastrichtuniversity.nl<http://www.maastrichtuniversity.nl/> macsbio.maastrichtuniversity.nl<http://macsbio.maastrichtuniversity.nl/> www.M2E2.nl<http://www.m2e2.nl/> Peter Debyeplein 1, 6229 HA, Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 3882971 F +31 43 3884128 M + 31 6 15623990 [cid:image002.jpg@01CFE4A8.DE3297D0] For more information: http://macsbio.maastrichtuniversity.nl/

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JOBS: several PhD-candidate and postdoc positions in systems biology
by Arts Ilja (EPID) 02 Nov '14

02 Nov '14

The Maastricht Centre for Systems Biology (MaCSBio) is now hiring!!! The 6 PhD-candidate and 6 postdoc positions are online at http://macsbio.maastrichtuniversity.nl/current-vacancies-0 and on Academic Transfer. Maastricht University, The Netherlands, is looking for several PhD candidates and postdocs who will work on the integration of biological data coming from different empirical domains using mathematical multi-scale modelling approaches. This research will occur within two highly integrated research lines in the new Maastricht Centre for Systems Biology (MaCSBio). The centre, which is a joint activity of three Faculties, will offer a dynamic, challenging environment with high profile multidisciplinary research. We are looking for candidates who are specialists in the approaches needed and who have the ambition and the competences to think and work outside the usual disciplinary boxes. Description research lines: Research line 1: SYStems biology approach TOwards targeted Personalised Prevention of chronic diseases in the ‘obese system’ (SYSTOPP) By studying the ‘obese system’, we aim to improve our mechanistic insight into the development of chronic diseases, and to identify new strategies for prevention and treatment based on personalised risk profiles for obese people. We will focus on data- and knowledge-driven approaches to integrate and mathematically model multi-omics data with phenotypic continuous traits and disease states, in the context of interacting environmental factors. We will use the large body of human data and samples available in Maastricht. Research line 2: A systems biology approach to model experience and disease-induced modifications in NEUral and GENetic NETworks (NeuGenNet) This multidisciplinary research programme has the overall goal of achieving new insights into the processes of normal and abnormal experience-induced modifications in brain and genetic networks, using mathematical tools and modelling approaches to bridge research domains and spatial scales of inquiry. The start-up of the programme will focus on advancing dynamic systems theories for modelling complex biological networks and applying these models to study: 1) the neural mechanisms of experience-induced changes in healthy brain networks and cognitive processes and 2) the genomic mechanisms underlying disease-induced changes in these networks and processes. [cid:image001.jpg@01CFE4A8.DE3297D0] Ilja C.W. Arts, PhD Professor of Molecular Epidemiology of Chronic Diseases Dept. of Epidemiology ilja.arts(a)maastrichtuniversity.nl <mailto:ilja.arts@maastrichtuniversity.nl> www.maastrichtuniversity.nl<http://www.maastrichtuniversity.nl/> macsbio.maastrichtuniversity.nl<http://macsbio.maastrichtuniversity.nl/> www.M2E2.nl<http://www.m2e2.nl/> Peter Debyeplein 1, 6229 HA, Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 3882971 F +31 43 3884128 M + 31 6 15623990 [cid:image002.jpg@01CFE4A8.DE3297D0] For more information: http://macsbio.maastrichtuniversity.nl/

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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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