- BBClist - maillist.psb.ugent.be

Data analysis engineer/Post-doctoral position
by Christophe Caron 22 Jan '15

22 Jan '15

This project is part of HAPAR French ANR (Head L. Guillou), in collaboration with the ABiMS platform (Analysis and Bioinformatics for Marine Science) and the University of Ghent (P. Rouzé/S. Rombauts) The Roscoff Marine Station provides to the scientific community a bioinformatics platform, ABiMS, in which the research will be conducted. The Ghent site on its side provides the ORCAE genome curation platform that will be used during the project. He / she will interact and move over long periods (several months) on the Ghent university site during half of his contract. The engineer will be located in Roscoff (with trips on Ghent). The engineer will be in charge of the genome and RNAseq data analyse. He will initially seek transposable elements in the genome in collaboration with the University of Ghent, using different strategies developed by the VIB team. Required Skills - Good experience of eukaryote genome annotation (structural and functional analysis, Transposable element) - Strong knowledge of NGS analysis tools and methods, and particularly in RNAseq analysis - Good knowledge of phylogeny - Good knowledge of statistical analysis - Advanced knowledge of scripting languages (Perl, Python,…) - Basic knowledge of Linux and Unix - Global knowledge in genetics and molecular biology - Rigour, autonomy and excellent relational and teamwork skills Limited term contract with funding available for 30 months, and available immediately. Salary : 1880 up to 2100 euros / month (depending on qualifications and experience) Send CV and cover letter to abims.job(a)sb-roscoff.fr before February, 15th. More information at: http://www.sfbi.fr/content/data-analysis-engineer -- Christophe Caron Station Biologique / Service Informatique et Bio-informatique Place Georges Teissier - CS 90074 29688 Roscoff Cedex Analysis and Bioinformatics for Marine Science http://abims.sb-roscoff.fr/ christophe.caron(a)sb-roscoff.fr tél: +33 (0)2 98 29 25 43 / +33 (0)6 07 83 54 77

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BioSB course on systems medicine: 8 seats left for 2015 Jan. 29-30
by Diman van Rossum | BioSB research school 22 Jan '15

22 Jan '15

BioSB course announcement <http://www.ncsb.nl/> BioSB course on personalized systems medicine Mailing date: 2015 January 22 Message for: BBC mailing list Email address: bbclist(a)psb.vib-ugent.be Dear Madam, Sir, The first course the BioSB research school organises in 2015 is a two-day course on personalized systems medicine. This course runs from January 29 to 30 - less than two weeks from now - at the VU University Amsterdam. There are still 8 seats open at this high-level course involving 18 lecturers. The course is designed for PhD students, postdocs and staff from academia and industry alike. You are welcome to register for this course, or otherwise to distribute this announcement within your organisation. <http://www.biosb.nl/course-systems-medicine/enrollment> Registration is still possible until next week Tuesday 2015 January 27. You may find detailed information on this systems medicine course here below. ............................................................................ .............................. Key course information Topic: O2 for personalized systems medicine: from inspiration to aspiration Dates: 2015 January (28,) 29-30, (Wed) Thu-Fri Venue: Room C648, Science Building, VU University Amsterdam De Boelelaan 1085, 1081HV Amsterdam Website: <http://www.biosb.nl/course-systems-medicine> www.biosb.nl/course-systems-medicine Programme: <http://www.icsb-nl.nl> www.icsb-nl.nl Registration: <http://www.biosb.nl/course-systems-medicine/enrollment> www.biosb.nl/course-systems-medicine/enrollment Deadline: 2015 January 27 (Tue) Lecturers: 18 lecturers (see below) Coordinators: <mailto:h.v.westerhoff@uva.nl> Hans Westerhoff (UvA, VU, University of Manchester), <mailto:b.m.bakker01@umcg.nl> Barbara Bakker (UMCG/RUG) ............................................................................ .............................. Eighteen (18!) course lecturers A total of 18 lecturers will give presentations on a wide array of aspects/topics of relevance for personalised systems medicine. Topics include metabolic diseases, pharmacology, sociological aspects, epigenetics, epidemiology, human metabolic map, cell cycle, stem cells, network analysis, malaria, microbial ecology, oncology, and bioinformatics. The following speakers are involved: Hans Aerts (UL), Ilja Arts (UM), Barbara Bakker (UMCG/RUG), Matteo Barberis (UvA), Jurgen Haanstra (VU), Jaap Heringa (VU), Thierry Mondeel (UvA), Gerard Muyzer (UvA), Marijana Radonjic (EdgeLeap), Gaston Remmers (HABITS/Inspire2Liv), Jaap Seidell (VU), Jacky Snoep (University of Stellenbosch-ZA), Renée van Amerongen (UvA), Piet Hein van der Graaf (UL), Ben van Ommen (TNO), Pernette Verschure (UvA), Lodewyk Wessels (NKI), Hans Westerhoff (UvA, VU, University of Manchester-UK). ............................................................................ ............................... Organised by BioSB Research School <http://biosb.nl/wp-content/uploads/2014/07/BioSB_Website_Image_400x67_20140 417.jpg> University of Amsterdam (UvA) <http://www.maastrichtuniversity.nl/> <http://biosb.nl/wp-content/uploads/2013/07/SBNL_Logo_100x29_20140731.jpg> VU University Amsterdam (VU) <http://www.maastrichtuniversity.nl/> <http://biosb.nl/wp-content/uploads/2013/07/SBNL_Logo_100x29_20140731.jpg> University Medical Centre Groningen (UMCG) <http://biosb.nl/wp-content/uploads/2014/08/MaCSBio_Logo_155x24_20140720.jpg > Infrastructure Systems Biology - Europe (ISBE) <http://biosb.nl/wp-content/uploads/2014/07/UM_Logo_256x198_20131014.jpg> ............................................................................ ............................... On behalf of the course coordinators, Hans Westerhoff and Barbara Bakker, Diman van Rossum, PhD Netherlands Bioinformatics and Systems Biology Research School (BioSB) c/o (Geert Grooteplein 28), PO Box 9101, 6500HB Nijmegen, The Netherlands Tel: +31-6-2260 7479 Email: <mailto:diman.van.rossum@biosb.nl> diman.van.rossum(a)biosb.nl Website: <http://www.biosb.nl> www.biosb.nl This message is distributed through the BBC mailing list.

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Master of Science in Bioinformatics at Ghent University
by Katrijn Vannerum 20 Jan '15

20 Jan '15

Dear, we are proud to announce that, with reservation of final approval by the Flemish Government, the new Master in Bioinformatics at Ghent University will start in the academic year 2015-2016! Read about it: http://www.nucleotides2networks.be/master and spread the word. With kind regards, Katrijn Vannerum PhD 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@01D034B3.C0401580]

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Big data course (in Dutch) at Ghent University
by Katrijn Vannerum 20 Jan '15

20 Jan '15

Dear, N2N is involved in the Big data 2015 Course (in Dutch) at Ghent University. * Module 1: Gegevensbeheer 26 februari, 5, 12, 19, 26 maart 2015 * Module 2: Gegevensanalyse 2, 23 en 30 april, 7 en 21 mei 2015 * Module 3: Visualisatie 28 mei en 4 juni 2015 Dit programma laat toe een getuigschrift van de Universiteit Gent te behalen. http://www.nucleotides2networks.be/node/327 Kind regards, Katrijn Vannerum PhD 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@01D03499.C8127D80]

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Life Science Courses at Avans University of Applied Sciences
by Sari van Heel - Vauhkala 16 Jan '15

16 Jan '15

Dear members of BBClist, We would like to draw your attention to three courses that the Research Group Analysis Techniques in Life Science (Avans University of Applied Sciences, Breda, the Netherlands) will be offering in April 2015: 1) Principles, parameters and applications of PCR; 7 April 2015 Registration fee: €400,- Website : http://www.alsavans.nl/avans-training-2545.htm 2) Real-time PCR in molecular diagnostics; 8-10 April 2015 Registration fee: €900,- Website: http://www.alsavans.nl/avans-training-2548.htm 3) Introduction to Next Generation Sequencing; technologies and data analysis; 14-17 April 2015 Registration fee: €1100,- Website: http://www.alsavans.nl/avans-training-2542.htm The digital registration form is available on the website. Should you have any questions, please do not hesitate to contact us by email at: si.vanheel-vauhkala(a)avans.nl<mailto:si.vanheel-vauhkala@avans.nl> Kind regards, Ms. Sari van Heel-Vauhkala Secretary Research Group Analysis Techniques in Life Science Disclaimer ( http://www.avans.nl/over-avans/e-mail-disclaimer )

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Postdoc Opportunity - Comparative Genomics, Horizontal Gene Transfer in Diatoms
by Katrijn Vannerum 15 Jan '15

15 Jan '15

From: Andrew James Alverson [mailto:aja@uark.edu] Sent: woensdag 14 januari 2015 19:27 To: Andrew James Alverson Subject: Postdoc Opportunity - Comparative Genomics, Horizontal Gene Transfer in Diatoms Dear Colleagues, We are conducting a search for a postdoctoral position at the Chicago Botanic Garden to work on an NSF-funded grant in genome reconstruction, horizontal gene transfer, and phylogenomics of diatoms (see the ad below). If you could forward the ad to anyone who might be interested in the position, we would appreciate your help in casting a wide net to find the best possible candidate. Thanks for your help, Andy Alverson and Norm Wickett …. Andrew Alverson University of Arkansas Department of Biological Sciences 1 University of Arkansas, SCEN 601 Fayetteville, AR 72701-1201 office: 479-575-7975 lab: 479-575-4886 http://alversonlab.com/ - - - POSTDOCTORAL RESEARCH ASSOCIATE IN COMPARATIVE GENOMICS AT THE CHICAGO BOTANIC GARDEN We are hiring a postdoctoral research associate for 2.5 years to lead the genome sequencing efforts of an NSF-funded, Phylogenetic Systematics grant titled “Evaluating the contributions of horizontally transferred bacterial genes and endogenous duplication events to the diversification of diatoms”. This project integrates transcriptomics, phylogenomics, and genome sequencing to understand the role of horizontal gene transfer and whole genome duplication in the diversification of diatoms. This project is a collaborative NSF research project between Andrew Alverson (University of Arkansas) and Norman Wickett (Chicago Botanic Garden & Northwestern University). The postdoc will be based at the Chicago Botanic Garden, where the genome sequencing, assembly, and annotation efforts will be based. START DATE: Spring - Fall, 2015 APPLICATION REVIEW: Begins immediately and will continue until filled DUTIES AND RESPONSIBLITIES: The postdoc will be responsible for coordinating and conducting the sequencing, assembly, and annotation of several diatom genomes. Additionally, the position includes the analysis of genome content and structure association with the diversification of diatoms, with an emphasis on the detection of horizontal gene transfer and whole genome duplication. Expectations are that postdoc will contribute to the preparation of numerous publications, many of which will be first-authored. Teaching and curriculum development opportunities will be provided through the Graduate Program in Plant Biology and Conservation, a joint program between the Chicago Botanic Garden and Northwestern University. Finally, the position includes involvement in the development of an exhibit on diatom biology to be hosted at the Chicago Botanic Garden. This PIs of this project are participating in the Oxford Nanopore MinION Access Programme and the postdoc hired for this position will be involved in testing its utility for the sequencing of diatom genomes. POSITION REQUIREMENTS: Applicants must have completed a Ph.D. in ecology and evolutionary biology, biology, bioinformatics, phycology, botany, or a related field by the start date. Some experience in bioinformatics is required, preferably in the area of genome assembly and annotation; skills in a scripting language (Perl/Python) and in a Linux/Unix computing environment are necessary. TO APPLY: Please email a single pdf file that includes a cover letter, CV, and contact information for three references to: nwickett(a)chicagobotanic.org<mailto:nwickett@chicagobotanic.org><mailto:nwickett@chicagobotanic.org> Please email if you have any questions or would like additional information. Katrijn Vannerum PhD 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@01D030BA.39B3A830]

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ICBO2015 - Call for workshops and tutorials
by Francisco Couto 15 Jan '15

15 Jan '15

The International Conference on Biomedical Ontology (ICBO, http://icbo2015.fc.ul.pt/callworkshops.html) will take place in beautiful Lisbon, Portugal July 26-30 2015. We would like to invite you to submit proposals to host tutorials and/or workshops. Other type of events (clinics, hackathon) will also be considered. TUTORIALS are educational events. They may be either for a full day or for a half day. They should focus on one specific topic presented by one or two experts and involve interaction with the audience. The organizers will be responsible for advertising the tutorial. Tutorials can include hands-on training, in which case the proposal should specify the anticipated requirements (laptops, software to install, etc.). WORKSHOPS provide a forum for the discussion of a specific topic through individual paper presentations; in particular, they should have a specific tangible outcome planned in advance. They may be for either a full day or a half day. The organizers will be responsible for advertising the workshop and reviewing and selecting the contributions. Workshops can also include interest group meetings, or meetings designed to disseminate the results of a research project on a specific topic. Workshop and tutorial proposals should be submitted to the easychair website: https://easychair.org/conferences/?conf=wsicbo2015, in the workshops and tutorials track. Each submission should include the title of the event, name, affiliation and e-mail addresses of the proposers. It should include also a description of the proposed event (maximum 200 words), including an explanation of how the workshop/tutorial will contribute to the field of biomedical ontology. Proposers should describe how they will advertise the event in order to receive a sufficient number of submissions and participants and explain the rationale for addressing their specific topic in the workshop/tutorial rather than in the main conference. One important argument would be to attract more people to ICBO. If the event has been organized in previous editions of ICBO, please indicate some statistics regarding previous attendance for better planning. For more information, please contact icbo2015(a)googlegroups.com, indicating "[icbo2015] workshops and tutorials" in the subject line. Important dates: Feb 10, 2015: Workshops and tutorials proposals submission deadline Feb 24, 2015: Notification of acceptance of workshops and tutorials Apr 13, 2015: Workshop papers submission deadline May 11, 2015: Notification of workshop paper acceptance May 25, 2015: Camera-ready copies submission deadline July 27-28, 2015: ICBO workshops and tutorials July 29-30, 2015: ICBO main conference

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short-term position in structural bioinformatics
by Prevost Martine 14 Jan '15

14 Jan '15

Please find description attached -------------------------------------------- Martine Prévost Structure et Fonction des Membranes Biologiques CP 206/2 Université Libre de Bruxelles Bld du Triomphe B-1050 Bruxelles Belgium Phone : 32-2-650 2049 Fax : 32-2-650 5382 E-mail: mprevost(a)ulb.ac.be --------------------------------------------

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symposium: "from big data to bedside" - Ghent
by Katleen De Preter 13 Jan '15

13 Jan '15

Dear Colleague, On the 2nd of April 2015, we are organising a symposium on translational bioinformatics "From big data to bedside: translational bioinformatics in cancer research". Several international and national top-speakers will present their data (see http://bigdata.cmgg.be) On the 1st of April a workshop will be organised for PhD students and young post-docs (see website for detailed program). Registration is open and can be done via http://bigdata.cmgg.be (be aware that seats are limited). A small registration fee is asked for the symposium (€ 50) and registration for the workshop is free. Hope to meet you soon at the symposium and/or workshop! Kind regards, organiser: Katleen De Preter co-organisers: Frank Speleman, Jo Vandesompele, Pieter Van Vlierberghe, Pieter Mestdagh

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N2N seminar Thursday, January 29 at 11 am: 'Bioinformatics in cancer research' By Prof. van Loo
by Katrijn Vannerum 09 Jan '15

09 Jan '15

Dear All, Prof. Peter van Loo will give a seminar on Thursday, January 29 at 11 am: 'Bioinformatics in cancer research'. (See abstract below) Please contact me if you would like to have a meeting with Prof. Peter van Loo in the afternoon. The lunch meeting is open to all PhD students, but lunch is only provided for students registered at the Doctoral Schools. Registration is still possible. With kind regards, Katrijn Vannerum PhD 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:image005.png@01D02C24.94E42990] [cid:image006.png@01D02C24.94E42990] "Bioinformatics in cancer research" Professor Peter van Loo KU Leuven, Department of Human Genetics, Leuven, Belgium January 29, 2014 (11:00) Lunch meeting for Doctoral Schools students 12:00-14:00 Jozef Schell seminar room, Technologiepark 927 - 9052 Zwijnaarde http://www.nucleotides2networks.be/node/232 http://www.nucleotides2networks.be/events Abstract Cancer evolves dynamically as clonal expansions supersede one another, driven by shifting selective pressures, mutational processes, and disrupted cancer genes. These processes mark the genome, such that a cancer's life history is encrypted in the somatic mutations present. We are developing algorithms to decipher this narrative from whole genome sequencing data and are applying them to several cancer types. We call such approaches "molecular archaeology of cancer", as we are using genomics and bioinformatics algorithms to infer a tumour's evolutionary history. I will discuss applications of our methods to breast cancer, allowing us to disentangle subclonal architecture from whole genome sequencing data, as well as time events such as chromosome duplications along a tumour's lifetime. In addition, I will describe how extending these molecular archaeology approaches to multiple sampling studies allow enhanced and unique insights into cancer evolution, and I will illustrate that using genomics studies on prostate cancer metastases, where we are able to elucidate the patterns of metastatic spread in unprecedented detail.

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