- BBClist - maillist.psb.ugent.be

open bioinformatics PhD position
by Katrijn Vannerum 27 Jan '15

27 Jan '15

Begin forwarded message: Date: 23 Jan 2015 17:35:06 CET From: Stefan Rensing <stefan.rensing(a)biologie.uni-marburg.de<mailto:stefan.rensing@biologie.uni-marburg.de>> To: undisclosed-recipients:; Subject: open bioinformatics PhD position Dear colleagues, I have a vacant bioinformatics PhD position and would be grateful if you could forward the announcement. Thanks a lot and best regards, Stefan -- Stefan A. Rensing, PhD Prof., Plant Cell Biology Faculty of Biology, University of Marburg Karl-von-Frisch-Str. 8, D-35043 Marburg, Fon +49 6421 28 21940 http://plantco.de/ stefan.rensing(a)biologie.uni-marburg.de<mailto:stefan.rensing@biologie.uni-marburg.de> "Everything is backwards now, like out there is the true world, and in here is the dream." 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@01D03A21.4DAFC100]

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VIB/BITS open upcoming Bioinformatics courses - NGS data / Python / RNA-seq
by Alexander Botzki | VIB | 24 Jan '15

24 Jan '15

Dear all, VIB BITS would like to give you a short overview of our Bioinformatics training courses which are now open for registration: * Introduction to NGS data analysis - 27 February and 6 March 2015 * Gentle hands-on introduction to Python programming - 9 and 16 March 2015 * RNA-Seq analysis for differential expression - 20 and 23 March 2015 Registration and more information via this link: http://www.vib.be/en/training/research-training/courses/Pages/default.aspx?… Best regards, Janick Mathys Contact: http://www.vib.be/en/training/research-training/Pages/Contact.aspx

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Vacant postdoc position in bacteria genomics and metagenomics at ITM Antwerp, Belgium
by Stijn Deborggraeve 23 Jan '15

23 Jan '15

Dear all, There is an exciting position vacant for a postdoc in bacteria genomics and metagenomics at the Institute of Tropical Medicine in Antwerp: Postdoctoral scientist in bacteria genomics Department of Biomedical Sciences - Unit of Diagnostic Bacteriology The Institute of Tropical Medicine (ITM) is internationally recognized as a center of excellence for education, research and service delivery in the field of tropical medicine. The Unit of Diagnostic Bacteriology at the Department of Biomedical Sciences is developing and validating innovative diagnostic tests for tropical bacterial infections. We recently launched several new projects in which we use metagenomics and genomics to identify and study pathogens in clinical samples. To support these activities and to develop new projects, we are looking for a postdoctoral scientist in genomics data analysis. Assignment: * Coordinate the bioinformatics activities at the Diagnostic Bacteriology Unit. * Develop and validate a metagenomics approach to identify bacteria in clinical samples. * Develop the data analysis for a study on whole genome sequencing of Salmonella isolates. * Assist in the data analysis of genomics, transcriptomics and proteomics projects in the unit. * Develop your own research lines and apply for competitive grants. * Coach MSc and PhD students. Profile: * You have a Master degree in biology, bioengineering or bioinformatics (or equivalent) and a PhD degree in sciences, preferably in the field of genomics or metagenomics. * You have strong skills in bioinformatic analysis of whole genome sequence data. * Additional skills in the analysis of transcriptomics and proteomics data are an asset. * Additional skills in bacteriology and molecular biology are an asset. * You have excellent knowledge of English. * You have proven that you can work in a multi-disciplinary context and lead research lines. Offer: * An intellectually stimulating, international and socially committed environment, with room for personal initiative. * A full time contract as postdoctoral scientist for one year, extendable. Starting date is as soon as possible. * A salary set according to the pay scales of the ITM and the Flemish universities. * Reimbursement of public transport costs, bicycle compensation and luncheon vouchers. * You will work at the ITM headquarter in the bustling city of Antwerp. Interested? For more information about this position, please contact Prof. Stijn Deborggraeve, Head of the Diagnostic Bacteriology Unit (sdeborggraeve(a)itg.be) Applications with motivation letter, application form and contact details of at least 3 references should be received by email at vacatures(a)itg.be by February 16, 2015. Please use the application form available as a download on www.itg.be/vacatures. * Please consider the environment before printing this e-mail Disclaimer: Http://www.itg.be/disclaimer Directions to our location(s): http://g.co/maps/ua89b

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Abstract submission open - ISCB Student Council Symposium 2015
by ISCBSC announcement 23 Jan '15

23 Jan '15

Call for Abstracts - 11th ISCB Student Council Symposium 2015 Submit your abstract now for the 11th Symposium of the International Society for Computational Biology Student Council, to be held on the 10th of July, 2015 in Dublin, Ireland, as a satellite meeting of the International Conference on Intelligent Systems for Molecular Biology (ISMB)! The Student Council Symposium 2015 will bring together young computational biologists from several research areas and regions of the world. As the central part of our symposium, several students will be selected to give oral presentations based on their submitted abstracts. This is your chance to present your work to an international audience of young scientists. We welcome abstracts covering scientific studies as well as novel tools and applications in the field of computational biology and bioinformatics. For more information please visit our website: *http://symposium.iscbsc.org/ <http://symposium.iscbsc.org/>* For preceeding directly to the abstract submission system: *http://bit.ly/1up4m6k <http://bit.ly/1up4m6k>* *Important Dates* Monday, January 19, 2015Symposium Submission Opens*Monday, April 27, 2015**Symposium Submission Closes*Firday, May 15, 2015Symposium Submission Acceptance Notification*Monday, May 25, 2015**Student Council Travel Fellowship Deadline*Thursday, June 4, 2015Student Council Travel Fellowship Acceptance NotificationFriday, May 29, 2015Symposium Late Poster Submission DeadlineMonday, June 8, 2015Symposium Late Poster Acceptance Notification*Friday, July 10, 2015**Student Council Symposium Date* We look forward to receiving your abstract, Katie Wilkins Chair, 11th ISCB Student Council Symposium 2015 Farzana Rahman Co-Chair, 11th ISCB Student Council Symposium 2015

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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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