- BBClist - maillist.psb.ugent.be

RECOMB-CG 2013 - Call for papers
by macha＠labri.fr 20 Apr '13

20 Apr '13

Eleventh Annual RECOMB Satellite Workshop on Comparative Genomics October 17-19, 2013, Lyon, France Website: rcg2013.sciencesconf.org Contributions to the workshop are welcomed on any theoretical and/or empirical approach to genome-wide comparison. This includes genome evolution, algorithms for genome rearrangement, comparative tools for assembly, gene identification or annotation, comparison of functional networks, genomic variation in humans and model organisms, cancer genomics, duplication patterns of genes, segments and whole genomes, and comparative epigenetics. We encourage paper submissions that offer new biological findings or otherwise highlight their relevance to biology. Refereed papers will be published as open-access manuscripts in the journal BMC Bioinformatics. -------- KEY DATES Paper submission deadline June 21, 2013 Acceptance notification July 19, 2013 Workshop October 17-19, 2013 - Lyon, France -------- CONFIRMED KEYNOTE SPEAKERS - Tal Dagan, Heinrich Heine Universität, Dusseldorf - Ludovic Orlando, Centre for GeoGenetics, natural History Museum of Denmark -------- THEME AND SCOPE The continuing advance of DNA sequencing technology has produced an avalanche of genome sequence and genome structural information across the evolutionary spectrum. Transforming that information into biological knowledge requires creative and innovative new computational and statistical methods for comparative genomics. The RECOMB Satellite Workshop on Comparative Genomics aims to provide the premier forum for new computational developments applied to all aspects of comparative genomics. We solicit contributions on topics including comparison of genome structure and organization, genome function, and evolution. We particularly encourage contributions that use new computational methods to acquire new insight into biological processes. Advances in computational theory are welcome, though all submissions should include genome-scale analyses informed by comparative data. All peer-reviewed and accepted RECOMB-CG manuscripts will be published in a supplement to BMC Bioinformatics as open-access, author-subsidized, articles. Specific topics of interest include but are not limited to: . Gene and genome duplication . Gene family evolution . Genome structural variation . Algorithms for comparative genomics . Genome rearrangements . Ancestral genome reconstruction . Multiple genome alignment . Genome sequence comparison . Modeling genome evolution . Comparative genomics for genome annotation . Gene tree reconciliation . Species and gene tree inference . Comparative metagenomics . Comparative genomics linked to proteomics, metabolomics, and other ~omic data . Comparative genomics and gene expression and regulation . Applications of comparative genomic methods . Paleogenomics -------- CALL FOR PAPERS Papers should be submitted via the EasyChair system: https://www.easychair.org/conferences/?conf=recombcg13. Submissions must be received in electronic form by 11:59pm (Samoa time), June 21th, 2013. Papers submitted for review should represent original, previously unpublished work. At the time the paper is submitted to the conference, and for the entire review period, the paper should not be under review by any other conference or scientific journal. At least one author per each successful submission is required to register and present the paper at the workshop. The paper will be included in the conference proceedings, which will be published in BMC Bioinformatics as open-access author-subsidized articles. Authors are encouraged to use the BMC document templates when preparing manuscripts. Templates are available in Microsoft and LaTeX formats. Otherwise, submissions should be typeset as double-spaced A4 pages with at least 1-inch margins all around in a minimum of 10 point font. Submissions should be limited to 16 pages, everything included (title, authors, addresses, abstract, references, figures, tables). Exceptions to this limit may be granted by consultation with the Program Committee Chairs. Submissions must include the corresponding author’s email address. When preparing your submission please follow the instructions for authors of BMC supplements: http://www.uff.br/recombcg/docs/Instructions-for-authors-BMC-Appendix-B.pdf. Submitted manuscripts must be rendered to PDF format prior to upload into EasyChair at the review stage. Address any questions to the program committee chairs: Macha Nikolski macha (at) labri (dot) fr and Yves Van de Peer yves (dot) vandepeer (at) psb (dot) vib (dash) ugent (dot) be -------- PROGRAM COMMITTEE Chairs: Macha Nikolski (LaBRI & CBiB, Université Bordeaux, France) Yves Van de Peer (VIB / Ghent University, Belgium) PROGRAM COMMITTEE (preliminary) Lars Arvestad Sweden Anne Bergeron Canada Mathieu Blanchette Canada Guillaume Blin France Guillaume Bourque Singapore Titus Brown United States Frederic Brunet France Marilia Braga Brasil Cedric Chauve Canada Aaron Darling Australia Alexei Drummond New Zealand Niklas Eriksen Sweden Martin Frith Japan Gerton Lunter United Kingdom Vsevolod Makeev Russia Kateryna Makova United States Guilherme Oliveira Brasil Francis Ouellette Canada Benedict Paten United States Ian Paulsen Australia Teresa Przytycka United States Ben Raphael United States Matt Rasmussen United States Hugues Roest-Crollius France Fredrik Ronquist Sweden Marie-France Sagot France Cathal Seoighe Ireland Joao Setubal Brasil Hayssam Soueidan Netherlands Jens Stoye Germany Krister Swenson Canada Eric Tannier France Glenn Tesler United States Raluca Uricaru France Miguel Vazquez Spain Christopher Workman Denmark Sophia Yancopoulos United States Louxin Zhang Singapore STEERING COMMITTEE Jens Lagergren (KTH Royal Institute of Technology and SciLifeLab Stockholm, Sweden) Aoife McLysaght (University of Dublin, Ireland) David Sankoff (University of Ottawa, Canada)

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Postdoc position in bioinformatics at Oslo University Hospital, Norway
by Maté Ongenaert 19 Apr '13

19 Apr '13

A one-year postdoc position is available at Institute for Cancer Research at Oslo University Hospital. Applications are invited from students holding a PhD in bioinformatics or molecular biology with experience in analysis of high throughput data. The post.doc will participate in the development of a gene based diagnostic test for detection of aggressive cervical cancer. A gene signature underlying the test has been identified, and validation and optimization of the signature in a new patient cohort will be major tasks. Extension of the post.doc period with two more years will be possible in case of a decision towards commercialization of the test. For more information: project leader Heidi Lyng, heidi.lyng(a)rr-research.no<mailto:heidi.lyng@rr-research.no> Web site: http://ous-research.no/lyng/ Application with CV to Heidi Lyng, heidi.lyng(a)rr-research.no<mailto:heidi.lyng@rr-research.no> Deadline: 29th of April 2013

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Marie-Curie Post-Doc Fellowship in Systems Biology - GSK Vaccines : Rixensart, Belgium
by Robert Van den Berg 19 Apr '13

19 Apr '13

Dear all, We are currently looking for a postdoc interested in writing a joint application for a Marie-Curie grant. The topic will be: Development of systems biology approaches to better understand the longitudinal development of the immune response after vaccination, and the relation of this development to vaccine efficacy. For more information please check: http://www.nature.com/naturejobs/science/jobs/318215-Marie-Curie-Post-Doc-F…. Feel free to share this further. Kind regards, Robert Robert van den Berg PhD Expert scientist Bioinformatics GlaxoSmithKline Vaccines Building B62J420 | Rue de l'Institut 89 | 1330 Rixensart | Belgium T: +3226568395 E: robert.x.van-den-berg(a)gsk.com<mailto:robert.x.van-den-berg@gsk.com> [Description: Description: cid:image001.jpg@01CD132C.27416BA0] Registered as GlaxoSmithKline Biologicals SA - Rue de l'Institut, 89 BE-1330 Rixensart - TVA BE 0440.872.918 RPM Nivelles. Deutsche Bank AG Bruxelles 826-0006444-59

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[Gtpb] GTPB Course Reminder - RNA-seq + Automatic Func. Annotation
by Pedro Fernandes 17 Apr '13

17 Apr '13

Course Reminder Applications are OPEN until May 7th 2013 Early decisions available. *TA-AFADM13* Transcriptome Assembly, Automatic Annotation and Data Mining with Ana Conesa and Fernando Garcia IMPORTANT DATES for TA-AFADM13 Deadline for applications: May 7th 2013 Notification of acceptance dates: EARLY: Apr 19th 2013 (on special request, see Application) NORMAL: May 8th 2013 Course date: May 20th - May 23rd 2013 http://gtpb.igc.gulbenkian.pt/bicourses/TA-AFADM13 This course is particularly suitable for those seeking training in using NGS data for tanscriptomics (RNA-seq), and in extensively annotating with Blast2GO, the most popular and powerful tool for this purpose. Course description: This is a combined course in RNA-seq and functional annotation aimed at scientists working in next generation sequencing transcriptomics who want to extract the best possible information from their data. The first part of the course is a practical tutorial on Blast2GO, the most popular framework for functional annotation of sequences. Participants will also learn how to generate de novo functional labels, such as GO terms and KEGG pathways, for their sequence data and how to extract relevant information from these annotations, i.e. visualization and enrichment analysis using the Gene Ontology. The second part of the course covers many relevant aspects of RNA-seq analysis, form quality control, to mapping, reconstruction of transcripts and differential expression. Participants will learn how to deal with RNAseq data both in the presence and absence of a reference genome. At the end of the course, participants can expect to have acquired skills to use multiple software tools to analise RNA-seq data and use Blast2GO. The course will be based on the use of Blast2GO application and will mainly comprise exercises and practical cases. Participants may bring their own data. *Who should attend?* Experimentalists and bioinformaticians working on EST, NextGeneration Sequencing and microarray design projects, specially (but not exclusively) of non-model species. No programming knowledge is required. *Course Pre-requisites:* Basic knowledge in Molecular Biology and Statistics. Pedro Fernandes GTPB Coordinator -- Pedro Fernandes 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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FW: Vacancy Full professor of Bioinformatics at Wageningen University - new link
by Vleghels, Ingrid 17 Apr '13

17 Apr '13

Because of an update on the Wageningen-UR site a new link for this vacancy: http://www.wageningenur.nl/nl/Werken-bij/Vacatures/Show/Full-Professor-of-B… With kind regards, Ingrid Veghels ________________________________ From: Vleghels, Ingrid Sent: 16 April 2013 16:59 To: 'bbclist(a)psb.ugent.be' Subject: Vacancy Full professor of Bioinformatics at Wageningen University Dear sirs, Wageningen University seeks to appoint a full professor in Bioinformatics. Please use the link to find more information on this vacancy http://www.wageningenur.nl/en/Jobs/Vacancies/Show/Full-Professor-Bioinforma…. I hope you will be so kind to forward this link to the people on your e-mail list. With kind regards, Ingrid Vleghels Dr. Ingrid Vleghels Graduate School ‘Experimental Plant Sciences’ (EPS) Droevendaalsesteeg 1 Building RADIX-East (bldg. nr. 107) Bode 180 6708 PB Wageningen The Netherlands T: +31 317 484757 E: ingrid.vleghels(a)wur.nl<mailto:ingrid.vleghels@wur.nl> W: www.graduateschool-eps.info<http://www.graduateschool-eps.info>

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Vacancy Full professor of Bioinformatics at Wageningen University
by Vleghels, Ingrid 16 Apr '13

16 Apr '13

Dear sirs, Wageningen University seeks to appoint a full professor in Bioinformatics. Please use the link to find more information on this vacancy http://www.wageningenur.nl/en/Jobs/Vacancies/Show/Full-Professor-Bioinforma…. I hope you will be so kind to forward this link to the people on your e-mail list. With kind regards, Ingrid Vleghels Dr. Ingrid Vleghels Graduate School 'Experimental Plant Sciences' (EPS) Droevendaalsesteeg 1 Building RADIX-East (bldg. nr. 107) Bode 180 6708 PB Wageningen The Netherlands T: +31 317 484757 E: ingrid.vleghels(a)wur.nl<mailto:ingrid.vleghels@wur.nl> W: www.graduateschool-eps.info<http://www.graduateschool-eps.info>

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ISCB SCS 2013 second call for abstracts / Arts & Science exhibition 2013 call for submissions
by ISCB Student Council Symposium 12 Apr '13

12 Apr '13

Dear students and young researchers, The ISMB/ECCB 2013 Conference is just a few months away and the opportunities to participate beyond attending are closing soon. The Student Council Symposium and the Art & Science Exhibition are highlighted below. ****************** _ISCB Student Council Symposium 2013_ *The ISCB Student Council Symposium will be held on July 19th (directly preceding ISMB/ECCB 2013) in Berlin, Germany.* *UPCOMING ABSTRACT SUBMISSIONS DEADLINE: Tuesday, April 16th* The Student Council Symposium is a forum for students, post docs, and young researchers in the fields of Computational Biology and Bioinformatics. Participants have the opportunity to present their work to an international audience, build a network within the computational biology community and develop important soft skills in an environment that fosters exchange of ideas and knowledge. We encourage you to submit an abstract and to bring a poster for showcasing your work at the Symposium's poster session. As a central part of the Symposium, ten abstracts will be selected for an oral presentation. We accept abstracts covering both scientific studies as well as novel tools and applications in the field of computational biology and bioinformatics. Travel fellowships will be available for accepted abstracts, and awards will be given to best posters and presentations. *LINKS* _Symposium website_: http://symposium.iscbsc.org/ _Submission link_: http://www.iscb.org/submissions/index.php?id=156 _Travel Fellowships information_: http://symposium.iscbsc.org/content/travel-fellowships *IMPORTANT DATES* April 16: Abstract submission deadline April 26: Travel Fellowship submission deadline April 30: Abstract acceptance notifications May 14: Travel fellowship acceptance notifications July 19th: Student Council Symposium 2013 ****************** _Art & Science Exhibition_ ISMB/ECCB brings together scientists from a wide range of disciplines, including biology, medicine, computer science, mathematics and statistics. In these fields we are constantly dealing with information in visual form: from microscope images and photographs of gels to scatter plots, network graphs and phylogenetic trees, and visual aids for problem-solving are omnipresent. For the ISMB/ECCB 2013 Art & Science Exhibition the organizers invite all interested conference attendees to submit such images and videos that have been generated as part of a research project. They are also soliciting images and videos resulting from creative efforts that involve scientific concepts or employ scientific tools and methods. All cover images produced by researchers for scientific journals are welcome as well. A cash award may be given for the winning image as voted by conference attendees. *LINKS* _Website_: https://www.iscb.org/ismbeccb2013-submission/ismbeccb2013-artandscienceexhi… _Submissions link_: http://www.iscb.org/submissions/index.php?id=149 *IMPORTANT DATES* May 13: Submissions deadline ****************** We look forward to receiving your submissions! Tomás Di Domenico (Chair, SCS2013) Milana Frenkel-Morgenstern (Chair, Art & Science Exhibition 2013)

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Call for Papers - VOC conference in Antwerp, May 31 2013
by Katrijn Van Deun 12 Apr '13

12 Apr '13

Second VOC Conference, May 31 2013 in Antwerp, Belgium Final Call for Papers Scope The Dutch/Flemisch Classification Society, VOC, aims at communicating scientific principles, methods, and applications of ordination and classification. The VOC is a member of the International Federation of Classification Societies. The VOC would like to invite you to attend its second conference. Contributed papers can be submitted on topics such as classification, clustering, scaling, data analysis, machine learning, pattern recognition, statistical modeling, and applications of classification and data analysis. Fee To encourage PhD students to participate, the conference fee is kept very low (±15€/35€ for members/non-members; lunch included). Keynote Stijn Vansteelandt, Ghent University and the London School of Hygiene and Tropical Medicine Important Dates / Deadlines April 30: deadline for abstract submission. May 10: notification of acceptance of presentation. May 17: deadline for inscription of non presenters. For more information, visit the conference website: https://ppw.kuleuven.be/english/mesrg/voc-conference-2013/registration-form… On behalf of the organizers: Ralph Rippe, Katrijn Van Deun, Jeroen Vermunt, Tom Wilderjans, Berrie Zielman

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Fwd: invitation to summerschool BioSCENTer 2013 - TechWatch4BIOS @ KU Leuven , Belgium
by mimi deprez 10 Apr '13

10 Apr '13

Summerschool BioSCENTer 2013 TechWatch4BIOS (Biosciences, Biomedicine, Bioscience Engineering, Bioinformatics) KU Leuven BioSCENTer offers a top notch summer school lectured by technology experts of KU Leuven, University of Ghent, University of Antwerp, VU Brussels, VIB and IMEC, BELGIUM. They will provide a bird’s eye perspective on several rapidly evolving technologies, including supercomputing, deep sequencing & genomics, proteomics & metabolomics, mass spectrometry (structure identification), NMR, crystallography, nano-biotech, electron & atomic force microscopy, transcriptomics, moleculal small animal imaging center, bioinformatics, imaging from single molecules cells and small animals, viral vectors, optogenetics.As part of the summer school program, 3 unique workshops for career development are offered that will be given by Leuven Inc. appointed professionals. In addition, participants are invited to a site visit at the IMEC headquarter and the NERFcentre for Neuroelectronics. dates: September 9-13 , 2013 venue: Faculty building Bioscience Engineering, Jozef Heuts auditorium, Kasteelpark Arenberg 20, 3001 Heverlee https://securehomes.esat.kuleuven.be/~bioiuser/bioscenter/summerschool_2013… registration: is now open - deadline before July 15th 2013 contact: prof. J. Winderickx Please feel free to forward this invitation to students and colleagues. We look forward to welcoming you at this exciting event in September 2013. Kindest regards, on behalf of the coordinator prof. J. Winderickx and local organizers

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Fwd: GCC2013 Talk Abstract Submission closes this Friday
by Dave Clements 09 Apr '13

09 Apr '13

Hello all, This is a final reminder that the *deadline for submitting an oral presentation abstract for the 2013 Galaxy Community Conference is 12 April, this Friday*. See http://wiki.galaxyproject.org/Events/GCC2013/Abstracts The poster presentation abstract deadline is 3 May. And in case you missed the announcement about GIgaScience and GCC2013 talks: We are pleased to announce that talks presented at the 2013 Galaxy Community conference will be eligible for consideration to be published in the journal *GigaScience <http://www.gigasciencejournal.com/>* and that BGI<http://www.genomics.cn/en/index>will generously cover the article processing fees for these articles. See the announcement <http://wiki.galaxyproject.org/News/GigaScienceGalaxyCFP>for details. Thanks, Dave C On Mon, Feb 25, 2013 at 3:40 AM, Dave Clements <clements(a)galaxyproject.org>wrote: > Dear Galaxy Community, > > We are pleased to announce that early registration<http://wiki.galaxyproject.org/Events/GCC2013/Register> > and paper and poster abstract submission<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts> are > now open for the 2013 Galaxy Community Conference (GCC2013)<http://wiki.galaxyproject.org/Events/GCC2013> > . GCC2013 will be held 30 June through July 2 in Oslo Norway, at the University > of Oslo <http://uio.no/>. > > GCC2013 <http://wiki.galaxyproject.org/Events/GCC2013> is an opportunity > to participate in two full days of presentations, discussions, poster > sessions, keynotes, lightning talks and breakouts, all about > high-throughput biology and the tools that support it. The conference also > includes a Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> for > the second year in a row, this year with more in-depth topic coverage, more > concurrent sessions, and more topics. > > If you are a biologist or bioinformatician performing or enabling > high-throughput biological research, then please consider attending. > GCC2013 is aimed at: > > - Bioinformatics tool developers and data providers > - Workflow developers and power bioinformatics users > - Sequencing and Bioinformatics core staff > - Data archival and analysis reproducibility specialists > > *Early registration<http://wiki.galaxyproject.org/Events/GCC2013/Register> > * *saves up to 75% off regular registration costs,* and is very > affordable, with combined registration (Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> + > main meeting) starting at ~ €95 for post-docs and students. Registering > early also assures you a spot in the Training Day workshops you want to > attend. Once a Training Day session becomes full, it will be closed to new > registrations. Early registration closes 24 May. > > *Abstract submission<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts> > * for oral presentations closes 12 April, and for posters on 3 May. > Please consider presenting your work. If you are working with big > biological data, then the people at this meeting want to hear about your > work. > > Thanks, and hope to see you in Oslo! > > The GCC2013 Organizing Committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers> > > PS: And please help get the word out<http://wiki.galaxyproject.org/Events/GCC2013/Promotion> > ! > -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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