- BBClist - maillist.psb.ugent.be

Job offer python developer @WIV-ISP
by Vanneste, Kevin 15 Jun '16

15 Jun '16

Dear all, The Belgian Institute of Public Health (www.wiv-isp.be<http://www.wiv-isp.be>) has one vacant position for a python developer to strengthen their NGS & bioinformatics platform. More details can be found in the job description added in attachment. Applications are possible using our job site (direct application link: http://wiv-isp.hr-technologies.com/content/login.asp?a=APPLY&jdkid=154&l=DU…) The position will remain open until a suitable candidate is found. Sincerely, Kevin [Description: Description: logo ISP-WIV]Kevin Vanneste Bioinformatician Platform Biotechnology and Molecular Biology Expertise, Service Provision and Customer Relations Rue Juliette Wytsmanstraat 14 | 1050 Brussels | Belgium T +32 (0)2 642 50 65 | F +32 (0)2 642 52 92 Email: kevin.vanneste(a)wiv-isp.be<mailto:kevin.vanneste@wiv-isp.be> | Skype: wiv-isp.kevin.vanneste Scientific Institute of Public Health | www.wiv-isp.be<http://www.wiv-isp.be/> ########################################################### Checked as being free of known viruses. Scientific Institute of Public Health, Brussels, Belgium Wetenschappelijk Instituut Volksgezondheid, Brussel, Belgi� Institut scientifique de Sant� publique, Bruxelles, Belgique Visit our website: http://www.wiv-isp.be ######################################################################## DISCLAIMER: Please see https://www.wiv-isp.be/Pages/EmailDisclaimer.aspx ########################################################################

1 0

Job offer clinical bioinformatician @WIV-ISP
by Vanneste, Kevin 15 Jun '16

15 Jun '16

Dear all, The Belgian Institute of Public Health (www.wiv-isp.be<http://www.wiv-isp.be>) has one vacant position for a clinical bioinformatician. More details can be found in the job description added in attachment. Applications are possible using our job site (direct application link: http://wiv-isp.hr-technologies.com/content/login.asp?a=APPLY&jdkid=153&l=DU…) The position will remain open until a suitable candidate is found. Sincerely, Kevin [Description: Description: logo ISP-WIV]Kevin Vanneste Bioinformatician Platform Biotechnology and Molecular Biology Expertise, Service Provision and Customer Relations Rue Juliette Wytsmanstraat 14 | 1050 Brussels | Belgium T +32 (0)2 642 50 65 | F +32 (0)2 642 52 92 Email: kevin.vanneste(a)wiv-isp.be<mailto:kevin.vanneste@wiv-isp.be> | Skype: wiv-isp.kevin.vanneste Scientific Institute of Public Health | www.wiv-isp.be<http://www.wiv-isp.be/> ########################################################### Checked as being free of known viruses. Scientific Institute of Public Health, Brussels, Belgium Wetenschappelijk Instituut Volksgezondheid, Brussel, Belgi� Institut scientifique de Sant� publique, Bruxelles, Belgique Visit our website: http://www.wiv-isp.be ######################################################################## DISCLAIMER: Please see https://www.wiv-isp.be/Pages/EmailDisclaimer.aspx ########################################################################

1 0

Job offer / Post_doc in Bio-Informatics
by Roels Dominique 15 Jun '16

15 Jun '16

Postdoctoral position in Bioinformatics and Computational Biology at the Breast Cancer Translational Research Laboratory (BCTL) Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium The BCTL directed by Prof. Christos Sotiriou MD, PhD, is located at the Institut Jules Bordet (Faculty of Medicine, Université Libre de Bruxelles), the only comprehensive cancer centre in Belgium. The current research projects of the lab include: - Molecular characterization of breast cancer using several "omics" techniques including NGS and CNA arrays to study tumour heterogeneity, disease progression and resistance to treatment(s); - Characterization at the molecular level of the minimal residual disease including the study of circulating tumor cells and circulating tumor DNA; - Several of the above translational research projects are part of international clinical studies. The candidate is expected to lead his/her own projects and mentor graduates students. He/she must be highly motivated, able to work independently, and show strong organizational skills. The candidate should hold a PhD in bioinformatics, computational biology or biostatistics and should show strong interest for breast cancer research, genomics, bioinformatics and translational medicine. Applicants should have prior experience in NGS and microarrays data analysis. Moreover, strong programming skills (R, Python/Perl) and familiarity with UNIX environment are required. Fluency in English is expected. Practical knowledge in French is a plus. The successful candidate will join an enthusiastic and interdisciplinary team of researchers, clinicians and bioinformaticians to work at the forefront of breast cancer translational research. Initial funding is available for 2 years, with possible extension for 2 additional years. How to apply: Applications including a letter of application, an up-to-date CV and at least two referees should be sent to Prof. Christos Sotiriou (christos.sotiriou(a)bordet.be<mailto:christos.sotiriou@bordet.be>) and Dr. Françoise Rothé (francoise.rothe(a)bordet.be<mailto:francoise.rothe@bordet.be>). Application deadline: 30 September 2016 Disclaimer : http://www.bordet.be/disclaimer/disclaimer.html

1 0

Call for Travel Fellowship Application for ESCS 2016 is now open
by ISCBSC announcement 14 Jun '16

14 Jun '16

Dear colleague, Call for travel fellowship application for European Student Council Symposium (ESCS) 2016 is now open. The abstract submission for oral and poster presentations are open until 24 June. ESCS will take place on Saturday 3rd September during ECCB 2016 in The Hague, Netherlands. Please visit submit.iscbsc.org/escs to submit your abstract and to apply for travel fellowship. Read more about the ESCS travel fellowship here <http://escs2016.iscbsc.org/2016-TF-Call-Guidelines> The ESCS is a biennial interdisciplinary symposium that brings together students and young researchers from computational biology, bioinformatics, systems biology, and related fields. This symposium offers you a great opportunity to present your research to an international audience, get insights into hot topics and newly developed methods and build a network within the computational biology community of Europe. We are pleased to announce our three confirmed keynote speakers Kris Laukens (University of Antwerp, Belgium), Yves Van de Peer (Ghent University, Belgium), and Nuria Lopez-Bigas (Universitat Pompeu Fabra, Spain). The symposium includes ice-breaking, oral presentations, keynote talks, poster presentations and an evening social event that offer you the opportunity to get to know fellow young scientists from all over Europe in a casual setting. Please visit our website http://escs2016.iscbsc.org/ regularily as more information will be announced soon. For registration details, please visit http://www.eccb2016.org/registration/. We welcome students and young researchers from all areas of computational biology to join our community. Please help us spread the word by sharing the event flyer (please find it attached), and using the hashtag #ESCS16 on social media. We look forward to welcome you in The Hague! Annika Jacobsen and Kevin Schwahn, chair and co-chair, ESCS 2016 <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DDB4FAA8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

1 0

Genomics Conference, Ghent, Belgium, 12-15 Sept - ABSTRACT SUBMISSION UNTIL 15 June
by Karel De Schamphelaere 10 Jun '16

10 Jun '16

Dear UGent genomicists and bioinformaticians, I would like to invite you to participate or contribute to our conference on “Environmental Genomics and Epigenetics: science, technology and applications” which will be held form 12-15 September, 2016 in Ghent, Belgium. Abstract submission<http://epigenetics.setac.eu/abstract_submission/?contentid=1079&pr_id=1067> is open until 15 June and you can register for the meeting until 15 August. We have lined up a nice list of keynote speakers<http://epigenetics.setac.eu/programme/keynote_speakers/?contentid=1114&pr_i…> and sessions<http://epigenetics.setac.eu/abstract_submission/?contentid=1079&pr_id=1067> on environmental, ecological, microbial, evolutionary, ecological, and stress genomics, as well sessions on metagenomics, and toxicogenomics. We welcome abstracts making use of all kinds of omics, including transcriptomics, proteomics, metabolomics, epigenomics, etc... Abstracts on new technological developments or novel bioinformatics analysis methods of omics datasets are also very welcome. I am quite sure that some of you have performed research that would fit with one of the conference’s sessions. If you are interested, but are unsure in which session you research would fit, don’t hesitate to ask. All further information can be found on the conference website<http://epigenetics.setac.org/> (see also flyer attached). Please note that you can also register just for the first two days of the conference (focus on ecology, evolution and genomics in general) or the last two days of the conference (focus on epigenetics in ecology and toxicology). Please also note that the registration fees include lunch, welcome reception, coffee during breaks and drinks during poster socials. Best regards, Karel De Schamphelaere On behalf of the Organizing Committee Karel De Schamphelaere, Ph D Associate Professor www.ecotox.ugent.be Follow us on Twitter@GhEnToxLab Ghent University (UGent) Laboratory of Environmental Toxicology and Aquatic Ecology Environmental Toxicology Unit (GhEnToxLab) Jozef Plateaustraat 22 B9000 Gent Belgium Tel. +32 9 264 3764 Fax +32 9 264 3766 skype karel.de.schamphelaere Researcher ID: http://www.researcherid.com/rid/A-1600-2008 Disclaimer: http://helpdesk.ugent.be/e-maildisclaimer.php

1 0

3-year Joint PhD studentship with the University of Birmingham and Maastricht University
by Coort Susan (BIGCAT) 09 Jun '16

09 Jun '16

Dear all, Apply now for a joint PhD position between the University of Birmingham and Maastricht University. The project is entitled: Integrative systems biology analysis of immune cell mRNA and miRNA expression by vitamin D. The data analysis part will be performed at Maastricht University and the lab work at the University of Birmingham. For a detailed description and the application procedure please go to: www.academictransfer.com/34302<http://www.academictransfer.com/34302> With kind regards, Susan ----------------------------------------------------------------------------- Susan LM Steinbusch-Coort, PhD Assistant Professor Department of Bioinformatics-BiGCaT NUTRIM School for Nutrition and Translational Research in Metabolism Maastricht University Email: susan.coort(a)maastrichtuniversity.nl<mailto:susan.coort@maastrichtuniversity.nl> Tel : +31 (0)43 3882913 Office : 1.306 (UNS50) In the office from Monday to Thursday

1 0

Open PhD position (bioinformatics) at UMC Utrecht Netherlands
by Ridder-4, J. de 03 Jun '16

03 Jun '16

You will join the recently established group of dr. de Ridder as a PhD student. The de Ridder lab is focussed on creating and applying advanced computational techniques to high-throughput molecular datasets and develops novel data integration strategies to further disease biology. You will participate in a research project funded by the Gieskes-Strijbis fund. The project is part of a collaboration between the research groups of Dr. W. Kloosterman (Genetics), Prof. H. Clevers, PhD, MD (Hubrecht Institute) and Prof. dr. E. Witteveen (Medical Oncology). Dr. Kloosterman has a strong background in (cancer) genomics and extensive expertise in the analysis of genome and transcriptome sequencing data. Prof. H. Clevers is director of the Princess Maxima Center for pediatric oncology and key scientist behind the organoid culture system. Prof. dr. E. Witteveen is an expert on ovarian cancer biology and focuses on testing of novel cancer drugs in clinical trials. The primary focus of the PhD project is the identification and computational characterization of novel mechanisms of drug sensitivity and resistance in ovarian cancer. This will be achieved by establishing and characterizing a “living” organoid biobank for ovarian cancer using organoid technology, thus capturing to a certain extent the genetic variability of this tumour type. A major part of this project will concern the analysis and interpretation of large-scale genome and transcriptome data and the selection and molecular characterization of novel genetic variations that are associated with response to chemotherapy or targeted drugs. The latter part involves experimental models, such as mouse, cell lines and organoids, followed by functional assays. If you are (or know someone who is) educated as a bioinformatician or computational biologist with a data analysis mindset, please get in touch! The ideal candidate should have affinity with machine learning, statistics and computational science in general and demonstrable knowledge of molecular biology and/or cancer biology. For more information: http://www.werkenbijumcutrecht.nl/vacatures/Paginas/phd-student-group-de-ri… Best Jeroen de Ridder ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

1 0

PhD position in Statistics for Biotech Data at GUGC
by Katrijn Vannerum 02 Jun '16

02 Jun '16

Recently a PhD position at GUGC in Korea is opened for research on (bio)statistics. Please see https://edit.ugent.be/en/work/vacancies/assisting/full-time-junior-assistan… or the attached document. Kind regards, Prof. Dr. Arnout Van Messem Centre for Biotech Data Science Ghent University Global Campus #315, 119 Songdomunhwa-Ro Yeonsu-Gu, Incheon, 406-840 South Korea E. Arnout.VanMessem(a)ghent.ac.kr<mailto:Arnout.VanMessem@ghent.ac.kr> T. +82 32 626 4210 F. +82 32 626 4109

1 0

Extended deadline for Bioinformatics meet Digital Pathology workshop at ECCB 2016
by Yves Sucaet 01 Jun '16

01 Jun '16

SECOND CALL FOR ABSTRACTS: CPW2016 - Bioinformatics and computational pathology summit Due to several requests we have decided to extend the MLSB 2016 submission deadline until Friday June 10. The workshop webpage (http://cpw.pathomation.com) has been updated to reflect the changes. When? Saturday, September 3, 2016. Where? Den Hague, Netherlands (during ECCB2016) Website? http://cpw.pathomation.com Digital pathology is increasingly used to study biological processes and diseases as novel molecular probing and imaging techniques allow the measurement of single molecules in whole tissue sections. Resulting multi-gigapixel images can be viewed on a computer screen via dedicated software. However, automated analysis of such large-scale datasets is challenging and their combination with omics data is not trivial. This workshop wants to facilitate bridging opportunities between the bioinformatics and tissue image analysis communities. This first edition is organized as a full-day workshop during ECCB 2016 (http://www.eccb2016.org) KEYNOTE SPEAKERS: The following keynote speakers have already agreed to speak at the conference: Jeroen Van der Laak, UMC Radboud Jeffrey Fine, Magee-Womens Hospital of UPMC SUBMISSIONS: The conference solicits oral talks, posters, and proceeding papers contributions of original work or work that was recently accepted or published in a peer-reviewed journal or at a high level international conference. In the latter case, the publication reference should be clearly mentioned, and the abstracts should be checked mainly for relevance, rather than receive a full review. Conference proceedings will be published by the Journal of Pathology Informatics (http://www.jpathinformatics.org) The program committee will decide which contributions are selected for an oral presentation, and which ones are presented during a poster session. For submission instructions, please refer to https://www.fourwav.es/view/265/info/. SCOPE: Computational pathology exists at the interphase between bioinformatics, machine learning, and digital pathology (microscopy). Submissions from all topics of interest are welcome (non-exhaustive list): Machine learning and image analysis for quantification in digital pathology (in 2D & 3D), Novel approaches (e.g. spatial or graph-based methods) to extract high-level features (e.g. molecular networks or spatial expression patterns) from tissue images for systems pathology, Software development methodologies and tools to ease the exploitation of large tissue images and integration with omics data, Novel molecular imaging techniques on tissues (molecular pathology, next generation pathology) and their analysis challenges, e.g. in situ hybridization, mass spectrometry imaging of formalin-fixed paraffin-embedded tissues, mass cytometry, and other spectroscopy techniques (Raman,...)... Research applications on non-human model organisms KEY DATES: Submission deadline: Friday June 10, 2016. Notification of acceptance: June 30, 2016. Conference: September 3, 2016. Organizing committee: Yves Sucaet, Vrije Universiteit Brussel, Belgium Jeroen Van der Laak, UMC Radboud, Netherlands Marius Nap, HistoGeneX, Belgium and Rigshospitalet Copenhagen, Denmark Zev Leifer, New York College of Podiatric Medicine, USA Yukako Yagi, Harvard Medical School & Massachusetts General Hospital, USA Raphaël Marée, Université de Liège, Belgium David Ameisen, IRIF, CNRS and Université Paris Diderot, France Paul Van Diest, UMC Utrecht, Netherlands

1 0

Bioinformatics Post-doctoral position @ INRA, France
by emmanuelle morin 31 May '16

31 May '16

*Postdoctoral Position in Comparative Genomics and Symbiosis Evolution * *Institution*: INRA, Lab of Excellence ARBRE *Location*: Nancy, France *Job Description: * A postdoctoral researcher position is available immediately in the lab of Francis Martin at the Tree-Microbe Interactions Department at INRA in Nancy, France. Martin’s lab uses computational approaches to study how saprotrophic and symbiotic (mycorrhizal) fungi evolve and adapt to their environments. Ongoing projects fall into the following broad areas: 1) Studying the emergence of the symbiotic mutualism in fungal and tree species by phylogenomics; 2) Characterization of symbiosis-related genes by using comparative transcriptomics; and 3) Deciphering genomic signatures of fungal adaptations to carbon decay and sequestration in forest habitats by metatranscriptomics. More information about Martin’s lab is available at http://mycor.nancy.inra.fr/blogGenomes/?page_id=149. Qualified applicant must have a Ph.D. in bioinformatics, computational biology, computer science, evolutionary biology or a related field with background and strong interest in molecular evolution of Fungi. The ideal candidate will already have some experience working with large genomic data sets from sequenced fungi or plants. This position requires a high level of proficiency in programming skills, and experience applying computational methods to genomic data is highly desirable. Applicants must possess good communication skills and be fluent in both spoken and written English (or French). Strong skills in the use of unix-based computer software, critical thinking, problem-solving abilities, and the ability to work semi-independently are also required. The responsibilities will include pipeline development for analyses of next-generation data sets and utilization of high-performance computing facilities. The successful candidate should anticipate contributing to a variety of ongoing collaborative research projects with the Joint Genome Institute, including the 1000 Fungal Genomes project and the Mycorrhizal Genomics Initiative, with teams across France, Europe and the United States. In addition to becoming a part of a vibrant research and educational environment, the incumbent can take advantage of professional development programs offered by Laboratory of Excellence ARBRE (http://mycor.nancy.inra.fr/ARBRE/?page_id=2&lang=en) The initial appointment is for one year with the possibility of renewal for up to two additional years contingent upon performance and funding. Review of applications will begin immediately and continue until the position is filled. Start date is July 1st, 2016 at the latest. *Interested applicants should send a single PDF file containing CV, one-page statement of research interests and contact information of three referees to Francis Martin at fmartin[at]nancy.inra.fr.* -- Emmanuelle MORIN UMR 1136 INRA/Université de Lorraine F-54280 Champenoux Tel : + 33 3 83 39 41 33 http://mycor.nancy.inra.fr

1 0