June 2016 - BBClist - maillist.psb.ugent.be

postdoctoral position in bioinformatics in University of Groningen
by Horvatovich, P.L. 20 Jun '16

20 Jun '16

Postdoc research position LC-MS/MS data preprocessing and statistical analysis (216165) Organisation The Faculty of Mathematics and Natural Sciences harbours a kaleidoscope of disciplines and research strengths. Our programmes in research and education range from nanomaterials and biomachinery to astronomy, from mathematics to pharmacy, from neurosciences to computer science, and from molecular and evolutionary biology to marine biology. Our researchers pursue fundamental key questions while collaborating with partners from industry, the medical world and other realms of society. Frontline research groups explore new fields such as synthetic biologyand sustainable energy use. Job description Development of single-stage LC-MS/MS data preprocessing and statistical analysis approaches for risk assessment of mycotoxin exposure through dietary intake in Qatar. This postdoctoral position is embedded within the interdisciplinary research groups of Analytical Biochemistry/Department of Pharmacy1 at the Faculty of Mathematics and Natural Science of the University of Groningen (RUG). Mycotoxins are the most ubiquitous carcinogenic contaminant in the human food supply leading to adverse consequences on human population such as hepatocellular carcinoma. Mycotoxin concentrations are regularly measured in food but their impact on human population health remain unclear. The aim of this project is to perform risk assessment of mycotoxin exposure of Qatar population through dietary intake in collaboration with scientists of the Anti Doping Lab Qatar2. In the research project the postdoctoral scientist is expected i) to develop and implement novel single stage, data dependent and data independent LC-MS(/MS) data pre-processing workflows based on Threshold Avoiding Proteomics3 pipeline and other open source tool such as OpenMS4, XCMS5 and mzMine6, and ii) statistical analysis of obtained molecular profile for mycotoxin exposure in pilot animal study and in human population and iii) perform risk assessment of human population in Qatar based on obtained data. The successful candidate will strongly benefit from working in a highly interdisciplinary research team composed of clinical researchers, analytical chemists, bioinformaticians and statisticians. The Analytical Biochemistry group has an excellent scientific infrastructure and track record in proteomics, proteogenomics and computational Mass Spectrometry1. Qualifications The candidate should have a strong background in mathematics and statistics and should have strong experience in C++, Matlab and/or R programming. Experience with data analysis in mass spectrometry would be a significant advantage. The candidate should be able to work in an interdisciplinary and multinational research team and have good communication skills. Conditions of employment The University of Groningen offers a salary that is determined in accordance with the rules as set out in the collective labour agreement for the Dutch Universities (CAO) and has a range between € 3,044 and € 3,997 (scale 10 Dutch Universities) gross per month depending on qualifications and experience based on a fulltime position. The position is temporary for one year. After a positive successful evaluation in the first year, the contract will be extended by 1.5 year. The University of Groningen offers an excellent research infrastructure and training programme to develop research skills of the successful candidate. Link references: 1 http://www.biomac.nl 2 http://adlqatar.net/ 3 Suits F, Hoekman B, Rosenling T, Bischoff R, Horvatovich P., Threshold-avoiding proteomics pipeline, Anal Chem. 2011, 15;83(20):7786-94. 4 Bertsch A, Gröpl C, Reinert K, Kohlbacher O., OpenMS and TOPP: open source software for LC-MS data analysis, Methods Mol Biol. 2011;696:353-67. 5 Mahieu NG, Genenbacher JL, Patti GJ., A roadmap for the XCMS family of software solutions in metabolomics, Curr Opin Chem Biol., 2016, 30:87-93. 6 Pluskal T, Castillo S, Villar-Briones A, Oresic M., MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data, BMC Bioinformatics. 2010, 11:395. Additional information and sending in of applications Applications with curriculum vitae and the names of three former or present supervisors who can be contacted as references should be sent until 14 July / before 15 July 2016 Dutch local time by means of the application form (click on the link below). Unsolicited marketing is not appreciated. Information For information you can contact: · Prof. P.L. Horvatovich, +31 50 3633341, p.l.horvatovich(a)rug.nl (please do not use for applications) *Apply <http://www.rug.nl/about-us/work-with-us/job-opportunities/overview?reply=00…>* or direct link: http://www.rug.nl/about-us/work-with-us/job-opportunities/overview?reply=00… -- Peter Horvatovich Associate Professor University of Groningen Faculty of Mathematics and Natural Sciences Department of Pharmacy Analytical Biochemistry Building 3226, Room 6.9 Antonius Deusinglaan 1 9713 AV Groningen Internal Zip Code XB20 P.O. Box 196 9700 AD Groningen The Netherlands Telephone: +31-(0)50-363 3341 Fax: +31 (0)50 363 7582 Mobile: +31 (0)6 2459 7203 Email: p.l.horvatovich(a)rug.nl Homepage: www.biomac.nl

1 0

Vacancy: The Netherlands Institute of Ecology is looking for a bioinformatician
by Mattias de Hollander 17 Jun '16

17 Jun '16

The Netherlands Institute of Ecology (NIOO-KNAW) offers the position of: *Bio-informatician * The bioinformatician has a general task to give support to researchers in each of the four NIOO-KNAW research departments. Sequencing projects are very diverse, ranging from bacteria and fungi to plants, insects, birds and genetic material recovered directly from soil or other environmental samples. The bioinformatician’s task involves close interaction with researchers and with ICT staff. Work is aimed at facilitating researchers to perform their bioinformatics analyses, both for sequencing-based and other data-rich research. This includes tutoring and help with data management, building in-house bioinformatic pipelines and facilitating downstream analyses. The ideal candidate has an academic background, excellent communication skills in English, several years of experience with high-throughput sequencing data, a strong motivation and social skills to support a broad range of different projects, a good network of contacts in the bioinformatics community, and a flexible and cooperative attitude. Requirements: * Experience with working in a UNIX environment * Affinity with system administration tasks for HPC systems * Good programming skills, preferably Python and R * Experience with workflow management systems, preferably Snakemake * Experience with version control systems like Git * Experience with web-services (R-studio, Gitlab, Galaxy, Genome browsers) * Motivated to give in-house trainings * Affinity with data management and stewardship More information: https://nioo.knaw.nl/en/vacatures/bio-informatician-embedded

1 0

Job offer - System administrator for ELIXIR Node in Luxembourg
by Venkata Pardhasaradhi SATAGOPAM 15 Jun '16

15 Jun '16

Dear all, We are looking for a System administrator for ELIXIR Luxembourg node. Please refer the attached PDF or URL http://emea3.mrted.ly/13fpu <http://emea3.mrted.ly/13fpu> for more details. Best regards, Venkata -- Venkata P. Satagopam Bioinformatics Core Luxembourg Centre For Systems Biomedicine (LCSB) University of Luxembourg Campus Belval, House of Biomedicine II 6, avenue du Swing L-4367 Belvaux T +352-466-644-6421 F +352-466-644-6949 venkata.satagopam(a)uni.lu <mailto:venkata.satagopam@uni.lu> http://lcsb.uni.lu <http://lcsb.uni.lu/> ----- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies. -----

1 0

3Gb-TEST Course; Next-generation sequencing in a diagnostic setting
by J.A.Lopez_Hernandez＠lumc.nl 15 Jun '16

15 Jun '16

3Gb-TEST Course; Next-generation sequencing in a diagnostic setting The 3Gb-Test Consortium, invite your participation in to the NGS 2016 course in Lisbon, Portugal. It is a 4-day course from 24th till 27th of October 2016 with focus is on clinical diagnostics using exome/genome sequences, variant identification and analysis including afternoon practical sessions. [cid:e05917bd-7821-4f69-b56b-9c6ddf2cdf36] Location Instituto Nacional de Saude, Lisboa, Portugal. http://www.insa.pt Some of the topics to be covered: Characteristics of the NGS methods Annotation and prioritization of variants Whole genome VS whole exome sequencing Functional validation of variants Targeting gene panels Exome sequencing Calling variants Afternoon practical sessions* More information at http://3gb-test.eu/24-27-october-2016-4-day-course-on-ngs-lisbon-portugal/ Please feel free to distribute this material

1 0

Postdoctoral position - Breast Cancer Translational Research Laboratory - Brussels
by Matthieu Defrance 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) and Dr. Françoise Rothé (francoise.rothe(a)bordet.be) Application deadline: 30 September 2016

1 0

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