July 2014 - BBClist - maillist.psb.ugent.be

bioinformatics PhD position in Wageningen
by stephane Rombauts 07 Jul '14

07 Jul '14

We have a Marie Curie ITN (COMREC) and the candidate has just bailed out and we need to find a non-Dutch bioinformatician before November to do the thesis with us. Do you mind to disseminate the attached announcement around? Thank you very much in advance, Gabino

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PhD student positions in computational proteomics
by Şule Yılmaz 07 Jul '14

07 Jul '14

The CompOmics group in Gent, Belgium is going to hire a new PhD student. In addition to this, there is also an opening for two joint PhD positions (one with Dr. René Zahedi, and one with Prof. Dr. Albert Sickmann) at ISAS in Dortmund, Germany. More details about it can be found here and also attached.* Job description * The group of Prof. Dr. Lennart Martens, located in Ghent, Belgium, focuses on the analysis and integration of high-throughput omics data. The group is currently looking for PhDs student to work on computational proteomics. The group of Prof. Martens is very internationally oriented, and has a very strong publication record. The group offers an open, highly dynamic, and challenging working environment, in which team work, initiative and originality are stimulated. The positions are available from 1st of September 2014 or earlier, based on availability. http://www.compomics.com http://www.vib.be/en/research/scientists/Pages/Lennart-Martens%20Lab.aspx * **Profile *You have (or will soon have) a Master’s degree in a relevant field (sciences, informatics, statistics, mathematics, (bio-)engineering). You combine a keen interest in bioinformatics and/or data mining with knowledge of algorithm design and/or Machine Learning. Any prior experience with proteomics informatics and/or software development is considered an advantage. *Contact *Please submit a cover letter, a full c.v., and two contact persons (with name, email, address, phone number) for letters of reference via email to * *lennart.martens(a)UGent.be, or via mail to: Lennart Martens, A. Baertsoenkaai 3, B-9000 Gent, BELGIUM.* Application deadline *Please submit applications before 1st of August 2014.

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Software developer, bioinformatician
by Şule Yılmaz 07 Jul '14

07 Jul '14

*Job description:* The research group of Prof. Dr. Lennart Martens at Ghent University and VIB in Ghent, Belgium, is specialized in the storage, processing and analysis of large data sets obtained from modern high-throughput analysis methods in the life sciences. This highly international and dynamic group is looking for a new team member to strengthen its software development and data analysis capabilities. The job entails software development in Java and Python, and data analysis using R and Python. The position is immediately available, and the successful candidate will be offered a three-year contract, that can be extended based on performance. The group is very internationally oriented, and has very close collaborations with groups in Luxembourg, Germany, Norway, Sweden and the UK, amongst others. The group offers an open, highly dynamic, and challenging working environment, in which team work, initiative and originality are strongly stimulated. http://www.compomics.com/ http://www.vib.be/en/research/scientists/Pages/Lennart-Martens%20Lab.aspx *Profile:* You have (or will soon have) a Bachelor or Master’s degree, preferably in (bio-) science, informatics or engineering. You combine an avid interest in software development and data analysis with a general interest in informatics, and are eager and able to acquire new skills under the guidance of experts. You can program in an object-oriented programming language, preferably Java and/or Python. Any experience you have with relational databases (e.g., MySQL) is an asset. You're also interested in front-end technologies (HTML5, JavaScript). Finally, you are a team worker, who enjoys solving problems in collaboration with others. *Contact:* Applications, including a cover letter, a full c.v., and two contact persons (with name, email, address, phone number) for references, should be sent via email to: lennart.martens(a)UGent.be, or via mail to: Lennart Martens, A. Baertsoenkaai 3, B-9000 Gent, BELGIUM. *Application deadline:* Please submit applications before 1st of August 2014

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Postdoc in Computational Cancer Biology
by l.wessels＠nki.nl 07 Jul '14

07 Jul '14

POSTDOC IN COMPUTATIONAL CANCER BIOLOGY PROJECT OUTLINE At the Netherlands Cancer Institute (NKI) several high throughput screens are performed, such as imaging-based high-content screens that aim to capture genotype-phenotype relations, and transposon reporter screens that are used to study the effect of chromatin organization on gene expression. Moreover, the size and number of publicly available datasets, such as ENCODE, TCGA and the drug screening datasets is increasing. In the Delft Bioinformatics Lab (bioinformatics.tudelft.nl) and the Computational Cancer Biology group at the NKI (ccb.nki.nl) we develop machine learning algorithms to extract biologically relevant structure from these data. However, integrally analyzing these heterogeneous data, while ensuring that the derived models remain amenable to biological interpretation is a major challenge. In this project we aim to develop machine learning based data integration algorithms that can deal with heterogeneous, partially unlabeled data. A special emphasis is placed on deriving models that are interpretable, thus maximizing the biological utility of such models. The successful candidate will - Be responsible for performing and supervising the research project; - Act as a liaison between the TUDelft and the NKI with the aim of identifying synergies between these institutions and developing these projects further; - Contribute to education at the BSc, MSc and PhD levels, as well as assist in the supervision of MSc and PhD students. REQUIREMENTS The candidates should have a strong computational background in bioinformatics or machine learning with a track-record in (cancer) genomics. The candidate must be able to work effectively in a multidisciplinary team environment and be able to partner with leading, worldwide institutions (university, government agencies, national labs, and professional organizations). The candidate must have exceptional communication skills, capable of interacting with peers and students and technical staff. EMPLOYER PROFILES The Delft Bioinformatics Lab at the TUDelft develops computer algorithms to further fundamental biological knowledge, apply these to advance the state-of-the-art in health care and industry. To this end, we closely collaborate with researchers in molecular and cell biology, medicine and biotechnology. The Computational Cancer Biology group at the NKI, focuses on developing novel computational approaches which exploit a wide variety of (high-throughput) data sources to further our basic understanding of cancer and to translate these findings to the clinic. CONTACT DETAILS Please contact Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels(a)nki.nl. When applying please ensure you include a CV, list of publications and the names and addresses of at least two persons that can be approached to obtain further information. Also see ccb.nki.nl for further information. CLOSING DATE: 1 MAY 2014

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Mark you calendar: Environmental Metagenomics Course & Symposium, 15-19 September 2014, Wageningen, the Netherlands
by Celia.vanGelder＠radboudumc.nl 05 Jul '14

05 Jul '14

Dear colleague, Metagenomics has quickly become one of the most important discovery tools in microbial ecology. Metagenomics is a powerful tool to study the organisms in microbial communities, that has numerous applications in many areas of biomedical science. By bypassing the need for laboratory culturing, this technology can unlock the massive uncultured microbial diversity, enabling the microbial component of specific environments to be surveyed, discover new organisms, and explore the dynamic ecology of microbial populations under changing conditions. The high throughput nature of metagenomics means that huge datasets are generated, and in order to extract biological information from these data, advanced bioinformatics and statistical tools are indispensable. >From 15-19 September 2014 we organize a five-day course at NIOO-KNAW in Wageningen. Participants will get hands on experience in the analysis and treatment of metagenomic data, including preprocessing and quality filtering, data handling and submission to public archives, annotation, multivariate statistical analyses, and metagenome assembly. On the last day of the course, 19 September 2014, we are organizing an Environmental Metagenomics Symposium which will bring together renowned scientists in microbial ecology and bioinformatics, who will present their recent explorations of the microbiota of different environments. Moreover, we will welcome the presentations of several students of the metagenomics course held in the week leading up to this symposium. Together, this will be an exciting opportunity to see the latest advances in environmental metagenomics from young talents as well as established leaders in the field. The symposium is open for everyone interested in environmental metagenomics. Attending the symposium is free of charge, but registration by email is required. All information about the programmes of course and symposium and about registration can be found in the attached pdf. Our website will be available soon: https://nioo.knaw.nl/en/metagenomics-course. The organization of course and symposium has been made possible with the generous support of AllBio.<http://www.allbioinformatics.eu/doku.php> If you are interested in participating in either the course or the symposium, please mark your calendar! You can also indicate your interest in participating by sending an email to Barbara van Kampen (Barbara.vanKampen(a)radboudumc.nl<mailto:Barbara.vanKampen@radboudumc.nl>). You will then be notified when registration is open. Best regards, Bas Dutilh (Utrecht University & Radboudumc) Eiko Kuramae (NIOO-KNAW) Celia van Gelder (Radboudumc) Dr. Celia W.G. van Gelder Projectleader Education NBIC/BioSB Coordinator Education CMBI Programme Manager Learning DTL tel. +31-(0)24-3666120 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:C.vanGelder@umcn.nl> websites: www.nbic.nl<http://www.nbic.nl/>, www.biosb.nl, www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.dtls.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre PO Box 9101 6500 HB Nijmegen The Netherlands Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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Bioinformatician at SkylineDx (1,0 fte)
by Erik van Beers 03 Jul '14

03 Jul '14

Bioinformatician (PhD, 1,0 fte) [zx21] Job Description The Bioinformatician will perform research, feasibility and development work for molecular diagnostic assays, including microarrays and next generation sequencing with the goal of improving existing and building new assays. Key domains for this Bioinformatician are collaborations with academic partners (Erasmus MC and other national and international groups) and SkylineDx's development team to evaluate and ensure the implementation and validation of clinically relevant scientific discoveries into reliable medical diagnostic assays for diagnosis, prognosis and drug effectiveness prediction that will ultimately contribute to improved patient care. The candidate will collaborate in a multidisciplinary team with biologists, medical doctors, bioinformaticians, statisticians, laboratory technicians, study directors, software development engineers and our QA and regulatory department. The candidate will substantially contribute to preparation of the assay registration files as well as scientific publications and presentations of the research and development of our diagnostic assays. Profile The candidate should preferably have a PhD degree in Bioinformatics with relevant experience in oncology and genomics. MSc with some experience are also invited to respond. A track record in machine learning combined with programming skills (e.g., R, Matlab, Perl, C++), and a fundamental knowledge of statistics is strongly preferred. Publication skills are an important asset. A keen interest in new developments and experience in high throughput assay design and analysis is a pre. The candidate shall have good communication and organization skills, and a service and result-oriented attitude. We offer SkylineDx offers you to become part of our challenge to translate state-of-the-art scientific achievements into diagnostic products that will contribute to improve patient care. We are a young and dynamic company offering excellent opportunities for personal growth and development. Skyline is well embedded in the infrastructure of the Hematology and Bioinformatics Departments of the Erasmus MC in Rotterdam, the Netherlands. Therefore, we believe the company can offer you the best of both worlds; a career in life sciences with emphasis on product development and clinical diagnostics in close collaboration with an academic environment. We offer a full-time position with an attractive salary, 25 holidays and travelling expenses compensation. Company description SkylineDx is a pioneer in the field of molecular diagnostics through developing and commercializing array-based diagnostic tests using gene signatures for personalized medicine in oncology that help to provide physicians and patients with the best individual care possible. At SkylineDx we transform life sciences into the daily practice of clinical diagnostics. SkylineDx has a dedicated team with unique expertise and the technology needed for a highly efficient identification of novel relevant biomarkers, development, registration and commercialization of (companion) diagnostics. Our mission is to improve therapeutic treatment selection through the development of reliable, clinically validated molecular diagnostic tests for blood cancers and thereby improving the quality of life of blood cancer patients. As an innovative company, SkylineDx is continuously seeking for ambitious colleagues with an academic and/or industrial background that are passionate about our mission. You are invited to send your application to e.vanbeers(a)skylinedx.com<mailto:e.vanbeers@skylinedx.com> [SkylineDX_logo_.XXXsmall] E.H. van Beers, PhD vice president science & technology. SkylineDx BV Rotterdam Science Tower Marconistraat 16 3029 AK Rotterdam The Netherlands Phone: +31 (0)10 70 43431 Web: www.skylinedx.com<http://www.skyline-diagnostics.com/> Follow us: [twitter]<http://twitter.com/skylinedx> [linkedIn] <http://www.linkedin.com/company/222765>

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Junior Principal Investigators Workshop at ISMB 2014
by Jeroen de Ridder - EWI 03 Jul '14

03 Jul '14

Junior Principal Investigators Workshop at ISMB 2014 Sunday July 13, 10:30am - 12:25 pm, Lunch 12:30-2:00pm Building on the success of the JPI meeting in 2013<http://iscb.us3.list-manage.com/track/click?u=4c0e7fa66594378a44ccd614e&id=…>, the JPI workshop will bring together scientists who recently started or expect to start their own research group. It will serve the purpose of launching a community of junior PIs within the broader field of Computational Biology, providing the ideal platform for networking opportunities and the sharing of valuable experiences<http://iscb.us3.list-manage.com/track/click?u=4c0e7fa66594378a44ccd614e&id=…>. Present your research During the workshop you will get the chance to present your research in a 2-3 minute elevator pitch using a single presentation slide. This will facilitate networking opportunities and help connect you with potential collaborators. If you want to present you must submit a presentation slide (see details below). Hear from one of the best An expert in the field (TBC) will deliver a keynote talk on how to successfully set up and lead your lab. Discuss the challenges of being a Junior PI with your peers There will be a series of round-table discussions at the JPI lunch (immediately following the workshop) at an offsite venue (TBC, tickets available soon). During this session we aim to learn from each other by discussing topics that are relevant to being a Junior PI. Examples: Grant writing, hiring and supervising, setting up collaborations, leading a team, and the role of social networks/media in maximizing research impact. Use the submission form to suggest topics relevant to you. Register your interest in attending the lunch during slide submission (details below). Submission guidelines Submission website: https://www.easychair.org/conferences/?conf=jpiismb2014<http://iscb.us3.list-manage.com/track/click?u=4c0e7fa66594378a44ccd614e&id=…>. Please include the following information in the abstract box on the submission website: * a short bio about you and your research to share with participants (maximum 200 words) * any topic recommendations for the round table discussions * whether you will attend the JPI lunch following the workshop to continue round table discussions (tickets sold separately) More information Workshop website: https://www.iscb.org/cms_addon/conferences/ismb2014/workshops.php<http://iscb.us3.list-manage.com/track/click?u=4c0e7fa66594378a44ccd614e&id=…> JPI COSI: http://cosi.iscb.org/wiki/JPI:Home<http://iscb.us3.list-manage.com/track/click?u=4c0e7fa66594378a44ccd614e&id=…> JPI linkedin group: http://www.linkedin.com/groups/PIs-in-Computational-Biology-4990102<http://iscb.us3.list-manage1.com/track/click?u=4c0e7fa66594378a44ccd614e&id…> Email: jpicontact(a)iscb.org<mailto:jpicontact@iscb.org>

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Fwd: Junior Principal Investigators Workshop at ISMB 2014
by Jeroen de Ridder - EWI 03 Jul '14

03 Jul '14

[cid:085523C0-D0E9-4769-B101-A2860C4997D9@tudelft.nl] Junior Principal Investigators Workshop at ISMB 2014 Sunday July 13, 10:30am - 12:25 pm, Lunch 12:30-2:00pm Building on the success of the JPI meeting in 2013<http://iscb.us3.list-manage.com/track/click?u=4c0e7fa66594378a44ccd614e&id=…>, the JPI workshop will bring together scientists who recently started or expect to start their own research group. It will serve the purpose of launching a community of junior PIs within the broader field of Computational Biology, providing the ideal platform for networking opportunities and the sharing of valuable experiences<http://iscb.us3.list-manage.com/track/click?u=4c0e7fa66594378a44ccd614e&id=…>. Present your research During the workshop you will get the chance to present your research in a 2-3 minute elevator pitch using a single presentation slide. This will facilitate networking opportunities and help connect you with potential collaborators. If you want to present you must submit a presentation slide (see details below). Hear from one of the best An expert in the field (TBC) will deliver a keynote talk on how to successfully set up and lead your lab. Discuss the challenges of being a Junior PI with your peers There will be a series of round-table discussions at the JPI lunch (immediately following the workshop) at an offsite venue (TBC, tickets available soon). During this session we aim to learn from each other by discussing topics that are relevant to being a Junior PI. Examples: Grant writing, hiring and supervising, setting up collaborations, leading a team, and the role of social networks/media in maximizing research impact. Use the submission form to suggest topics relevant to you. Register your interest in attending the lunch during slide submission (details below). Submission guidelines Submission website: https://www.easychair.org/conferences/?conf=jpiismb2014<http://iscb.us3.list-manage.com/track/click?u=4c0e7fa66594378a44ccd614e&id=…>. Please include the following information in the abstract box on the submission website: * a short bio about you and your research to share with participants (maximum 200 words) * any topic recommendations for the round table discussions * whether you will attend the JPI lunch following the workshop to continue round table discussions (tickets sold separately) More information Workshop website: https://www.iscb.org/cms_addon/conferences/ismb2014/workshops.php<http://iscb.us3.list-manage.com/track/click?u=4c0e7fa66594378a44ccd614e&id=…> JPI COSI: http://cosi.iscb.org/wiki/JPI:Home<http://iscb.us3.list-manage.com/track/click?u=4c0e7fa66594378a44ccd614e&id=…> JPI linkedin group: http://www.linkedin.com/groups/PIs-in-Computational-Biology-4990102<http://iscb.us3.list-manage1.com/track/click?u=4c0e7fa66594378a44ccd614e&id…> Email: jpicontact(a)iscb.org<mailto:jpicontact@iscb.org> Register to Attend ISMB'14<http://iscb.us3.list-manage.com/track/click?u=4c0e7fa66594378a44ccd614e&id=…> Conference Reception<http://iscb.us3.list-manage2.com/track/click?u=4c0e7fa66594378a44ccd614e&id…> Become an ISCB Member<http://iscb.us3.list-manage1.com/track/click?u=4c0e7fa66594378a44ccd614e&id…> ISMB'14 Career Fair<http://iscb.us3.list-manage.com/track/click?u=4c0e7fa66594378a44ccd614e&id=…> Copyright © 2014 International Society for Computational Biology, All rights reserved. ISCB announcements Our mailing address is: International Society for Computational Biology 9500 Gilman Drive MC 0505 San Diego, CA 92093-0505 Add us to your address book<http://iscb.us3.list-manage1.com/vcard?u=4c0e7fa66594378a44ccd614e&id=04453…> unsubscribe from this list<http://iscb.us3.list-manage.com/unsubscribe?u=4c0e7fa66594378a44ccd614e&id=…> update subscription preferences<http://iscb.us3.list-manage.com/profile?u=4c0e7fa66594378a44ccd614e&id=0445…> [Email Marketing Powered by MailChimp]<http://www.mailchimp.com/monkey-rewards/?utm_source=freemium_newsletter&utm…>

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Call for Abstracts - The 1st Unified Workshop on Proteome and Metabolome Informatics @ ECCB 2014
by Andrew Dowsey 02 Jul '14

02 Jul '14

Abstract submission deadline: Monday July 14th Dear colleagues, We invite you to submit an abstract for oral or poster presentation at The 1st Unified Workshop on Proteome and Metabolome Informatics, to be held at ECCB 2014, Strasbourg, France on Saturday 6th September. This workshop will be of interest to all researchers in proteomics or metabolomics, whether at the wet-lab or informatics level. It will also be of relevance to systems modellers and network biologists who integrate proteomics and metabolomics data and who wish to gain a greater understanding of how upstream processing of this data is performed. The core aim for this workshop is for there to be an equal proportion of talks on proteome and metabolome informatics. In particular, we will prefer talks that already describe some synergy between the two fields. Speakers are advised to ensure metabolomics concepts are accessible to a proteomics audience, and vice versa. The agenda with invited speakers and further details is available from http://www.cadetbioinformatics.org/workshops/eccb14/ Here you can also find the abstract submission form and details for registering. The abstract submission deadline is Monday July 14th. Hope to see you in Strasbourg! The Organsing Committee, Andrew Dowsey Simon Rogers Rainer Breitling Richard Unwin Andrew Dowsey PhD Lecturer and CADET Bioinformatics Research Lead Institute of Human Development, The University of Manchester t: +44 161 701 0244 f: +44 161 701 0242 http://www.manchester.ac.uk/research/andrew.dowsey<http://www.manchester.ac.uk/research/andrew.dowsey/> Centre for Advanced Discovery and Experimental Therapeutics (CADET) Central Manchester University Hospitals NHS Foundation Trust Oxford Road Manchester M13 9WL UK

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Vacature Data analist, Afdeling Klinische Genetica, VU Medisch Centrum Amsterdam
by Beek, Daphne van 02 Jul '14

02 Jul '14

Vacature: Data analist 36 uur, vast contract, bepaalde tijd Analyseren van Next Generation Sequencing data binnen de diagnostiek Werkomgeving De afdeling klinische genetica is verantwoordelijk voor het diagnosticeren van (mogelijke) genetische/erfelijke afwijkingen, zowel bij kinderen en volwassenen maar ook steeds meer bij embryo's vroeg in de zwangerschap. Er wordt hierbij intensief gebruik gemaakt van in-house Next Generation Sequencing capaciteit. Zo gebruikt onze afdeling momenteel deze techniek voor analyse van genpakketten, exomen (WES) en niet-invasieve prenatale diagnostiek (NIPT). Vanwege de enorme toename van het gebruik van NGS is de afdeling is op zoek naar uitbreiding van haar bioinformatica team met een data analist. Deze heeft de verantwoordelijkheid de grote datastromen die hiermee gegenereerd worden te beheersen en op een efficiënte en effectieve manier beschikbaar te maken in de praktijk van de kliniek. Werkzaamheden Als Data analist zijn je voornaamste taken: * Het runnen van verschillende diagnostische pipelines/flows; * Uitvoeren van periodieke checks en genereren van statistieken ten behoeve van quality control; * Troubleshooting binnen onze bioinformatische pipelines; * Managen van de data die door de sequencing faciliteit gegenereerd wordt; * Beheren en ontwikkelen van de soft- en hardware infrastructuur; * Schrijven van pipelines om data te kunnen verwerken; * Testen van software voor gebruik in de diagnostiek (validatie); * Opstellen en reviseren van protocollen (SOPs); * Het signaleren van afwijkende resultaten. Jouw profiel Wij zoeken een Data analist die de volgende kennis en ervaring met zich meebrengt: * Afgeronde WO/HBO opleiding informatica/bioinformatica; * Ervaring met het werken met pipelines; * Ervaring met Python en Bash in een Linux omgeving; * Ervaring met het werken met cluster computers is een pré; * Ervaring in de genetica is niet nodig, interesse hierin is echter wenselijk; * Je neemt initiatief, bent analytisch, stressbestendig en inventief. Wij bieden Salarisschaal 9: 2689 tot 3704 euro bruto bij een fulltime dienstverband (afhankelijk van opleiding en ervaring). Inschaling in salarisschaal 10 is bij de juiste opleiding en ervaring bespreekbaar. Naast een uitstekend basissalaris bieden we onder andere 8,3% eindejaarsuitkering en 8% vakantietoeslag. Voor meer informatie over onze voorwaarden zie: http://www.werkenbijvumc.nl/vumc/arbeidsvoorwaarden/ Wij bieden in eerste instantie een contract voor 12 maanden, dat bij goed functioneren kan worden verlengd. Pas jij bij VUmc? Doe de test! http://www.werkenbijvumc.nl/vumc/cultuur/ Bijzonderheden Voor meer informatie over de selectieprocedure kunt je terecht bij Wessel Haytink, recruiter, via telefoonnummer: 06 - 1066 7718. Interesse? Wil je meer informatie over de functie dan kun je contact opnemen met dr. E.A. Sistermans, hoofd genoomdiagnostiek via 020-4448346 of met Daphne van Beek, bio-informaticus via 020-4443092. Je kunt uiterlijk tot 8 juli 2014 solliciteren via deze link<http://www.werkenbijvumc.nl/vacatures/D5.2014.00070WH/?Data+analist>.

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