January 2015 - BBClist - maillist.psb.ugent.be

Life Science Courses at Avans University of Applied Sciences
by Sari van Heel - Vauhkala 16 Jan '15

16 Jan '15

Dear members of BBClist, We would like to draw your attention to three courses that the Research Group Analysis Techniques in Life Science (Avans University of Applied Sciences, Breda, the Netherlands) will be offering in April 2015: 1) Principles, parameters and applications of PCR; 7 April 2015 Registration fee: €400,- Website : http://www.alsavans.nl/avans-training-2545.htm 2) Real-time PCR in molecular diagnostics; 8-10 April 2015 Registration fee: €900,- Website: http://www.alsavans.nl/avans-training-2548.htm 3) Introduction to Next Generation Sequencing; technologies and data analysis; 14-17 April 2015 Registration fee: €1100,- Website: http://www.alsavans.nl/avans-training-2542.htm The digital registration form is available on the website. Should you have any questions, please do not hesitate to contact us by email at: si.vanheel-vauhkala(a)avans.nl<mailto:si.vanheel-vauhkala@avans.nl> Kind regards, Ms. Sari van Heel-Vauhkala Secretary Research Group Analysis Techniques in Life Science Disclaimer ( http://www.avans.nl/over-avans/e-mail-disclaimer )

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Postdoc Opportunity - Comparative Genomics, Horizontal Gene Transfer in Diatoms
by Katrijn Vannerum 15 Jan '15

15 Jan '15

From: Andrew James Alverson [mailto:aja@uark.edu] Sent: woensdag 14 januari 2015 19:27 To: Andrew James Alverson Subject: Postdoc Opportunity - Comparative Genomics, Horizontal Gene Transfer in Diatoms Dear Colleagues, We are conducting a search for a postdoctoral position at the Chicago Botanic Garden to work on an NSF-funded grant in genome reconstruction, horizontal gene transfer, and phylogenomics of diatoms (see the ad below). If you could forward the ad to anyone who might be interested in the position, we would appreciate your help in casting a wide net to find the best possible candidate. Thanks for your help, Andy Alverson and Norm Wickett …. Andrew Alverson University of Arkansas Department of Biological Sciences 1 University of Arkansas, SCEN 601 Fayetteville, AR 72701-1201 office: 479-575-7975 lab: 479-575-4886 http://alversonlab.com/ - - - POSTDOCTORAL RESEARCH ASSOCIATE IN COMPARATIVE GENOMICS AT THE CHICAGO BOTANIC GARDEN We are hiring a postdoctoral research associate for 2.5 years to lead the genome sequencing efforts of an NSF-funded, Phylogenetic Systematics grant titled “Evaluating the contributions of horizontally transferred bacterial genes and endogenous duplication events to the diversification of diatoms”. This project integrates transcriptomics, phylogenomics, and genome sequencing to understand the role of horizontal gene transfer and whole genome duplication in the diversification of diatoms. This project is a collaborative NSF research project between Andrew Alverson (University of Arkansas) and Norman Wickett (Chicago Botanic Garden & Northwestern University). The postdoc will be based at the Chicago Botanic Garden, where the genome sequencing, assembly, and annotation efforts will be based. START DATE: Spring - Fall, 2015 APPLICATION REVIEW: Begins immediately and will continue until filled DUTIES AND RESPONSIBLITIES: The postdoc will be responsible for coordinating and conducting the sequencing, assembly, and annotation of several diatom genomes. Additionally, the position includes the analysis of genome content and structure association with the diversification of diatoms, with an emphasis on the detection of horizontal gene transfer and whole genome duplication. Expectations are that postdoc will contribute to the preparation of numerous publications, many of which will be first-authored. Teaching and curriculum development opportunities will be provided through the Graduate Program in Plant Biology and Conservation, a joint program between the Chicago Botanic Garden and Northwestern University. Finally, the position includes involvement in the development of an exhibit on diatom biology to be hosted at the Chicago Botanic Garden. This PIs of this project are participating in the Oxford Nanopore MinION Access Programme and the postdoc hired for this position will be involved in testing its utility for the sequencing of diatom genomes. POSITION REQUIREMENTS: Applicants must have completed a Ph.D. in ecology and evolutionary biology, biology, bioinformatics, phycology, botany, or a related field by the start date. Some experience in bioinformatics is required, preferably in the area of genome assembly and annotation; skills in a scripting language (Perl/Python) and in a Linux/Unix computing environment are necessary. TO APPLY: Please email a single pdf file that includes a cover letter, CV, and contact information for three references to: nwickett(a)chicagobotanic.org<mailto:nwickett@chicagobotanic.org><mailto:nwickett@chicagobotanic.org> Please email if you have any questions or would like additional information. Katrijn Vannerum PhD Project manager N2N (From Nucleotides to Networks) Multidisciplinary Research Partnership Bioinformatics and Systems Biology Ghent University http://www.nucleotides2networks.be/ twitter: @N2N_UGent Katrijn.Vannerum(a)UGent.be<mailto:Katrijn.Vannerum@UGent.be> Technologiepark 927 9052 Gent, Belgium +32 (0)9 331 36 85 [cid:image001.png@01D030BA.39B3A830]

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ICBO2015 - Call for workshops and tutorials
by Francisco Couto 15 Jan '15

15 Jan '15

The International Conference on Biomedical Ontology (ICBO, http://icbo2015.fc.ul.pt/callworkshops.html) will take place in beautiful Lisbon, Portugal July 26-30 2015. We would like to invite you to submit proposals to host tutorials and/or workshops. Other type of events (clinics, hackathon) will also be considered. TUTORIALS are educational events. They may be either for a full day or for a half day. They should focus on one specific topic presented by one or two experts and involve interaction with the audience. The organizers will be responsible for advertising the tutorial. Tutorials can include hands-on training, in which case the proposal should specify the anticipated requirements (laptops, software to install, etc.). WORKSHOPS provide a forum for the discussion of a specific topic through individual paper presentations; in particular, they should have a specific tangible outcome planned in advance. They may be for either a full day or a half day. The organizers will be responsible for advertising the workshop and reviewing and selecting the contributions. Workshops can also include interest group meetings, or meetings designed to disseminate the results of a research project on a specific topic. Workshop and tutorial proposals should be submitted to the easychair website: https://easychair.org/conferences/?conf=wsicbo2015, in the workshops and tutorials track. Each submission should include the title of the event, name, affiliation and e-mail addresses of the proposers. It should include also a description of the proposed event (maximum 200 words), including an explanation of how the workshop/tutorial will contribute to the field of biomedical ontology. Proposers should describe how they will advertise the event in order to receive a sufficient number of submissions and participants and explain the rationale for addressing their specific topic in the workshop/tutorial rather than in the main conference. One important argument would be to attract more people to ICBO. If the event has been organized in previous editions of ICBO, please indicate some statistics regarding previous attendance for better planning. For more information, please contact icbo2015(a)googlegroups.com, indicating "[icbo2015] workshops and tutorials" in the subject line. Important dates: Feb 10, 2015: Workshops and tutorials proposals submission deadline Feb 24, 2015: Notification of acceptance of workshops and tutorials Apr 13, 2015: Workshop papers submission deadline May 11, 2015: Notification of workshop paper acceptance May 25, 2015: Camera-ready copies submission deadline July 27-28, 2015: ICBO workshops and tutorials July 29-30, 2015: ICBO main conference

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short-term position in structural bioinformatics
by Prevost Martine 14 Jan '15

14 Jan '15

Please find description attached -------------------------------------------- Martine Prévost Structure et Fonction des Membranes Biologiques CP 206/2 Université Libre de Bruxelles Bld du Triomphe B-1050 Bruxelles Belgium Phone : 32-2-650 2049 Fax : 32-2-650 5382 E-mail: mprevost(a)ulb.ac.be --------------------------------------------

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symposium: "from big data to bedside" - Ghent
by Katleen De Preter 13 Jan '15

13 Jan '15

Dear Colleague, On the 2nd of April 2015, we are organising a symposium on translational bioinformatics "From big data to bedside: translational bioinformatics in cancer research". Several international and national top-speakers will present their data (see http://bigdata.cmgg.be) On the 1st of April a workshop will be organised for PhD students and young post-docs (see website for detailed program). Registration is open and can be done via http://bigdata.cmgg.be (be aware that seats are limited). A small registration fee is asked for the symposium (€ 50) and registration for the workshop is free. Hope to meet you soon at the symposium and/or workshop! Kind regards, organiser: Katleen De Preter co-organisers: Frank Speleman, Jo Vandesompele, Pieter Van Vlierberghe, Pieter Mestdagh

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N2N seminar Thursday, January 29 at 11 am: 'Bioinformatics in cancer research' By Prof. van Loo
by Katrijn Vannerum 09 Jan '15

09 Jan '15

Dear All, Prof. Peter van Loo will give a seminar on Thursday, January 29 at 11 am: 'Bioinformatics in cancer research'. (See abstract below) Please contact me if you would like to have a meeting with Prof. Peter van Loo in the afternoon. The lunch meeting is open to all PhD students, but lunch is only provided for students registered at the Doctoral Schools. Registration is still possible. With kind regards, Katrijn Vannerum PhD Project manager N2N (From Nucleotides to Networks) Multidisciplinary Research Partnership Bioinformatics and Systems Biology Ghent University http://www.nucleotides2networks.be/ twitter: @N2N_UGent Katrijn.Vannerum(a)UGent.be<mailto:Katrijn.Vannerum@UGent.be> Technologiepark 927 9052 Gent, Belgium +32 (0)9 331 36 85 [cid:image005.png@01D02C24.94E42990] [cid:image006.png@01D02C24.94E42990] "Bioinformatics in cancer research" Professor Peter van Loo KU Leuven, Department of Human Genetics, Leuven, Belgium January 29, 2014 (11:00) Lunch meeting for Doctoral Schools students 12:00-14:00 Jozef Schell seminar room, Technologiepark 927 - 9052 Zwijnaarde http://www.nucleotides2networks.be/node/232 http://www.nucleotides2networks.be/events Abstract Cancer evolves dynamically as clonal expansions supersede one another, driven by shifting selective pressures, mutational processes, and disrupted cancer genes. These processes mark the genome, such that a cancer's life history is encrypted in the somatic mutations present. We are developing algorithms to decipher this narrative from whole genome sequencing data and are applying them to several cancer types. We call such approaches "molecular archaeology of cancer", as we are using genomics and bioinformatics algorithms to infer a tumour's evolutionary history. I will discuss applications of our methods to breast cancer, allowing us to disentangle subclonal architecture from whole genome sequencing data, as well as time events such as chromosome duplications along a tumour's lifetime. In addition, I will describe how extending these molecular archaeology approaches to multiple sampling studies allow enhanced and unique insights into cancer evolution, and I will illustrate that using genomics studies on prostate cancer metastases, where we are able to elucidate the patterns of metastatic spread in unprecedented detail.

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Registration open: BioSB course on the systems-biology of individualized medicine, 28-30 January 2015, Amsterdam
by Celia.vanGelder＠radboudumc.nl 09 Jan '15

09 Jan '15

BioSB course on the systems-biology of individualized medicine: O2 for Personalized Medicine: from inspiration to aspiration Date: 28-30 January, 2015 Location: Amsterdam Course Organizers: Barbara Bakker (University Medical Centre Groningen (UMCG), Matteo Barberis, Gerard Muyzers and Hans V. Westerhoff (Centre for Integrative Systems Biology Amsterdam CISBA), in collaboration with ISBE@NL Website: http://www.isbe-nl.nl/ On 28-30 January 2015 a course on the systems-biology of individualized medicine will be organized in Amsterdam. Human individuals are all a bit different, yet very much the same. We may all succumb to heart disease, arthritis or cancer, but there is no certainty for any one of us; just probabilities. The probability that a medicine applied to a diseased individual works, is 30%. Einstein contended that probabilities only exist by virtue of ignorance. Systems Biology has the potential to reduce this ignorance. A recent example is provided by the genome-wide human metabolic network, which has been reconstructed by systems biology on the basis of a thorough bioinformatics-aided integration of experimental data. By inserting an individual's genome sequence plus lifestyle data and by calibrating with functional genomics and physiological data, differences between individuals become understood. 'Next generation systems biologists' may soon create an individualized medicine with a 50 % hit rate for each therapy and with actual cures for some of our multifactorial diseases. This course is for PhD students, postdocs and staff from academia and industry, aspiring to becoming these next generation systems biologists. It reviews recent progress and future potential in this endeavor, with some in silico hands-on practicing. Best regards Celia van Gelder Dr. Celia W.G. van Gelder Education Manager NBIC/BioSB Coordinator Education CMBI Programme Manager Learning DTL/ELIXIR-NL 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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Registration open: NBIC/BioSB Course Pattern Recognition (4th edition), 23-27 March 2015, Amsterdam
by Celia.vanGelder＠radboudumc.nl 09 Jan '15

09 Jan '15

NBIC/BioSB Course Pattern Recognition (4th edition) Date: 23-27 March, 2015 Location: Amsterdam Course Coordinator: Perry Moerland (AMC) Website: http://biosb.nl/education/course-portfolio/pattern-recognition/ Registration: http://biosb.nl/education/enrollment-pattern-recognition-course-4th-edition/ On March 23-27, 2015, NIBC/BioSB organises the fourth edition of the PhD Course Pattern Recognition in Amsterdam. The course aims at PhD students with a background in bioinformatics, computer science or a related field. The course introduces basic techniques from the fields of pattern recognition and machine learning to solve bioinformatics problems. After having followed this course, a student should have an overview of basic pattern recognition techniques and be able to recognize what method is most applicable to classification problems (s)he encounters in bioinformatics applications. The course is aimed at PhD students with a background in bioinformatics, computer science or a related field; a working knowledge of basic statistics and linear algebra is assumed. Preparation material on statistics and linear algebra will be distributed before the course, to be studied by students missing the required background. This course is part of the Education Programme of BioSB, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education for in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl. Best regards Celia van Gelder Dr. Celia W.G. van Gelder Education Manager NBIC/BioSB Coordinator Education CMBI Programme Manager Learning DTL/ELIXIR-NL 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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Tenure track position Big Data Science at UGent
by Katrijn Vannerum 07 Jan '15

07 Jan '15

Dear Colleague, At Ghent University we are pleased to open a tenure track position dedicated to research in Big Data Science. This is part of a larger set of vacancies advertised on our website: http://www.ugent.be/en/work/vacancies/professorial-staff/3-assistant-profes… for the Dutch version, see: http://www.ugent.be/nl/vacatures/zap/drie-voltijdse-ambten-van-docent-tenur… We are looking for a promising candidate and hope we may call on you to help us spread the ad below. Please note that the closing date for applications is 31 January 2015. The university application form is available via the following link: https://www.ugent.be/nl/vacatures/zap/sollicitatieformulieren-zap/sollboftt… For further information you can also contact: Lieven.Clement(a)ugent.be<mailto:Lieven.Clement@ugent.be> Peter.Dawyndt(a)ugent.be<mailto:Peter.Dawyndt@UGent.be> Els.Goetghebeur(a)ugent.be<mailto:Els.Goetghebeur@ugent.be> Stijn.Vansteelandt(a)ugent.be<mailto:Stijn.Vansteelandt@ugent.be> Many thanks for your help and our best wishes for 2015, Lieven Clement Job position at the Department of Applied Mathematics, Computer Science and Statistics (WE02). Contact: prof. W. Govaerts, department chair (tel. +32 (0) 9 264 48 93 or e-mail: willy.govaerts(a)ugent.be<mailto:willy.govaerts@ugent.be>). Ghent University, Belgium, invites applications for a full time tenure track position dedicated to research in Big Data Science. This field draws on computer science and statistics to solve through computational, numerical and statistical means methodological problems encountered when aiming to extract in real time reliable and relevant information from massive data sets characterized by the 5 V's: "Volume, Velocity, Variety, Value and Veracity". The position, funded by the Special Research Fund (BOF), is a tenure track position launched within the Faculty of Sciences. We seek an upcoming research leader with outstanding scientific record situated in the broad domain of Scientific Computing and/or Statistics and specific interests in information extraction from Big Data. The ideal candidate has experience analyzing large data sets and developing and making appropriate use of big data technology. He or she will engage in research to develop mathematical, computational and statistical methods to deal with increasingly large numbers of heterogeneous data and to enable reliable extraction and reporting of relevant and reproducible information in real time and in an ethical manner. This should be done with a focus on available or obtainable "big data" for important real-world applications. Our candidate is motivated to build a research group in the domain of Big Data science and will play a major role in the Big Data Science Technology platform linked to the high performance computing infrastructure at Ghent University. The successful candidate will be hosted within the Department of Applied Mathematics, Computer Science and Statistics and is expected to collaborate closely with colleagues from this and other Departments. Specific requirements: * candidates should hold a PhD with a doctoral thesis in quantitative sciences with a strong computing component, preferably in Computer Science, Engineering, Mathematics or Statistics, or a discipline that is declared admissible by the evaluation committee; or a degree recognized as equivalent; * a growing proficiency in Big Data science is expected; * candidates should show a keen interest in the development and application of advanced computational techniques for the design and analysis of large to massive data sets. Katrijn Vannerum PhD Project manager N2N (From Nucleotides to Networks) Multidisciplinary Research Partnership Bioinformatics and Systems Biology Ghent University http://www.nucleotides2networks.be/ twitter: @N2N_UGent Katrijn.Vannerum(a)UGent.be<mailto:Katrijn.Vannerum@UGent.be> Technologiepark 927 9052 Gent, Belgium +32 (0)9 331 36 85 [cid:image001.png@01D02A8D.9289BCC0]

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PhD position Bioinformatics - Plant Regulatory Genomics (Ghent, Belgium)
by Klaas Vandepoele 06 Jan '15

06 Jan '15

Dear colleague, The Comparative & Integrative Genomics lab <http://bioinformatics.psb.ugent.be/cig/> (Ghent University - VIB, Belgium) is currently looking for a *PhD student in Bioinformatics* to work on a research project focusing on Plant Regulatory Genomics. More info here: http://bioinformatics.psb.ugent.be/cig/RegulGenomics_jobdescription2015.pdf Thanks to forward this message to potential candidates in your network. -- Prof. Dr. Klaas Vandepoele Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium --------------------------------------------------------- Lab website: http://bioinformatics.psb.ugent.be/cig/ N2N MRP: http://www.nucleotides2networks.be/ Twitter: http://twitter.com/plaza_genomics ---------------------------------------------------------

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