January 2012 - BBClist - maillist.psb.ugent.be

NBIC PhD course on Managing Life Science Information: registration is open!
by Celia van Gelder 01 May '13

01 May '13

*NBIC PhD Course on Managing Life Science Information (2nd edition) *Course coordinators: Marco Roos, Scott Marshall _Date:_ 17-21 October 2011 (one week of tutorials) and a final workshop on Friday 28 October 2011 to discuss project results _Location:_ Science Park, Amsterdam _Registration:_ http://www.nbic.nl/education/nbic-phd-school/enrolment/ _Website: _http://www.nbic.nl/education/nbic-phd-school/course-schedule/managing-life-science-information/ Did you ever suspect that the data that you need is somewhere but neither discoverable nor accessible? Have you ever produced valuable data that nobody can use anymore, including yourself? Have you ever wondered how to create a federation of distributed data sources? If you do not want your data to end up in a data graveyard, and for many other information management issues, we have organised a course for you. In this course we will teach you methods to make data shareable and self-describing. You will learn how: 1. the 'Linked Data' principle works and how it can be applied for 'meaningful' data integration 2. to expose your local data (including relational databases) for use in other systems. 3. Web Services can be used to analyse data from anywhere. 4. text mining can be applied to link resources such as biobanks. 5. human knowledge can be made computable and associated with data. 6. to make your data publishable artifacts for which you can get scientific credit. 7. to use tools such as MolGenis <http://www.molgenis.org/>, Taverna <http://www.taverna.org.uk/>, SPARQL <http://www.w3.org/TR/sparql11-query/>, D2RQ <http://www4.wiwiss.fu-berlin.de/bizer/d2rq/>, SWObjects <http://tinyurl.com/swobjects-swat4ls>, NCBO's BioPortal <http://bioportal.bioontology.org/>, Anni <http://www.biosemantics.org/index.php?page=anni-2-0>, LarKC <http://larkc.org/>(Large Knowledge Collider). 8. to collaboratively solve an information management problem _Program_ (tentative) Monday: Introduction by leading Semantic Web expert Prof. Dr. Frank van Harmelen; Hands-on with RDF and SPARQL (Scott Marshall) Tuesday: XML, RDF, Minimal information models, and exposing data from local databases (Scott Marshall); hands-on with MolGenis (Erik Roos) Wednesday: Data integration with Web Services (Katy Wolstencroft); hands-on with Taverna (Katherine Wolstencroft) Thursday: Knowledge management and nano-publication (Andrew Gibson); hands-on federated queries with SWObjects (Scott Marshall) Friday: Text mining for linking biobanks and hands-on with Anni (Marco Roos, Kristina Hettne); Hands-on with LarKC (Spyros Kotoulas); DRINKS!!! -- Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: C.vanGelder(a)cmbi.ru.nl websites: www.cmbi.ru.nl, www.nbic.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands

2 2

Bioinformatics Postdoc
by Lodewyk Wessels 02 Dec '12

02 Dec '12

POST DOCTORAL BIOINFORMATICIAN IDENTIFICATION AND VALIDATION OF NEW TARGETS FOR COLORECTAL CANCER OVERALL OBJECTIVES The aim of this project is to redefine colorectal cancer (CRC) at the molecular level, by identifying and validating new activated pathways and specific drug targets for defined CRC patient populations. The project will employ the complementary expertise and tools at Astra Zeneca, two academic laboratories (those of Lodewyk Wessels and Rene Bernards at the Netherlands Cancer Institute, Amsterdam) and a leading diagnostics company with an established presence in oncology (Agendia BV, Amsterdam). PROJECT OUTLINE AND STRATEGY We will first use computational approaches to perform a ‘pathway’ or ‘module’ level integration of molecular profiling (gene expression and next generation sequencing data) and extensive clinical annotation data from a collection of 400 CRC tumours to identify and prioritise pathways that are deregulated in each CRC sub-disease. Next, we will define for each pathway, targets that are amenable to drug discovery efforts, and that can be validated in cell culture models. To enable target validation, we will develop approaches to identify, based on molecular profiling data, CRC cell lines in the AZ collection that represent each molecular sub-disease. Once these are in place, target validation experiments will be conducted, using established RNAi methodology. Targets whose functions are shown to be essential for cell viability in the appropriate cell line models will then be recommended for new drug discovery projects. These results will be fed back to refine the target section procedure based on the tumor data. EMPLOYER INFORMATION The Netherlands Cancer Institute is a dedicated cancer center conducting research in all major areas of cancer, with a strong emphasis on translational research. The Bioinformatics and Statistics group (Wessels lab.) provides leadership on the collection and analysis of data for the research programs of the institute, by developing novel compuational approaches and performing state of the art analyses of a wide array of data types, including laboratory and animal experiments, clinical trials, and epidemiologic studies. REQUIREMENTS The ideal candidate is a highly motivated postdoc with a strong background in bioinformatics or computational biology. The vacancy is a research position within the field of bioinformatics/computational biology and the research will be carried out in close collaboration with the involved partners: Bernards lab, Astra Zeneca and Agendia. The ideal candidate has a background in the analysis of high throughput molecular data, computational diagnostics, bioinformatics, computer science, statistics or physics with strong analytical and algorithmic skills. EMPLOYMENT CONDITIONS The temporary employment will be for a period of three years. The gross monthly salary for a Postdoc will range from €3140,- to €3.495,- and depends on previous experience. We can help you find housing. The NKI-AVL has been listed in the top 25 of ‘Best Employers’ in 2009 offering a specialized cancer research institute and hospital with good working conditions and an excellent atmosphere. INTERESTED? Please contact Dr. Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels(a)nki.nl or Dr George Orphanides, Director of Discovery Medicine, tel. +44 1625 232312 or e-mail George.Orphanides(a)astrazeneca.com. 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. http://bioinformatics.nki.nl CLOSING DATE 1 May 2011

1 2

Integrative Bioinformatics 2011: 2nd call for abstracts
by Jack Leunissen 16 Jul '12

16 Jul '12

Dear colleague, The 2011 International Symposium on Integrative Bioinformatics (IB2011) will take place on March 21-23, 2011 in Wageningen (the Netherlands). This seventh meeting on Integrative Bioinformatics will be of interest to bioinformaticians, computer scientists and all working in, or interested in the developing area of integrative bioinformatics. There will be opportunities to present and discuss methods, theoretical approaches, and their practical applications. We invite you to register for the conference, and to send in an abstract for a presentation at the conference. Accepted abstracts will be invited for a presentation at the conference, and will also be invited to send in a full manuscript, to be published (after peer reviewing) in the IB2011 Special Issue of the Journal of Integrative Bioinformatics. The deadline for sending in an extended abstract is January 15th; submissions should not exceed 4 pages. Authors will be informed of acceptance before February 1st. There are also opportunities for presenting posters and software demonstrations at the Symposium. The deadline for sending in abstracts for posters or a software demo is February 15th, 2011. The best poster will receive an award sponsored by IMBio e.v. The conference website is open for registration and abstract submission, and can be found at www.bioinformatics.nl/ib2011/ and www.imbio.de/ib2011/. We hope to meet you in March in Wageningen. On behalf of the organizing committee, Jack Leunissen Wageningen UR IB2011 is organized by Wageningen University, the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, and IMBio e.V. == Disclaimer: We have tried our best to remove duplicate e-mail addresses from our mailing list to reduce the amount of clutter in your mailbox. It may nevertheless still happen that you receive this mail via different channels. We apologize if you receive this mail more than once.

3 3

BBC11: Key information and updates
by Francisco Azuaje 14 Mar '12

14 Mar '12

Dear colleagues, submission of abstracts is well underway and approaching its deadline: Friday, 28 October. Also I remind you that updates on conference venue and travel are now available at: http://www.bbc11.lu/index.php?page=location We look forward to receiving your abstracts soon. All the best. Francisco Azuaje. (On behalf of the BBC11 Organisation).

2 1

annonce CDD bioinformatician
by Marc Lensink 31 Jan '12

31 Jan '12

----- Forwarded message from Helene Touzet <helene.touzet(a)lifl.fr> ----- --------------------- The University of Lille is seeking a talented software engineer in computational biology to contribute to the development of Lille Bioinformatics Platform. RESPONSIBILITIES: the candidate will work in close collaboration with research teams from the biology department of the University, and will act as a support person to conduct bioinformatics analyses and to implement custom platforms. PROFILE: Relevant backgrounds include formal training or notable experience in a quantitative discipline, such as bioinformatics, computational biology, computer sciences,...: - Proficiency in database management - Programming in JAVA - Scripting languages, such as python and/or perl and/or PHP - Competence in usual bioinformatics tools and bioanalysis (alignment, phylogeny,...) - Strong notions in biology and genetics. TERMS: A French CDD contract 12 months will be offered to the successful candidate. Salary according experience, between 1400 and 1800 euros. This contract is renewable. LOCALISATION: Lille (France) HOW TO APPLY: please submit a statement of interest and a CV to Helene.Touzet(a)lifl.fr ----- End forwarded message ----- -- Marc F. Lensink, CR1, PhD Interdisciplinary Research Institute (IRI) - USR3078 CNRS Computational Biology marc.lensink(a)iri.univ-lille1.fr Parc de la Haute Borne, 50 Avenue de Halley, BP 70478 F-59658 Villeneuve d'Ascq, France tel: +33 3 62 53 17 28 fax: +33 3 62 53 17 01

1 0

Bioinformatics Research Assistant position at Plant Research Internation, Wageningen UR
by Haarst, Jan van 30 Jan '12

30 Jan '12

Dear people, In our group we are looking for a new bioinformatics research assistant. Details and appliaction form is available at: https://www20.i-grasp.com/fe/tpl_wageningen_ur_01.asp?newms=jj&id=43245&new… Please feel free to forward to anyone interested. With kind regards, -- Jan van Haarst Assistant Researcher Bioinformatics Wageningen UR, Plant Research International Applied Bioinformatics P.O Box 167, 6700 AD, Wageningen, the Netherlands Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands ++31-317480756 msn:jan.vanhaarst@wur.nl www.pri.wur.nl<http://www.pri.wur.nl/> www.appliedbioinformatics.wur.nl<http://www.appliedbioinformatics.wur.nl/> www.disclaimer-uk.wur.nl<http://www.disclaimer-uk.wur.nl/>

1 0

Call for Papers - VOC conference at Tilburg University, 25 May 2012
by Katrijn Van Deun 26 Jan '12

26 Jan '12

New Style VOC Conference, May 25 2012 at Tilburg University Call for Papers Scope The Dutch/Flemisch Classification Society, VOC, is an interdisciplinary society that aims at communicating scientific principles, methods, and applications of ordination and classification. The VOC is a member of the International Federation of Classification Societies. The VOC would like to invite you to attend its first new style conference. Contributed papers can be submitted on topics such as classification, clustering, scaling, data analysis, machine learning, pattern recognition, statistical modeling, and applications of classification and data analysis. Fee PhD students are encouraged to actively participate; therefore, the conference fee is kept very low. Keynote Emmanuel Lesaffre, Department of Biostatistics, Erasmus University Rotterdam and Leuven Biostatistics and Statistical Bioinformatics Centre Important Dates / Deadlines March 30: deadline for abstract submission. April 15: notification of acceptance of presentation. May 11: deadline for inscription of non presenters. For more information, visit the conference website: http://www.tilburguniversity.edu/voc-conference On behalf of the organizers: Ralph Rippe, Katrijn Van Deun, Michel van de Velden, Jeroen Vermunt, Tom Wilderjans, Berrie Zielman

1 0

JOB: Academic position in computational biology and statistical genomics
by Stijn Vansteelandt 25 Jan '12

25 Jan '12

Ghent University, Belgium, invites applications for a full time tenure track position dedicated to research in Computational Biology and Statistical Genomics. The position, funded by the Special Research Fund (BOF), is one of five tenure track positions in Bioinformatics launched as part of the Multidisciplinary Research Partnership in Bioinformatics `From Nucleotides to Networks' (N2N: http://www.nucleotides2networks.be/) This interdisciplinary field joins the expertise of scientists with different backgrounds to solve problems in (molecular) biology through computational means. Ghent University has identified it as one of its five areas of excellence. We seek an upcoming research leader with an outstanding scientific record situated in the broad domain of Computational Biology generally and with specific interest in Statistical Genomics. The ideal candidate is motivated to play a major role in the high profile Multidisciplinary Research Partnership in Bioinformatics. Her or she will engage in research related to one or more work packages identified by the partnership (www.nucleotides2networks.be) to 1) build streamlined pipelines to deal with increasingly large numbers of heterogeneous data, 2) integrate these data for further downstream analyses, 3) develop novel tools and approaches for systems biology (inferring and modeling biological networks), and 4) apply these tools and approaches to Sustainable Agriculture and Successful Aging. The successful candidate will be hosted within the Statistics research group at the Department of Applied Mathematics and Computer Science and is expected to collaborate closely with colleagues from the Bioinformatics research groups of Ghent University and the Flemish Institute of Biotechnology. The Statistics research group is internationally recognized, primarily for its research on causal inference and robust statistics. It builds on this expertise to develop targeted applied research for innovation in the private and public sector through the consortium Stat-Gent CRESCENDO (www.statgent.be) The primary focus there is on life sciences, the analysis of electronic health records and genetics data. Bioinformatics groups at Ghent University are world-renowned for their expertise in genomics and proteomics, applied to areas of research that have to do with successful aging and sustainable agriculture. This position will initially be a five-year temporary appointment in a Tenure Track system dedicated to research, with a limited teaching load. The appointment will be made in the starting rank of assistant professor. Upon positive evaluation by the university board, the position will lead to a permanent position starting at the level of associate professor. Profile: the candidate should: - meet the degree requirements (PhD based on a doctoral thesis or equivalent recognized diploma), indicated in Article 83 of the Decree of 12 July 1991 concerning universities within the Flemish Community; the PhD or equivalent should have been obtained after 1 October 2005, but no later than 1 October 2010; - hold a PhD with a doctoral thesis in sciences with a strong quantitative statistical component, by preference in Physical Sciences, including Statistics and Mathematics, Life Sciences, Bioscience engineering, or a degree recognized as equivalent; - have carried out outstanding scientific research in Computational Biology and/or Statistical Genomics, that is proven by research output of a high level in peer-reviewed international publications (journals and/or books). A growing proficiency in statistical genomics is expected; - show a keen interest in the development and application of advanced statistical techniques in genetics; - have strong didactic, communicative and organizational skills; - experience in leading research projects and/or coaching PhD students is an asset; - international academic experience is an asset. The governing language at Ghent University is Dutch. However, research is primarily conducted in English. Persons who do not speak Dutch as a native language are very welcome to apply and are expected to acquire a working knowledge of the language. Method of application Applications must be sent in duplicate by registered mail to the Vice-Chancellor of Ghent University, Vice-Chancellor’s Office, Sint-Pietersnieuwstraat 25, 9000 Ghent, using the necessary application form, together with proof of suitability (e.g., copies of the applicant’s diplomas); After pre-selection, candidates will be asked to submit a research project plan which fits into the research objectives of the Multidisciplinary Research Partnership. A brief description will be made available; The deadline is 1 March 2012. The date of posting is accepted as the date of receipt. Further information concerning these vacancies can be requested by contacting Stijn Vansteelandt (Stijn.Vansteelandt(a)Ugent.be) or Els Goetghebeur (Els.Goetghebeur(a)Ugent.be) The required application form is available on the internet: http://www.ugent.be/nl/werken/aanwerving/formulieren/zap/formulier.doc/view. It can also be requested from Ghent University, F.A.O. Department of Personnel and Organization, Sint-Pietersnieuwstraat 25, 9000 Ghent, or requested via telephone on +32 (0)9 264 95 48 or +32 (9) 264 31 28.

1 0

MLG seminar: Modular protein interaction domains - Evolution, Selectivity and Complexity
by Tom Lenaerts 23 Jan '12

23 Jan '12

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Joined ULB Machine Learning Group (MLG) and VIB/VUB Molecular Recognition unit (MoRe) S E M I N A R %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Apologies for cross-postings. Please send it to interested colleagues and students. Thanks! Title: "Modular protein interaction domains - Evolution, Selectivity and Complexity" by: Dr. Piers D. Nash, The Ben May Department for Cancer Research The University of Chicago Chicago, IL, USA When: 14 February 2012 at 11:00 (until 12:30) Where: Building D Room D.005 (lower level) link to campus map: http://www.vub.ac.be/infoover/campussen/etterbeek.html Vrije Universiteit Brussel, Pleinlaan 2 1050 Bruxelles For those coming by car please email tlenaert_(a)_ulb.ac.be for a barcode to access the VUB campus. Abstract: Modular protein interaction domains (PIDs), such as the SH2 domain, are a common feature of many proteins, particularly those involved in cellular signal transduction. The SH2 domain recognizes phosphotyrosine modified peptide sequences, and in doing so couples tyrosine kinases to downstream signaling networks. We have examined the evolution of SH2 domains and find that they expand rapidly with the emergence of multicellularity and subsequent expansions concomitant with leaps in organismal complexity within the animal lineage. Increasing connectivity within and between SH2 proteins may underlie more highly interconnected and robust signal transduction networks. Yet the rapid evolutionary expansion of SH2 domains comes at some cost to selectivity so that the extant SH2 domains explore only a small region of the available peptide ligand sequence space. The ability of PIDs to nucleate highly selective interactions is essential for signal fidelity yet relies on limited peptid e sequence information. For instance, SH2 domains may appear to have simple binding motifs characterized by a few residues surrounding a phosphotyrosine (eg. pY-X-X-P/L). We have recently shown that by reading both permissive and non-permissive residues and longer regions of adjacent sequence, the SH2 domain is able to make use of a wider information channel to prescribe selective interactions. This results in a complex language for SH2 domain-peptide interactions in which the SH2 domain is readily able to distinguish physicochemically similar amino acids. Thus, despite evolutionary constraints, individual SH2 domains have distinct recognition profiles and exhibit a remarkable degree of selectivity. Speaker:Dr. Piers D. Nash is a world-renowned scientist who investigates protein-protein interactions involved in signal transduction, and the molecular mechanisms by which cells respond to external cues. After completing a postdoctoral position in the lab of Tony Pawson in Toronto, he became Assistant Professor in The Ben May Department for Cancer Research and a Scientist of the Comprehensive Cancer Center at The University of Chicago. His current work focuses on understanding the SH2 domain at a systems level and investigating the role of ubiquitination in controlling endocytosis and modulating signal transduction. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% MLG http://mlg.ulb.ac.be/ MORE http://more.vub.ac.be/ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

1 0

VIB-BGI Genomics Meeting 15 February 2012
by Mark Veugelers 19 Jan '12

19 Jan '12

Dear scientist, Please find attached a Pdf-flyer for the joint VIB-BGI Genomics meeting taking place on 15 February in Leuven. We have an exciting program featuring the top scientists and executive management of BGI, as well as VIB scientists which have worked together with BGI. You can register for the meeting at: www.vib.be/VIB-BGI-Meeting<http://www.vib.be/VIB-BGI-Meeting> Greetings, Mark Veugelers, Ph.D. Integration Manager VIB

1 0