- BBClist - maillist.psb.ugent.be

BeneLearn and PMLS 2012: Call for Abstracts and Full Papers
by Willem Waegeman 05 Feb '12

05 Feb '12

(Apologies for multiple postings) BENELEARN 2012 -- PMLS 2012 The 21st annual Machine Learning Conference of Belgium and The Netherlands Workshop Predictive Modeling for the Life Sciences www.benelearn2012.ugent.be <http://www.benelearn2012.ugent.be> May 24th and 25th, 2012 Ghent University, Belgium Call for Abstracts and Full Papers BeneLearn is the annual machine learning conference of Belgium and The Netherlands. It serves as a forum for researchers to exchange ideas, present recent work, and foster collaboration in the broad field of Machine Learning and its applications. The 21st edition of the annual Belgian-Dutch Conference on Machine Learning (BeneLearn) will be organized in Ghent, in conjunction with a workshop on Predictive Modeling in Life Sciences (PMLS). This year we have chosen for a two-day program to showcase the use of predictive modeling in the life sciences. This is in part motivated by the increasing focus on applicability of scientific research. The joint event takes place on the 24th and 25th of May 2012 at the Faculty of Bioscience Engineering of Ghent University. It is organized by the research unit Knowledge-based Systems (KERMIT). Scope We invite the submission of abstracts or full papers on all aspects of machine learning and related disciplines, including, but not limited to Kernel Methods Bayesian Learning Case-based Learning Ensemble Methods Computational Learning Theory Data Mining Evolutionary Computation Hybrid Learning Systems Graphical Models Inductive Logic Programming Knowledge Discovery in Databases Online Learning Web/Link Mining Learning in Multi-Agent Systems Learning in Dynamic Domains / Data Streams Multi-Strategy Learning Neural Networks Reinforcement Learning Robot Learning Feature Selection and Dimensionality Reduction Scientific Discovery Multi-task and Transfer Learning Statistical Learning Ranking / Preference Learning / Information Retrieval Computational models of Human Learning Structured Output Prediction / Learning from Multi-Label Data Learning for Language and Speech Image, Video, Audio and Text Analysis Applications of Machine Learning Learning and Ubiquitous Computing In addition to theoretical and applied work in machine learning in general, we warmly welcome applications for the PMLS workshop, in areas such as: Bioinformatics Medicine / Biomedical Engineering Systems Biology / Microbiology Chemometrics / Computational Drug Discovery Ecology / Environmental Sciences Agriculture and Soil Management Food Sciences Geographical Information Systems Weather and Climate Forecasting Submission One can submit full papers up to 6 pages or one-page abstracts. Full papers need to report original, unpublished work and they are meant for researchers that prefer to obtain an official publication via BeneLearn, including feedback from the program committee. Abstracts can also concern work in progress and past published work, if the precise references to the original publication are mentioned. This way we aim to provide the same broad overview as in previous years, and make it attractive and easy to attend by both senior as well as junior researchers, from both academia and industry. To attract as many people as possible, registration fees will be low and three international speakers are invited for a keynote talk. We consider a single submission procedure for the main conference and its satellite workshop. The program committee will make a selection for oral presentations among abstracts and full papers to ensure a program that has academic quality but is also interesting and inspiring for the attendees. The remainder of the submissions will be presented during a poster session and poster spotlight presentations. Abstracts and papers should be submitted electronically, no later than Friday March 2nd, 2012. Notification of acceptance is on Friday April 6th. Please follow the guidelines that are mentioned on our website: http://www.benelearn2012.ugent.be/submission.php During submission authors will be able to indicate their preference for an oral or a poster presentation. Submissions that concern an application in the life sciences will be considered for PMLS, all other submissions will be considered for the main conference day. Organizing Committee Bernard De Baets, Michaël Rademaker, Willem Waegeman (UGent) Bernard Manderick (VUB)

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NGS course
by Martie Verschuren 03 Feb '12

03 Feb '12

Dear reader, We organise an international shortcourse on next generation sequencing in Breda in March. Please visit the course website for detailed information: http://www.alsavans.nl/avans-training-2542.htm Looking forward to meeting you in BReda Best regards Martie C.M. Verschuren Avans university of applied science p.o. box 90116 4800 RA Breda The Netherlands --------------------------------------------------------------------------- Op deze e-mail zijn de volgende voorwaarden van toepassing: The following conditions apply to this e-mail: http://emaildisclaimer.avans.nl ---------------------------------------------------------------------------

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NSBM Spring Meeting April 25th CALL FOR ABSTRACTS
by Barbara van Kampen 02 Feb '12

02 Feb '12

NETHERLANDS SOCIETY ON BIOMOLECULAR MODELLING Spring Meeting April 25th 2012 in conjunction with the Netherlands Bioinformatics Conference 2012 Venue: Congrescentrum De Werelt, Lunteren CALL FOR ABSTRACTS The NSBM cordially invites you to visit its spring meeting, which is being held in conjunction with the Netherlands Bioinformatics Conference 2012. During the parallel session, the floor will be given to PhD students and post-docs who study protein structure and/or structural bioinformatics or related topics (see a list below). Speakers and attendees will have the opportunity to join the NBIC 2012 activities and visit key note lectures by Gerard Kleywegt of the European Bioinformatics Institute, Cambridge and by Dorus Gadella, of the Centre for Advanced Microscopy (CAM) at the University of Amsterdam. Abstract Format Abstracts should be limited to a maximum of 10 lines, with 12-pt font and single-spaced text, giving a short description of the research done. Please include a title in bold. The name(s) and affiliation(s) of the author(s) should follow the title. The opportunity will be given to present a poster, though this is not mandatory. If you wish to present a poster, please indicate so. Abstract Submission All abstracts, also for those who already registered for the NBIC meeting, should be submitted electronically in MSWord via e-mail attachment to g.nicolaes(a)maastrichtuniversity.nl The deadline for receipt of all abstracts is April 15th 2012. Selected candidates will be notified no later than April 18th 2012. Presentations will be 20 min, including a 5 min discussion. Starting PhD students are particularly encouraged to present their research. For questions regarding the abstract or meeting please contact Gerry Nicolaes, +31-(0)43 3881688, g.nicolaes(a)maastrichtuniversity.nl Registration Registration can be performed through the NBIC site at: http://www.nbic.nl/about-nbic/nbic-conferences/nbic-conference-2012/registr… The 1-day conference fee amounts €62,50 for NBIC members and € 75,- for non-NBIC members and includes participation to the conference and poster sessions on April 25th, lunch, coffee/tea during breaks, internet access. Should a lack of funding be a hurdle for visiting the NSBM Spring Meeting, please contact prof. Gert Vriend at vriend(a)cmbi.ru.nl so that an arrangement can be made. Topics for presentations may include, but are not limited to: • Computational Biology and Bioinformatics • Computer-aided drug design • Drug design and drug discovery • Grid computing • Homology modelling • Molecular and supramolecular dynamics • Molecular modeling and simulation • Mutational analysis • Protein crystallography • Protein NMR • Protein structure analysis • Protein structure prediction • Protein-protein interactions • Protein-small molecules interaction • Protein software design • Proteomics • Structural bioinformatics • Structure-function analysis • Text mining & information extraction • Virtual screening Links http://www.nbic.nl/about-nbic/nbic-conferences/nbic-conference-2012/program… -- Barbara van Kampen CMBI 260 Radboud University Nijmegen-Medical Centre / NCMLS CMBI Office / Room 0.02 PO Box 9101 Geert-Grooteplein 26-28 6500 HB Nijmegen 6525 GA Nijmegen Phone: +31(0)24 36 19390 Fax: +31 (0)24 36 19395 www.cmbi.ru.nl

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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

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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/>

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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

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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.

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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/ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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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

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Bioinformatics position at Keygene, Wageningen
by Antoine Janssen 18 Jan '12

18 Jan '12

Dear collegues, Please find attached an ad for a bioinformatics position at Keygene. I would very much appreciate if you could forward it to your contacts. Thanks a lot for your help! Antoine Janssen Team Leader Bioinformatics [cid:imageb6d6f3.jpg@2a262fe6.cad54c8d] Keygene N.V. P.O. Box 216 6700 AE Wageningen The Netherlands Tel. (+31) 317 46 68 66 Fax. (+31) 317 42 49 39 Web: http://www.keygene.com<http://www.keygene.com/> The information contained in this message, and attachments if any, may be privileged and/or confidential and is intended to be received only by persons entitled to receive such information. Use of any part of this message and/or its attachments if any, in any other way than as explicitly stated by the sender is strictly prohibited. Should you receive this message unintentionally please notify the sender immediately, and delete it together with all attachments, if any. Thank you. The transmission of messages and/or information via the Internet is not secured and may be intercepted by third parties. KeyGene assumes no liability for any damage caused by any unintentional disclosure and/or use of the content of this message and attachments if any.

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