April 2009 - BBClist - maillist.psb.ugent.be

Bioinformatics Postdoc, Amsterdam, NL
by Lodewyk Wessels 05 Aug '09

05 Aug '09

BIOINFORMATICS POSTDOC Topic: Pathway-based tumour characterisation by alignment against cell panels along multiple molecular dimensions. Research: Astra Zeneca Oncology has constructed large cell panels to serve as in vitro models for drug response. These cell panels have been extensively characterized by mutation analysis, mRNA expression, aCGH, response to a wide variety of drugs, micro-RNA expression and phosphoprotein characterization. In parallel, the same measurements are being performed on a collection of colorectal samples. In this project two aims are pursued. First, a comparative analysis will be performed between the cell line data and the tumor data to determine the multi-dimensional molecular states spanned by the cell lines and whether these states faithfully recapitulate the space spanned by a representative and clinically relevant selection of tumor samples. Guided by this mapping and by following a pathway-based approach, integrative modeling will be applied on the cell line panel data to construct models predictive of resistance. Job description: The successful candidate will be responsible for the bioinformatics analysis of the cell line and tissue data. More specifically, these tasks include 1) constructing a comprehensive gene list of the PI3K and ERK network; 2) Molecular characterisation of the colorectal cell panel and tumour samples through integrative analysis of the various data sources within the space spanned by the identified network genes and 3) Pathway-based alignment of cell panel to tumours to determine the extent to which the cell panel recapitulates the heterogeneity in the tissue set. Location: The position is embedded within the Bioinformatics and statistics group lead by Dr Lodewyk Wessels (http://bioinformatics.nki.nl) at the Netherlands Cancer Institute, Amsterdam and the Oncology Informatics group, Discovery Medicine, Astra Zeneca, Alderley Park, UK lead by Dr Tim French. We plan to have regular meetings, and the postdoc will also spend time at both locations. Requirements: Candidates should fulfill the following criteria. - MSc or PhD in one of the following areas: bioinformatics, engineering, computer science, statistics, physics, biotechnology, or biology. - Knowledge of fundamental aspects of cancer biology, especially signalling pathways. - Knowledge of fundamental aspects of computer science (algorithms and data structures, programming languages). - Knowledge or experience of informatics. - Knowledge of statistics, artificial intelligence or bioinformatics is highly desirable. Conditions of Employment: The successful candidate will be employed by the Netherlands Cancer Institute. The employment conditions follow general employment rules as laid down in the 'CAO' for hospitals. The salary will be determined depending on education and experience. Contact and Applications: Dr. Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels(a)nki.nl or Dr Tim French Discovery Medicine, Cancer Bioscience, tel. +44 1625-519922 or e-mail: Tim.French(a)AstraZeneca.com. Applicants should send a CV, list of publications and the names and addresses of at least two persons that can be approached to obtain further information. Website: http://bioinformatics.nki.nl Closing date: 30 January 2009 L.F.A.Wessels, Ph.D Bioinformatics and Statistics The Netherlands Cancer Institute Plesmanlaan 121, 1066 CX Amsterdam The Netherlands Tel: +31 (0)20 5127987 Fax: +31 (0)20 6691383 Mobile: +31 (0)634485714 http://bioinformatics.nki.nl/ L.F.A.Wessels, Ph.D Bioinformatics and Statistics The Netherlands Cancer Institute Plesmanlaan 121, 1066 CX Amsterdam The Netherlands Tel: +31 (0)20 5127987 Fax: +31 (0)20 6691383 Mobile: +31 (0)634485714 http://bioinformatics.nki.nl/

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International Computational Drug Discovery Course 2009
by Celia van Gelder 25 Apr '09

25 Apr '09

*International Computational Drug Discovery Course 2009 * June 29 – July 10, 2009 Nijmegen, the Netherlands From June 29 - July 10 2009, the Computational Drug Discovery (CDD) Group from the Centre of Molecular and Biomolecular Informatics (CMBI) will present the seventh annual Computational Drug Discovery Course. This course was developed by the CDD group together with the pharmaceutical company Schering-Plough (former Organon) and is supported by NBIC. The two-week course discusses recent advances in drug discovery informatics, with a focus on the application of e-science to real life problems. The course is targeted at MSc students, PhD students, and postdocs, who are interested in the field of computational target and drug discovery. For more information see the course website (http://www.cmbi.ru.nl/ICDD2009) -- 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

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Call for papers: Machine Learning in Systems Biology, Slovenia, 5-6 September
by Pierre Geurts 24 Apr '09

24 Apr '09

[apologies for multiple postings] ************************** Call for Papers ********************************* MLSB 09 Third International Workshop on Machine Learning in Systems Biology 5-6 September 2009, Ljubljana, Slovenia ****************************************************************************** http://mlsb09.ijs.si/ MOTIVATION Molecular biology and all the biomedical sciences are undergoing a true revolution as a result of the emergence and growing impact of a series of new disciplines/tools sharing the "-omics" suffix in their name. These include in particular genomics, transcriptomics, proteomics and metabolomics, devoted respectively to the examination of the entire systems of genes, transcripts, proteins and metabolites present in a given cell or tissue type. The availability of these new, highly effective tools for biological exploration is dramatically changing the way one performs research in at least two respects. First, the amount of available experimental data is not a limiting factor any more; on the contrary, there is a plethora of it. Given the research question, the challenge has shifted towards identifying the relevant pieces of information and making sense out of it (a "data mining" issue). Second, rather than focus on components in isolation, we can now try to understand how biological systems behave as a result of the integration and interaction between the individual components that one can now monitor simultaneously (so called "systems biology"). Taking advantage of this wealth of "genomic" information has become a conditio sine qua non for whoever ambitions to remain competitive in molecular biology and in the biomedical sciences in general. Machine learning naturally appears as one of the main drivers of progress in this context, where most of the targets of interest deal with complex structured objects: sequences, 2D and 3D structures or interaction networks. At the same time bioinformatics and systems biology have already induced significant new developments of general interest in machine learning, for example in the context of learning with structured data, graph inference, semi-supervised learning, system identification, and novel combinations of optimization and learning algorithms. OBJECTIVE The aim of this workshop is to contribute to the cross-fertilization between the research in machine learning methods and their applications to systems biology (i.e., complex biological and medical questions) by bringing together method developers and experimentalists. We encourage submissions bringing forward methods for discovering complex structures (e.g. interaction networks, molecule structures) and methods supporting genome-wide data analysis. LOCATION AND CO-LOCATION The workshop will take place 5-6 September 2009 at the Jozef Stefan Institute, Ljubljana, Slovenia. It will immediately precede ECML PKDD 2009, taking place 7-11 September 2009 in Bled, Slovenia (Bled is 30 miles from Ljubljana, transport will be organized). SUBMISSIONS INSTRUCTIONS For an oral presentation, please submit an extended abstract of maximum eight pages. Formatting instructions are available on the website of the workshop. Extended abstracts should be submitted online by 1 June 2009 via the Easychair submission system at http://www.easychair.org/conferences/?conf=mlsb09. The accepted submissions will be collected in the proceedings of the workshop. KEY DATES 01 June: deadline for submission of extended abstracts for oral presentation 03 July: notification for oral presentations 03 August: deadline for submission of abstracts for poster presentations 10 August: notification for posters & camera ready versions due 5-6 September: workshop TOPICS A non-exhaustive list of topics suitable for this workshop is given below: Methods Machine learning algorithms Bayesian methods Data integration/fusion Feature/subspace selection Clustering Biclustering/association rules Kernel methods Probabilistic inference Structured output prediction Systems identification Graph inference, completion, smoothing Semi-supervised learning Applications Sequence annotation Gene expression and post-transcriptional regulation Inference of gene regulation networks Gene prediction and whole genome association studies Metabolic pathway modeling Signaling networks Systems biology approaches to biomarker identification Rational drug design methods Metabolic reconstruction Protein function and structure prediction Protein-protein interaction networks Synthetic biology CONFIRMED INVITED SPEAKERS Ross D. King, Aberystwyth University, UK William Stafford Noble, University of Washington, USA MLSB09 PROGRAM CHAIRS Sašo Džeroski, Jozef Stefan Institute, Ljubljana, Slovenia Pierre Geurts, Department of EE and CS & GIGA-Research, University of Liège, Belgium Juho Rousu, Department of Computer Science, University of Helsinki, Finland SCIENTIFIC PROGRAM COMMITTEE Florence d'Alché-Buc, University of Evry, France Saso Dzeroski, Jozef Stefan Institute, Slovenia Paolo Frasconi, Università degli Studi di Firenze, Italy Cesare Furlanello, Fondazione Bruno Kessler, Trento, Italy Pierre Geurts, University of Liège, Belgium Mark Girolami, University of Glasgow, UK Dirk Husmeier, Biomathematics & Statistics Scotland, UK Samuel Kaski, Helsinki University of Technology, Finland Ross D. King, Aberystwyth University, UK Neil Lawrence, University of Manchester, UK Elena Marchiori, Vrije Universiteit Amsterdam, The Netherlands Yves Moreau, Katholieke Universiteit Leuven, Belgium William Stafford Noble, University of Washington, USA Gunnar Rätsch, FML, Max Planck Society, Tübingen Juho Rousu, University of Helsinki, Finland Céline Rouveirol, University of Paris XIII, France Yvan Saeys, University of Gent, Belgium Guido Sanguinetti, University of Sheffield, UK Ljupco Todorovski, University of Ljubljana, Slovenia Koji Tsuda, Max Planck Institute, Tuebingen Jean-Philippe Vert, Ecole des Mines, France Louis Wehenkel, University of Liège, Belgium Jean-Daniel Zucker, University of Paris XIII, France Blaz Zupan, University of Ljubljana, Slovenia LOCAL ORGANIZATION Ivica Slavkov, Dragi Kocev, Tina Anžič, Jozef Stefan Institute, Ljubljana, Slovenia

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Call for participation: Workshop on Feature Selection in Bioinformatics
by Pierre Geurts 22 Apr '09

22 Apr '09

[apologies for multiple postings] ************** Call for Participation ******************** FSBIO 09 Feature Selection in Bioinformatics Workshop May 25th, 2009 Ghent, Belgium http://www.psb.ugent.be/~yvsae/fsbio09/ ********************************************************* MOTIVATION Feature or variable selection is an important topic in Bioinformatics, Systems Biology, and related fields. Important advantages of feature selection in these fields include the ability to create better and more compact models, as well as gaining a better insight into the processes described by the data. This workshop focuses on recent challenges for feature selection in Bioinformatics, such as the design of feature selection algorithms that scale well to high-dimensional spaces, can deal with small sample sizes, design robust feature sets and are able to support interactions or dependencies between variables. PROGRAM 09.50h Welcome 10.00h Badih Ghattas, Institut de Mathématiques de Luminy, Marseille, France Comparing different strategies for variable selection in large dimensions 11.00h Carolin Strobl, Institut für Statistik, Ludwig-Maximilians- Universität München, Germany Unbiased measures of variable importance for random forests 12.00h Alexandros Kalousis, Department of Computer Science, University of Geneva, Switzerland Stability of Feature Selection Algorithms LOCATION Department of Plant Systems Biology Ghent University Technologiepark 927 B-9052 Gent (Zwijnaarde) Belgium REGISTRATION Registration to the workshop is free of charge. In order to register, send a mail with your name and contact details to yvan.saeys(a)psb.ugent.be ORGANIZATION Yvan Saeys, Bioinformatics and Evolutionary Genomics group, Ghent University, Belgium Pierre Geurts, Department of EE and CS & GIGA-Research, University of Liège, Belgium

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NBIC PhD-Course: Managing life science information
by Celia van Gelder 17 Apr '09

17 Apr '09

*NBIC PhD-Course: Managing life science information* Date: 25-29 May 2009 Location: Science Park, Amsterdam, the Netherlands Course Coordinator: Marco Roos, UvA. This course introduces modern techniques for the management of life science data and knowledge for bioinformatics applications. Students will gain insight into Semantic Web languages and tools, XML and XQuery, data integration, data warehouses, federated databases, (Taverna) workflows, and Web2.0. More information about the course can be found on the NBIC-website: http://www.nbic.nl/biowise/school/EduProg/InfoMan09/ . Please note: the course is free for PhD students working in a BioRange project. Others can participate as well when paying a course fee (see course information on website). This course is part of the Education Programme of the NBIC PhD School. The PhD School is an initiative of NBIC together with a number of universities to organize high level education and training for PhD-students in bioinformatics. More information about the latest developments of the NBIC PhD School can also be found on the NBIC website: http://www.nbic.nl/biowise/school/ . Best regards, Celia van Gelder Projectleader Education NBIC ------------ 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, celia.van.gelder(a)nbic.nl websites: www.cmbi.ru.nl, www.nbic.nl NBIC Office Phone: +31 (0)24 36 19500 E-mail: office(a)nbic.nl Netherlands Bioinformatics Centre 260 NBIC P.O. Box 9101 6500 HB Nijmegen Fax: +31 (0)24 36 19395

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Business Personality of the Year 2009 !
by benjdami＠bioxpr.be 09 Apr '09

09 Apr '09

Good day, Here is an unusual request on this mailing-list. My name in Benjamin Damien, manager of BioXpr (bioinformatics service company in Belgium) and one of the 10 finalists of the "business personality of the year" contest. This final step is the results of several rounds of selection and trials. For the last trial, I need to gather as much votes as possible on the website : http://www.bpy2009.be This kind of prize is usually given to more "casual" businesses (marketing, sales, fashion,...) and it would be great to see biotech (and bioinformatics) win that kind of contest for once. Moreover, the "winner" will be able to communicate in the media regularly in the next 12 months (tv and newspapers), and I plan to use this platform to promote entrepreneurship and the scientific/technical careers (biotech first of all, of course). So I need your help to win this trial (I'm in second position, and the votes are closing on sunday 12/04), and to vote on http://www.bpy2009.be Thanks for your help in advance, and best regards, Benjamin

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[Biomath-ned] Positions in biological modeling and simulation
by Roeland Merks 08 Apr '09

08 Apr '09

Positions in biological modeling and simulation in Amsterdam, The Netherlands Within the Netherlands Consortium for Systems Biology (NCSB), biologists, computer scientists, physicists and mathematicians of Dutch universities and research institutes have joint forces to develop innovative systems biology approaches for tackling challenging, multi-factorial biological problems related to human health, plant sciences, and white biotechnology. Computer modeling and simulation are central to this highly multidisciplinary effort. NCSB’s core modeling group Biomodeling and Biosystems Analysis at CWI, the Dutch national research institute for mathematics and computer science, develops innovative simulation approaches and coordinates modeling projects at the participating institutes. The Biomodeling and Biosystems Analysis group invites applications for the following positions: Postdoctoral researcher Modeling dynamics and evolution of hierarchically regulated, eukaryotic gene networks See: http://www.cwi.nl/en/node/1044 PhD student Cell-based modeling of blood vessel formation See http://www.cwi.nl/en/node/1045 Scientific programmer / PhD student Bringing modeling and simulation to the biologist’s lab bench See http://www.cwi.nl/en/node/1043 Requirements for all positions: - A scientific background in simulation and modeling: a degree in theoretical biology or computational physics, computational science, or equivalent experience - Able to communicate with scientists in biology and mathematics - Good programming skills in C++ or equivalent - Minimum academic degree: for postdoc, PhD; for PhD, M.Sc.; for programmer, B.Sc. Information For full description of these positions, see http://www.cwi.nl/en/ jobs. For more information about CWI, NISB, NCSB and the Biomodeling and Biosystems Analysis group, visit http://www.cwi.nl, http://www.sysbio.nl , and http://www.cwi.nl/~merks. Contact: Roeland Merks, CWI, Roeland.Merks(a)sysbio.nl, Tel. +31-20-5624117 Application deadline is May 1st, 2009. ----- Roeland M. H. Merks Netherlands Institute for Systems Biology (NISB) and Centrum Wiskunde & Informatica (CWI) Science Park 123, 1098 XG Amsterdam, The Netherlands Mailing address: P.O. Box 94079, 1090 GB Amsterdam CWI Office Room M136 Roeland.Merks(a)sysbio.nl / Roeland.Merks(a)cwi.nl http://www.cwi.nl/~merks Phone +31 20 592 4117 Fax +31 20 592 4199 _______________________________________________ Biomath-ned mailing list Biomath-ned(a)few.vu.nl http://mailman.few.vu.nl/mailman/listinfo/biomath-ned

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