June 2008 - BBClist - maillist.psb.ugent.be

Postdoc position bioinformatics for toxicometabolomics NTC
by Jack Leunissen 30 Jun '08

30 Jun '08

Dear colleagues, Please bring the following vacancy to the attention of anyone interested (and suitable ;). Thanks, Jack -- Prof dr JAM Leunissen Lab of Bioinformatics Wageningen University -- *SCIENTIST BIOINFORMATICS FOR TOXICOMETABOLOMICS F/M* At RIKILT - Institute of Food Safety, research cluster Toxicology & Effect Monitoring. job opening number: RIK.801.2008-01 *Job description* You will be working at RIKILT in the field of bioinformatics for metabolomics within the Netherlands Toxicogenomics Centre (_www.toxicogenomics.nl <http://www.toxicogenomics.nl/>_). The most important tasks will be the establishment of a pipeline and database for the available metabolomics data from LC-MS, GC(GC)MS and NMR. You will implement preprocessing strategies (p.e. _www.metalign.nl <http://www.metalign.nl/>_) , quality control, data mining and statistics. You will interact with NTC participants in metabolome data analysis of toxicological experiments. You will also make interactions possible with text-mining and pathway programs. A tight collaboration will be set up with the chair of Bioinformatics at WUR (Prof. dr. Jack Leunissen) (_www.bioinformatics.nl <http://www.bioinformatics.nl/>_) as well as the other bioinformatics participants within NTC. Within the Cluster Toxicology & Effect monitoring at RIKILT you will be co-responsible for the acquisition, implementation and management of food safety projects in this field. *What we ask* A Ph.D. with solid experience in the area of informatics or bioinformatics, programming and databasing, preferably with experience in analytical chemistry and biochemistry. You are a real team player, innovator and stimulator. You are driven, result-oriented and you have excellent communication and writing skills. *What we offer* A stimulating position in pleasant and high-level work surroundings. We offer a fulltime position for three years with possibilities for a two-year extension. Salary ranging is from 2812–4371 Euro per month depending upon experience. *Information* For further information on this position please contact Dr. Arjen Lommen (arjen.lommen(a)wur.nl) tel.: +31-317-480264 and/or Dr. Ad Peijnenburg (ad.peijnenburg(a)wur.nl) tel.: +31-317-480284. For Further information: _http://www.rikilt.wur.nl/UK/_ *Application* Please submit your application letter with CV before the 2^nd of July 2008 by e-mail to: _vacatures.rikilt(a)wur.nl <mailto:vacatures.rikilt@wur.nl>_.

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PhD defense Morgane Thomas-Chollier
by Morgane THOMAS-CHOLLIER 23 Jun '08

23 Jun '08

PhD Public defense - Morgane Thomas-Chollier Title: "Evolutionary study of the Hox gene family with matrix-based bioinformatics approaches" joint PhD supervision between the Vrije Universiteit Brussel (Prof. L. Leyns - Laboratory of Cell Genetics) and the Université Libre de Bruxelles (Prof J. van Helden - Service de Bioinformatique des Génomes et des réseaux (BiGRe)) June 27, 2008, at 16:00 Vrije Universiteit Brussel - Campus Etterbeek Pleinlaan 2, 1050 Brussels Building D, room D2.01 « promotiezaal » Access : http://www.vub.ac.be/image/3brussel_large.jpg Hox genes belong to the family of homeobox transcription factors characterised by a 60 amino acids region called homeodomain. These genes are evolutionary conserved and play crucial roles in the development of animals. In vertebrates, this family of genes can be divided into 14 groups of homology. The first goal of this thesis was to design an automated approach to assign the growing number of Hox sequences into their groups of homology. The resulting program, HoxPred, classifies Hox sequences on the basis of their scores for a combination of protein generalised proﬁles. This program was applied to clarify the evolutionary history of the HoxC1a genes in teleost fish. As transcription factors, Hox proteins regulate target genes by specifically binding DNA on cis-regulatory elements. Only a few of these target genes have been identified so far. The second goal of this work was to evaluate whether it is possible to apply computational approaches to detect Hox cis-regulatory elements in genomic sequences. For this, we participated to the development of matrix-based pattern matching approaches in the Regulatory Sequence Analysis Tools. After having performed a statistical validation of the pattern-matching scores, we focused on a study case based on the vertebrate HoxB1 protein, which binds DNA with its cofactors Pbx and Meis. The study aimed at predicting combinations of cis-regulatory elements for these three transcription factors. Contact person : morgane(a)bigre.ulb.ac.be

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Workshop in Louvain-la-Neuve, Belgium. "When modelers meet biologists: why modeling should become instrumental in plant biology."
by Roeland Merks 13 Jun '08

13 Jun '08

[Apologies for cross posting] Workshop: When modelers meet biologists: a series of case studies illustrating why modeling should become instrumental in plant biology. Not a "How to?" but a "What for?" The Belgian Plant Science Doctoral School organizes a workshop on plant modeling, September 8 and 9, 2008, in Louvain-la-Neuve, Belgium, http://www.eddsaib.org/plant_science. This workshop is a partner event to the summer school "Computational and Mathematical Modeling for Plant Systems Biology", September 1-5, VIB Department of Plant Systems Biology and Ghent University, Ghent, Belgium. See http://www.psb.ugent.be/plantmodels. The Ghent summer school will give both a scientific and practical introduction to modelling in plant sciences, going from the molecular level up to the level of the whole plant. The follow-up workshop in Louvain-la-Neuve shows participants what modelling has to offer to the plant sciences, without giving a practical introduction. It focuses on whole plant models and physiological and tissue-level models. The programs of both events are included below. ------ When modelers meet biologists: a series of case studies illustrating why modeling should become instrumental in plant biology. Not a "How to?" but a "What for?". Organizers: Xavier Draye, Université Catholique de Louvain, Louvain-la-Neuve, Belgium Claire Périlleux, Université de Liège, Liège, Belgium Roeland Merks, VIB Plant Systems Biology and Ghent University, Ghent, Belgium September 8-9, 2008, Université catholique de Louvain, Louvain-la-Neuve, Belgium. Organized by the "Plant Science" Doctoral School of the belgian scientific community (FRS-FNRS). This workshop is organized for PhD students or researchers looking for an introduction to what computational modeling is offering to plant science. It is not a practical initiation to modeling. Session 1 : Models of plant structure and growth dynamics Loïc Pagès, INRA Avignon, 3D-models of plant structure Jean-François Ledent, University of Louvain, Modelling growth and the genesis of plant 3D geometry of maize. Session 2 : Models that bring structure and function : from cells to crops Roeland Merks, University of Ghent, Cell-based, biomechanical tissue modeling in plant research Gerhard Buck-Sorlin, Wageningen UR, Virtual Rose - A Functional-Structural Plant Model to predict crop quality and quantity of cut roses Session 3 : Eco-physiological models Kathy Steppe, University of Ghent, The added value of plant modelling for ecophysiological research Gaby Deckmyn, University of Antwerp, Complex physiological models as tools for forestry: why choose the hard way?" Session 4 : Modeling plant-environment interactions Mathieu Javaux, University of Louvain, Forward and inverse 3-D root water uptake modelling based on a deterministic water flux model in soil and roots Achim Walter, Juelich Research Centrum, Leaf and root growth dynamics: How can plant organs reach their full growth potential in a dynamically fluctuating environment? For more information and registration, please visit : http://www.eddsaib.org/plant_science ------ Summer school: Computational and Mathematical Modeling for Plant Systems Biology September 1-5, 2008, VIB Department of Plant Systems Biology and Ghent University, Ghent, Belgium http://www.psb.ugent.be/plantmodels Plant science is evolving from a reductionistic view on gene function to an integrated systems biology approach, in which gene functions are studied in the context of the dynamic behavior of physiological, cellular, or developmental processes. Mathematical and computational modeling play a central role in this multiscale systems biology approach. This summer school will bring together a wide range of computational systems biologists, working on problems at different organizational levels, relevant to plant biologists. The course will start with phenomena occurring at the subcellular and cellular scale, including photosynthesis, cell cycle regulation and the organization of the cytoskeleton. Then it will gradually "scale up" to the tissue, organ, and whole plant levels. It will conclude with pattern formation in tissues, the mechanics of growth, and whole plant development and evolution. Organizers: Roeland Merks Gerrit Beemster Dirk Inzé VIB Plant Systems Biology and Ghent University, Ghent, Belgium Xavier Draye Université Catholique de Louvain, Louvain-la-Neuve, Belgium Roeland Merks (roeland.merks(a)psb.ugent.be) Gerrit Beemster Dirk Inzé VIB Plant Systems Biology and Ghent University, Ghent, Belgium Xavier Draye Université Catholique de Louvain-la-Neuve, Louvain-la-Neuve, Belgium Monday, 1st September 2008 Genetic and metabolic networks 10:00-11:00 Xin-Guang Zhu (Urbana, IL, USA). Dynamic models of photosynthetic metabolism 11:15-12:15 Joe Pomerening (Bloomington, IN, USA). Coupled positive and negative feedback loops drive transitions in embryonic and somatic cell cycles Tuesday, 2nd September 2008 Single cell shape and mechanics 10:00-11:00 François Nédélec (Heidelberg, Germany). Models of microtubule organization in fission yeast 11:15-12:15 Bela Mulder (Amsterdam/Wageningen, Netherlands). Modelling cellulose biosynthesis and plant cell wall architecture Wednesday, 3rd September 2008 Multicellular pattern formation 9:00-10:00 Hans Meinhardt (Tübingen, Germany). Models of biological pattern formation applied to plant development 10:15-11:15 Verônica Grieneisen (Utrecht, Netherlands). Auxin fluxes in the developing root. 11:30-12:30 Richard Smith (Bern, Switzerland). Simulation models of auxin transport-based patterning in plants. Thursday, 4th September 2008 Plant growth mechanics 10:00-11:00 Alain Goriely (University of Arizona, Tucson, AZ, USA). Continuum models of plant growth and remodeling 11:15-12:15 Roeland Merks (VIB Department of Plant Systems Biology, Ghent, Belgium). Cell-centered modeling of plant tissues Friday, 5th September 2008 Whole plant development and evolution. 10:00-11:00 Xavier Draye (Louvain-la-Neuve, Belgium). Model integration: building multidisciplinary, soil, plant and atmosphere models 11:15:12:00 Przemyslaw Prusinkiewicz (Calgary, Canada). Whole plant modeling and evo-devo of plants -- ================================================================== Roeland Merks Group Leader "Plant Systems Modeling" Tel:32 (0)9 3313823 Fax:32 (0)9 3313809 VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY, UGent Technologiepark 927, 9052 Gent, BELGIUM roeland.merks(a)psb.ugent.be http://www.psb.ugent.be ==================================================================

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Final CFP Machine Learning in Systems Biology (deadline extended)
by Pierre Geurts 13 Jun '08

13 Jun '08

[apologies for multiple postings] Deadline for submission has been extended to ** JUNE 22 ** ********************** Last Call for Papers **************************** 2nd International Workshop on Machine Learning in Systems Biology 13-14 September 2008, Brussels, Belgium ************************************************************************ http://www.montefiore.ulg.ac.be/services/stochastic/mlsb08 MOTIVATION Molecular biology and also 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 theirname. 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 of all, the amount of available experimental data is not at all a limiting factor any more; on the contrary, there is a plethora of it. The challenge has shifted towards identifying the relevant pieces of information given the question, and how to make sense out of it (a "data mining" issue). Secondly, rather than to focus on components in isolation, we can now try to understand how biological systems behave as the 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 more generally in biomedical sciences. 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 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. A non-exhaustive list of topics suitable for this workshop: 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 Structure Prediction Protein Function Prediction Protein-protein interaction networks SUBMISSIONS OF EXTENDED ABSTRACTS We invite to submit an extended abstract of maximum 8 pages. Each extended abstract must be submitted by *June 22 2008* (extended) electronically via the Easychair submission system: http://www.easychair.org/conferences/?conf=mlsb08 Formatting instructions can be found on the workshop website http://www.montefiore.ulg.ac.be/services/stochastic/mlsb08 The extended abstracts will be reviewed by the scientific programme committee. The papers will be selected for oral or poster presentation according to their originality and relevance to the workshop topics. Electronic versions of the extended abstracts will be accessible to the participants prior to the conference and will be made publicly available on the conference web site after the conference. It is also planned to publish these papers in a special volume of a bioinformatics journal. SUBMISSION OF POSTER PRESENTATIONS We invite you also to apply for poster presentations on topics of relevance to the workshop. Each poster presentation should be described in a 1 page summary and be submitted by August 20, 2008 via the Easychair submission system: http://www.easychair.org/conferences/?conf=mlsb08 Poster summaries must follow the same formatting instructions as the extended abstract, but should not exceed one page. IMPORTANT DATES - ** 22 June ** deadline for submissions of extended abstracts - 15 July: notification of acceptance to authors - 25 August: camera-ready versions of extended abstracts - 20 August: deadline for submissions of poster presentations - 25 August: notification of acceptance to authors - 13-14 September: workshop LOCATION The workshop will take in place Brussels at the Palais des Académies of Académie royale des Sciences, des Lettres et des Beaux-Arts de Belgique. CONTACT For further information, please contact mlsb08(a)gmail.com or see the conference website: http://www.montefiore.ulg.ac.be/services/stochastic/mlsb08 MLSB08 CHAIRS Louis Wehenkel and Pierre Geurts, GIGA-Research, University of Liège, Belgium Florence d’Alché-Buc, IBISC CNRS FRE 2873, University of Evry-Val d’Essonne, France Yves Moreau, ESAT, Katholieke Universiteit Leuven, Belgium SCIENTIFIC PROGRAMME COMMITTEE Florence d’Alché-Buc (University of Evry, France) Christophe Ambroise (University of Evry, France) Pierre Geurts (University of Liège, Belgium) Mark Girolami (University of Glasgow, UK) Samuel Kaski (University of Helsinki, Finland) Kathleen Marchal (Katholieke Universiteit Leuven, Belgium) Elena Marchiori (Vrije Universiteit Amsterdam, The Netherlands) Yves Moreau (Katholieke Universiteit Leuven, Belgium) 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) Rodolphe Sepulchre (University of Liège, Belgium) Koji Tsuda (Max Planck Institute, Tuebingen) Jacques Van Helden (Université Libre de Bruxelles, Belgium) Kristel Van Steen (University of Liège, Belgium) Jean-Philippe Vert (Ecole des Mines, France) Louis Wehenkel (University of Liège, Belgium) David Wild (University of Warwick, UK) Jean-Daniel Zucker (University of Paris XIII, France)

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2 postdoc positions Computational Biology and Structural Bioinformatics, Barcelona, Spain
by Jacques van Helden 07 Jun '08

07 Jun '08

Two Postdoc Positions Computational Biology and Structural Bioinformatics, in the context of Systems Biology Institut de Neurociències Universitat Autònoma de Barcelona (Spain) Two postdoc positions for either three or two years and starting early 2008 are open in the laboratory of Jesús Giraldo1 (Institut de Neurociències2. Universitat Autònoma de Barcelona3) to work on the modeling of G protein-coupled receptor function. REQUIREMENTS: Applicants should have a PhD in Bioinformatics, Computational Biology, Mathematics, Physics, Chemistry or Engineering. Send CV and names of 3 references to Jesus.Giraldo(a)uab.es . 1 http://servet.uab.es/biomathematics 2 http://servet.uab.es/neurociencies/ 3 http://www.uab.es/ Contact Jesús Giraldo, PhD Grup Biomatemàtic de Recerca Institut de Neurociències i Unitat de Bioestadística Facultat de Medicina Universitat Autònoma de Barcelona 08193 Bellaterra (Spain) Phone: +34 93 581 3813 Fax: +34 93 581 23 44 E-mail: Jesus.Giraldo(a)uab.es http://servet.uab.es/biomathematics

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postdoc in systems biology
by Marianne Rooman 06 Jun '08

06 Jun '08

Please find in the attached file the advertisement for a 2-years post-doc position in Brussels. -- -------------------------------------------- Marianne Rooman Bioinformatique génomique et structurale Université Libre de Bruxelles 50 avenue Franklin Roosevelt, CP 165/61 B-1050 Bruxelles Belgium Phone : 32-2-650 2067/5572 Fax : 32-2-650 3575 E-mail: mrooman(a)ulb.ac.be --------------------------------------------

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