August 2008 - beg-sysbiol@psb.ugent.be

[Beg-sysbiol] Systems biology: Reverse engineering the cell. [Nature. 2008] - PubMed Result
by Yves Van de Peer 31 Aug '08

31 Aug '08

http://www.ncbi.nlm.nih.gov/pubmed/18756243?dopt=Abstract -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-sysbiol] [Fwd: Machine Learning in Systems Biology - 13-14 Sept, Brussels, Belgium]
by Yves Van de Peer 29 Aug '08

29 Aug '08

Maybe Eric, Tome and Nathalie could attend and present something? Yves -------- Original Message -------- Subject: Machine Learning in Systems Biology - 13-14 Sept, Brussels, Belgium Date: Fri, 29 Aug 2008 13:14:01 +0200 (CEST) From: Yvan Saeys <yvan.saeys(a)psb.ugent.be> Reply-To: yvan.saeys(a)psb.ugent.be To: beg(a)psb.ugent.be Dear colleagues, The MLSB workshop in Brussels this year will also be an occasion to present ourselves withing the Bioframe project, but so far only a few people have registered for the event. It would be good if we could motivate some more people, as the invited talks are of very high quality, and not only restricted to machine learning. best regards, yvan [apologies for multiple postings] ********************** First Call for Participation********************* 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 15 2008 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 - 15 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 AcadÃ©mies of AcadÃ©mie royale des Sciences, des Lettres et des Beaux-Arts de Belgique. MLSB08 CHAIRS Louis Wehenkel and Pierre Geurts, GIGA-Research, University of LiÃ¨ge, Belgium Florence dâAlchÃ©-Buc, IBISC CNRS FRE 2873, University of Evry-Val dâEssonne, France Yves Moreau, ESAT, Katholieke Universiteit Leuven, Belgium SCIENTIFIC PROGRAMME COMMITTEE Florence dâAlchÃ©-Buc (University of Evry, France) Christophe Ambroise (University of Evry, France) Pierre Geurts (University of LiÃ¨ge, 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 RÃ¤tsch (FML, Max Planck Society, TÃ¼bingen) Juho Rousu (University of Helsinki, Finland) CÃ©line Rouveirol (University of Paris XIII, France) Yvan Saeys (University of Gent, Belgium) Rodolphe Sepulchre (University of LiÃ¨ge, Belgium) Koji Tsuda (Max Planck Institute, Tuebingen) Jacques Van Helden (UniversitÃ© Libre de Bruxelles, Belgium) Kristel Van Steen (University of LiÃ¨ge, Belgium) Jean-Philippe Vert (Ecole des Mines, France) Louis Wehenkel (University of LiÃ¨ge, Belgium) David Wild (University of Warwick, UK) Jean-Daniel Zucker (University of Paris XIII, France) -- ================================================================== Dr. Yvan Saeys, PhD DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 331 38 09 BIOINFORMATICS TEAM Tel:32 (0)9 331 36 95 GHENT UNIVERSITY, Technologiepark 927, B-9052 Gent, Belgium Vlaams Instituut voor Biotechnologie VIB mailto:yvan.saeys@ugent.be http://bioinformatics.psb.ugent.be/ http://www.psb.ugent.be/~yvsae/ ================================================================== -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-sysbiol] @home
by Eric Bonnet 28 Aug '08

28 Aug '08

hi there, working at home today, see you guys tomorrow! Eric

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[Beg-sysbiol] [Fwd: Meta Analysis of Gene Expression Data within and Across Species.]
by Klaas Vandepoele 21 Aug '08

21 Aug '08

Great review from Kathleen her group about comparative transcriptomics. Klaas -- Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ --------------------------------------------------------- Come on if you think, come on if you think You can take us on, you and whose army?

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[Beg-sysbiol] @home
by Eric Bonnet 20 Aug '08

20 Aug '08

hi there, I'm working at home this morning. see you guys this afternoon. Eric

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[Beg-sysbiol] [Fwd: FW: TG/SCREEN/012]
by Yves Van de Peer 19 Aug '08

19 Aug '08

-------- Original Message -------- Subject: FW: TG/SCREEN/012 Date: Tue, 12 Aug 2008 14:17:31 +0200 From: Rudy Dekeyser <Rudy.Dekeyser(a)vib.be> To: Yves Van de Peer <yves.vandepeer(a)psb.ugent.be> CC: Barbara Leyman <Barbara.Leyman(a)vib.be> Yves, ter info,rudy *From:* Jan Tavernier [mailto:Jan.Tavernier@UGent.be] *Sent:* dinsdag 12 augustus 2008 13:53 *To:* Rudy Dekeyser *Subject:* RE: TG/SCREEN/012 Rudy: De Cell paper is uit en staat op PubMed. De data zijn open-source: dit is wel een “fragmentoom”-map. Ik kan ook zorgen voor toegang tot de S. cerevisiae interactoommap (verschijnt binnenkort in Science). Ik check de beschikbaarheid van de C. elegans an mens-mappen. Bedankt voor de tip: ik kijk het octrooi na. Greetz, Jan ------------------------------------------------------------------------ *From:* Rudy Dekeyser [mailto:Rudy.Dekeyser@vib.be] *Sent:* 12 August 2008 13:17 *To:* Jan Tavernier *Subject:* FW: TG/SCREEN/012 Dag Jan, Twee zaken (ter info) : 1) Gezien yves van de peer en zijn team momenteel hun systeem biologie software ah uitbreiden zijn en ze interesse hebben om meer eiwit-eiwit data te integreren heb ik heb yves daarnet verteld dat jij met marc vidal een groot project hebt op eiwit-eiwit interacties en dat er binnenkort in Cell een publicatie staat. Het zou knn dat yves je contacteert om te checken of hij toegang kan hebben tot de data. 2) In de attached file : een octrooiaanvrage die we lang geleden indienden. Je moet ze vooral NIET lezen, maar ‘ns kijken naar figuur 1. Daar staat een methode om op snelle wijze combinaties van hypotheses te evalueren via een “3D-aanpak”. Ik vroeg me af of die aanpak in een gemodificeerde vorm bruikbaar zou zijn in jouw arrayMAPPIT. Bye for now,rudy -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-sysbiol] (no subject)
by Greg Amoutzias 14 Aug '08

14 Aug '08

I accidentally came across this photo :-) --- Greg Amoutzias, Ph.D VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3758 Fax: +32 (0)9 331 3809 email: gramo(a)psb.ugent.be

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[Beg-sysbiol] working @ home tomorrow morning
by Nathalie Pochet 06 Aug '08

06 Aug '08

Hi, Somebody from Belgacom will come tomorrow somewhere between 8h and noon to check my phone connection, so I will be working at home till they have left. Kind regards, Nathalie

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