March 2006 - beg-sysbiol@psb.ugent.be

[Beg-sysbiol] I hope you can all be there next Tuesday afternoon?
by Yves Van de Peer 30 Mar '06

30 Mar '06

Thanks in advance, Yves -------- Original Message -------- Subject: Bioinformatics for Agribusiness Date: Wed, 22 Mar 2006 17:38:59 +1100 From: <David.Mitchell(a)csiro.au> To: <yvdp(a)psb.ugent.be> Dear Yves, Koen Bruynseels from CropDesign suggested that I drop you a line. I am the leader of the Biotechnology and Health Informatics program in CSIRO's Division of Mathematical and Information Sciences. My background is in molecular biology, but I now have the pleasure of leading a group of about 40 statisticians, mathematicians and image analysts. The group works in three main areas, bioinformatics for human health and agribusiness, imaging in biotechnology and health informatics. I've written more about our research in detail below. My colleague David Lovell (who heads up our Bioinformatics for Agribusiness group) and I will be in Gent on Tuesday 4th of April visiting CropDesign. Koen suggested that a visit to the Plant Systems Biology Department at VIB and gave me your email. As a group we are interested in Systems Biology but are still discussing how to really get some engagement. If you have some time on Tuesday afternoon, would it be possible to come for a chat? I would be happy to give a short presentation on some of our statistical bioinformatics stuff, particularly the network building. Kind Regards David ------------------------------------------------------------------------------------ CSIRO is Australia's national science agency and one of the largest in the world. CSIRO research delivers solutions for agribusiness, energy and transport, environment and natural resources, health, information technology, telecommunications, manufacturing and mineral resources. The Division of Mathematical and Information Sciences consists of mathematicians and statisticians with a focus on smarter information use in Biotechnology and Health, the Environment, and Decision Technologies. CSIRO Bioinformatics are specialists in the analysis of the types of data being generated by the current range of high throughput platforms. Our initial focus was on expression microarray data, where the number of measurements (genes) per sample vastly exceeds the number of samples. We call this type of data p>n data, because in statistics p often refers to the number of measurements (or variables) and n refers to the number of samples. Of course, p>n data occurs in many other settings and we are now active not only in expression microarrays (both Affymetrix and cDNA types) but in DNA (SNPs), proteomics (including LC/MS) and metabolomics. Our proprietary technology is focused mainly in the area of classification of samples using p>n data. For example, seeking simple combinations of gene expression parameters that are diagnostic of disease or finding combinations of SNPs that are indicative of a certain predisposition. The philosophy of our technology is multivariate; in particular, we generate classifiers using combinations of small numbers of genes, but all genes are candidates not just those preselected by univariate differential expression measures. There are two main threads to our technology; one based on the use of sophisticated Bayesian priors and an EM algorithm[1] <BLOCKED::outbind://20/#_edn2>, and the other a highly efficient variant of more a traditional stepwise approach. The Bayesian approach is able to generate sparse predictive models of complex phenotypes, including classification, survival and quantitative traits. We have also used our Bayesian approach to build "sparse" networks of genes. We have found this to be particularly useful as we are able to cross validate the linkages to build a robust network (Poster attached). While much of our work has been on data from medical applications, we have a group working on agribusiness applications as well. They have been looking at 2 phase designs for microarray experiments, building a LIMS database for managing rice breeding and looking at various problems using mathematical modelling approaches. We are also just starting work in objective measurement of plant phenotypes using imaging. ------------------------------------------------------------------------ [1] <outbind://20/#_ednref2> (“A Bayesian approach to variable selection when the number of variables is very large”, in /Science and Statistics: A Festschrift for Terry Speed/, volume 30 of Lecture Notes - Monograph Series, Institute of Mathematical Statistics, Hayward, California, 2003, Kiiveri, H. T.). David Mitchell PhD, MEI Research & Business Leader Biotechnology & Health Informatics CSIRO Mathematical & Information Sciences Locked Bag 17 North Ryde, NSW, 1670 AUSTRALIA T: +61 2 9325 3256 F: +61 2 9325 3200 M: +61 402 304 801 E: david.mitchell(a)csiro.au <mailto:david.mitchell@csiro.au> -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Department of Plant Systems Biology 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://www.psb.ugent.be/bioinformatics/

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[Beg-sysbiol] A Chemical Kinetic Model of Transcriptional Elongation
by Roeland Merks 14 Mar '06

14 Mar '06

-------- Original Message -------- Subject: q-bio daily Subj-class mailing 8 1 Date: Tue, 14 Mar 2006 05:04:33 -0500 From: no-reply(a)arXiv.org (send mail ONLY to q-bio) Reply-To: q-bio(a)arXiv.org To: rabble(a)arXiv.org (q-bio daily title/abstract distribution) ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ send mail only to q-bio(a)arXiv.org, do not reply to no-reply@... send any complaints regarding submissions directly to submitter. use a single `get' to request multiple papers, `list macros' for available macro packages, and `help' for a list of available commands and other info. ------------------------------------------------------------------------------ point your www client at http://arXiv.org/ To unsubscribe, e-mail To: q-bio(a)arXiv.org, Subject: cancel ------------------------------------------------------------------------------ Submissions to: Subcellular Processes received from Fri 10 Mar 06 21:00:02 GMT to Mon 13 Mar 06 21:00:02 GMT ------------------------------------------------------------------------------ %-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%- ------------------------------------------------------------------------------ \\ Paper: q-bio.BM/0603012 Date: Sun, 12 Mar 2006 02:50:18 GMT (77kb) Title: A Chemical Kinetic Model of Transcriptional Elongation Authors: Yujiro Richard Yamada, Charles S. Peskin Comments: 12 pages, 4 figures Subj-class: Biomolecules; Subcellular Processes \\ A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. Unlike previous models that attempt to explain the motion of RNA polymerase using internal strain and stresses, we propose a chemical kinetic model which governs the discrete movement of the RNA polymerase along a DNA tether, with no consideration given to elastic effects. The model's novel concept is a ``look-ahead'' feature, in which nucleotides bind reversibly to the DNA prior to being incorporated covalently into the nascent RNA chain. Results are presented for specific DNA sequences that have been used in single-molecule experiments of the random walk of RNA polymerase along DNA. \\ ( http://arXiv.org/abs/q-bio/0603012 , 77kb) %%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%% %%%---%%%---%%%---%%%---%%%---%%%---%%%---%%%---%%%---%%%---%%%---%%%---%%%--- -- Roeland Merks Department of Plant Systems Biology VIB / Ghent University Technologiepark 927 B-9052 Ghent, Belgium http://www.psb.ugent.be Tel. +32-(0)9-33 13825 email: post(a)roelandmerks.nl http://www.roelandmerks.nl weblog: http://biolog.volkskrantblog.nl

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[Beg-sysbiol] meeting on systems biology ...
by Yves Van de Peer 08 Mar '06

08 Mar '06

Dear All, Since it is very difficult to have a meeting where everybody can be present, and since we do not want to postpone this (first) meeting too much, let's have it on April 10th at 10:30 (sorry Dirk, we will keep you posted and we will have a second meeting later ...). Hope this works out for most of you. See you then. Yves PS. Marnik, Martin will fill you in on this (Martin?) -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Department of Plant Systems Biology 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://www.psb.ugent.be/bioinformatics/

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[Beg-sysbiol] next beg-sysbiol meeting confirmed for March 28th, 10:00 am. please mark your agendas!
by Yves Van de Peer 08 Mar '06

08 Mar '06

-- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Department of Plant Systems Biology 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://www.psb.ugent.be/bioinformatics/

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[Beg-sysbiol] paper Steven on yeast modules (confidential)
by Steven Maere 08 Mar '06

08 Mar '06

-- ================================================================== Steven Maere Dept. of Plant Systems Biology, Biocomputing research group Ghent University / VIB tel: +32 9 33 13 692 Technologie Park 927 fax: +32 9 33 13 809 B-9052 Gent BELGIUM email: stmae(a)psb.UGent.be http://www.psb.UGent.be http://www.psb.ugent.be/cbd/ ==================================================================

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[Beg-sysbiol] review friedman
by Steven Maere 08 Mar '06

08 Mar '06

status of probabilistic graphical models anno 2004, both segal and pe'er are discussed S -- ================================================================== Steven Maere Dept. of Plant Systems Biology, Biocomputing research group Ghent University / VIB tel: +32 9 33 13 692 Technologie Park 927 fax: +32 9 33 13 809 B-9052 Gent BELGIUM email: stmae(a)psb.UGent.be http://www.psb.UGent.be http://www.psb.ugent.be/cbd/ ==================================================================

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[Beg-sysbiol] another date for the meeting on systems biology ...
by Yves Van de Peer 08 Mar '06

08 Mar '06

Dear All, This seems to be a difficult mission :-) Since Dirk is not here on April 10 and April 11, but would like to attend the meeting, I'd like to propose April 27th (morning) or April 28th (whole day). Please let me know your preferences. Thanks in advance, Yves -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Department of Plant Systems Biology 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://www.psb.ugent.be/bioinformatics/

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[Beg-sysbiol] meeting on Systems Biology
by Yves Van de Peer 07 Mar '06

07 Mar '06

Dear All, The Bioinformatics and Computational Biology groups are working hard to develop top-down Systems Biology approaches (where regulatory networks are being inferred from large amounts of transcriptome data), and we would like to discuss these with some of the 'experimental' people to see how we can integrate transcriptome data that are generated in the Department with approaches that we develop, for instance to elucidate transcriptional regulation in developing leafs. I would like to propose to have a meeting on this on either April 10th or April 11th. Could you please let me know whether this fits you? Many thanks in advance, Best regards, Yves -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Department of Plant Systems Biology 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://www.psb.ugent.be/bioinformatics/

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[Beg-sysbiol] change of plans ... sorry.
by Yves Van de Peer 07 Mar '06

07 Mar '06

Dear All, I have just found out that I have a meeting at 4pm tomorrow, and I cannot afford to miss that. Therefore, I suggest to have our meeting at 11am. I hope that's ok with all of you. Sorry about that. Thanks, Yves -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Department of Plant Systems Biology 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://www.psb.ugent.be/bioinformatics/

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[Beg-sysbiol] (no subject)
by Yves Van de Peer 07 Mar '06

07 Mar '06

Will you guys be here at Monday 10 and/or Tuesday 11 April? Please confirm. Yves -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Department of Plant Systems Biology 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://www.psb.ugent.be/bioinformatics/

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