- beg-sysbiol@psb.ugent.be - maillist.psb.ugent.be

[Beg-sysbiol] [Fwd: BioMagNet Newsletter October 2007]
by Klaas Vandepoele 27 Sep '07

27 Sep '07

Anything to report concerning the BioMagnet project? Klaas

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[Beg-sysbiol] ESF proposal
by Eric Bonnet 27 Sep '07

27 Sep '07

Hi there, Here is the ESF proposal that I compiled with data from Steven, Greg and Tom. Feel free to comment, we have til monday midnight to submit. Eric

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[Beg-sysbiol] Extracting the hierarchical organization of complex systems
by Roeland Merks 25 Sep '07

25 Sep '07

In PNAS this week: *PHYSICAL SCIENCES / APPLIED PHYSICAL SCIENCES* * Extracting the hierarchical organization of complex systems* * Marta Sales-Pardo, Roger Guimerà, André A. Moreira, and Luís A. Nunes Amaral^* * Department of Chemical and Biological Engineering and Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL 60208 Edited by H. Eugene Stanley, Boston University, Boston, MA, and approved July 22, 2007 (received for review April 23, 2007) Extracting understanding from the growing "sea" of biological^ and socioeconomic data is one of the most pressing scientific^ challenges facing us. Here, we introduce and validate an unsupervised^ method for extracting the hierarchical organization of complex^ biological, social, and technological networks. We define an^ ensemble of hierarchically nested random graphs, which we use^ to validate the method. We then apply our method to real-world^ networks, including the air-transportation network, an electronic^ circuit, an e-mail exchange network, and metabolic networks.^ Our analysis of model and real networks demonstrates that our^ method extracts an accurate multiscale representation of a complex^ system.^ cellular metabolism | complex networks | multiscale representatiom http://www.pnas.org/cgi/content/abstract/104/39/15224?etoc I haven't seen the paper itself yet. Cheers, Roeland

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Re: [Beg-sysbiol] Esf meeting?
by Yves Van De Peer 25 Sep '07

25 Sep '07

Hoi Steven, Ik zit momenteel in Atlanta te wachten om naar huis te gaan ... Al in labo's geweest of nog aan't rondcruisen? Yves -----Original Message----- From: beg-sysbiol-bounces(a)psb.ugent.be <beg-sysbiol-bounces(a)psb.ugent.be> To: beg-sysbiol(a)psb.ugent.be <beg-sysbiol(a)psb.ugent.be> Sent: Tue Sep 25 05:28:47 2007 Subject: Re: [Beg-sysbiol] Esf meeting? No objection if I get stuck in California a little longer ? I like it here! Sunny greetings from Berkeley, Steven > On 24 Sep 2007, at 21:16, Yves Van De Peer wrote: >> Hi guys, >> >> I hope all is well? >> Maybe you've heard but I got stuck in Ecuador for a little longer. >> > > No, what happened? > >> I'll probably (at least that's what I hope) be back Thursday but I >> was wondering whether yiu guys made any progress on the Esf meeting >> proposal? >> > We are working on it. I'm pretty confident we will meet all the > deadlines of the upcoming days/weeks, but not necessarily by more > than a few hours :-) > > > > Tom > > -- > Tom Michoel > <http://www.psb.ugent.be/~tomic/> > _______________________________________________ > Beg-sysbiol mailing list > Beg-sysbiol(a)psb.ugent.be > https://maillist.psb.ugent.be/mailman/listinfo/beg-sysbiol > _______________________________________________ Beg-sysbiol mailing list Beg-sysbiol(a)psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/beg-sysbiol

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[Beg-sysbiol] Esf meeting?
by Yves Van De Peer 25 Sep '07

25 Sep '07

Hi guys, I hope all is well? Maybe you've heard but I got stuck in Ecuador for a little longer. I'll probably (at least that's what I hope) be back Thursday but I was wondering whether yiu guys made any progress on the Esf meeting proposal? Best regards, Yves

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[Beg-sysbiol] Systems biology conference
by Greg Amoutzias 24 Sep '07

24 Sep '07

FYI http://www.genomestosystems.org/prog.html Its a very good and well organised conference, I 've been a couple of times and I would suggest it. --- 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] Re: technical research project - REMINDER
by Steven Maere 14 Sep '07

14 Sep '07

Hi Sylvie, Here are two projects, one for the first semester and one for the second. Best, Steven Sylvie De Buck wrote: > Dear, > Last week, I already send you a mail concerning the technical research > projects that students of the first Master have to do in our lab. Let > me first of all thank all the people that already submitted such a > proposal. Thank you very much for your cooperation ! > Some groups however, did not send a proposal yet. Can I please ask > them to still do this before monday evening (17/09/07). Also projects > for the focus "Bioinformatics and Systems Biology" are very welcome > and still needed. > In attach, you find again the form that you should fill in if you want > to submit a proposal. Please also indicate if you want a student in > the first and/or second semester. > > Thank you very much, > Sylvie > -- ================================================================== Steven Maere, PhD Dept. of Plant Systems Biology Bioinformatics & Evolutionary Genomics research group VIB / Ghent University Technologiepark 927 B-9052 Gent BELGIUM tel: +32 9 331 3810 fax: +32 9 331 3809 email: stmae(a)psb.UGent.be http://www.psb.UGent.be http://bioinformatics.psb.ugent.be/ ==================================================================

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[Beg-sysbiol] Re: Combined analysis of mRNA co-expression patterns, promoter motifs and transcription factors
by Klaas Vandepoele 13 Sep '07

13 Sep '07

Could be relevant for you SB boys/girls as well... Klaas Stefanie De Bodt wrote: > http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&dopt=AbstractPlus&db=… > > Research article . Putative cold acclimation pathways in Arabidopsis thaliana identified by a combined analysis of mRNA co-expression patterns, promoter motifs and transcription factors Aakash Chawade , Marcus Brautigam , Angelica Lindlof , Olof Olsson and Bjorn Olsson BMC Genomics 2007, 8:304 doi:10.1186/1471-2164-8-304 Background With the advent of microarray technology, it has become feasible to identify virtually all genes in an organism that are induced by a certain developmental or environmental change. However, relying solely on gene expression data may be of limited value if the aim is to infer the underlying genetic networks. Development of computational methods to obtain more complex networks is therefore desirable. Here we propose one such method and, using cold acclimation in Arabidopsis as an example, demonstrate that the resulting network can be used to identify hitherto un-described putative regulatory pathways. Results A putative network of cold-related genes is identified by applying our proposed method to previously published Arabidopsis microarray data from cold acclimated plants at six different time points and promoter motif sequence data extracted from ~24,000 Arabidopsis promoters, followed by a functional annotation analysis of interacting genes. The inferred network includes some of the previously characterised cold acclimation pathways, and hitherto un-described putative regulatory interactions between transcription factor (TF) genes and other genes, which encode TFs or other proteins. Part of the obtained transcription factor regulatory network is presented here. More detailed information can be accessed from the supplementary data. Conclusions Microarray gene expression data is of tremendous value to characterise global gene expression during environmental stress or during specific developmental stages, but is of even more value when combined with other information sources. Here we applied a rule-based method that combines microarray gene expression data with promoter motif structures inferred from genomic DNA and previous knowledge of the specific transcription factors involved. By using this method to study the cold acclimation process in Arabidopsis, more complex putative genetic regulatory networks than previously described were elucidated. -- ================================================================== 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/ ==================================================================

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[Beg-sysbiol] LeMoNe web/gui startup
by Tom Michoel 12 Sep '07

12 Sep '07

Thomas wrote a nice webstart application for LeMoNe: http://www.psb.ugent.be/~thpar/ws/ The idea is to help a new user choose parameter settings (though currently the "help" only contains the comments from the properties file, will be updated later), write a properties file and give the option to run LeMoNe without opening a command line. You can also run the Run class with option --gui to run the application locally, and all code is under svn (requires java 1.6 to compile). Tom -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] ongoing conference
by Vanessa Vermeirssen 10 Sep '07

10 Sep '07

http://www.rothamsted.bbsrc.ac.uk/bab/conf/ib07/prog.php -- ================================================================== Vanessa Vermeirssen, PhD Tel:+32 (0)9 331 38 23 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM vamei(a)psb.ugent.be http://www.psb.ugent.be ==================================================================

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