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

[Beg-sysbiol] Toward accurate reconstruction of functional protein networks.
by Klaas Vandepoele 12 May '09

12 May '09

Dear Tom/Anagha and other sysbiol-folks, I recently read this paper and found it intruiging how different ways of finding subnetworks/modules in a ppi-network could reveal complementary aspects of the underlying biology. Do you think these local/global methods could be used to dissect other types of networks (we use in the lab) as well? If yes, should we ellaborate on this study during the brainstorm? best, Klaas Toward accurate reconstruction of functional protein networks. Yosef N, Ungar L, Zalckvar E, Kimchi A, Kupiec M, Ruppin E, Sharan R. Mol Syst Biol. 2009;5:248. Genome-scale screening studies are gradually accumulating a wealth of data on the putative involvement of hundreds of genes/proteins in various cellular responses or functions. A fundamental challenge is to chart out the protein pathways that underlie these systems. Previous approaches to the problem have either employed a local optimization criterion, aiming to infer each pathway independently, or a global criterion, searching for the overall most parsimonious subnetwork. Here, we study the trade-off between the two approaches and present a new intermediary scheme that provides explicit control over it. We demonstrate its utility in the analysis of the apoptosis network in humans, and the telomere length maintenance (TLM) system in yeast. Our results show that in the majority of real-life cases, the intermediary approach provides the most plausible solutions. We use a new set of perturbation experiments measuring the role of essential genes in telomere length regulation to further study the TLM network. Surprisingly, we find that the proteasome plays an important role in telomere length regulation through its associations with transcription and DNA repair circuits. http://www.ncbi.nlm.nih.gov/pubmed/19293828

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[Beg-sysbiol] kiwi
by Eric Bonnet 11 May '09

11 May '09

I've created a section called "presentations" on the existing wiki page "Brainstorm 2009" https://bioinformatics.psb.ugent.be/knowledge/wiki-bioinformatics/Brainstor… with a dedicated page for the sysbiol session: https://bioinformatics.psb.ugent.be/knowledge/wiki-bioinformatics/Sysbiol_s… Now it's up to you guys ;-) Eric

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[Beg-sysbiol] brainstorm systems biology/transcription regulation
by Vanessa Vermeirssen 08 May '09

08 May '09

Hi all, shall we have a short meeting to start preparing for the brainstorm on monday after lunch 1 pm? The idea would be that everybody starts already thinking along the lines Yves proposed in his email (state of the art/opportunities/threats/discussion topics) and that we then bundle our ideas. Vanessa if I forgot anybody, please forward... -- ================================================================== Vanessa Vermeirssen, PhD Tel:+32 (0)9 331 38 10 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM vamei(a)psb.vib-ugent.be http://www.psb.vib-ugent.be ==================================================================

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[Beg-sysbiol] The challenges of systems biology (DREAM2 proceedings)
by Tom Michoel 06 May '09

06 May '09

For those who are interested, I recieved a print copy of this volume: http://www3.interscience.wiley.com/journal/122295267/issue Tom -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] [Fwd: Re: Computational Systems Biology]
by Tom Michoel 28 Apr '09

28 Apr '09

This book <http://www.springer.com/humana+press/book/978-1-58829-905-5> will be in the library soon, apparently some of you asked for it as well. Tom -------- Original Message -------- Subject: Re: Computational Systems Biology Date: Tue, 28 Apr 2009 09:42:51 +0200 From: Jacques De Laet <jalae(a)psb.vib-ugent.be> To: Tom Michoel <tom.michoel(a)psb.vib-ugent.be> CC: psblib >> "psblib(a)psb.ugent.be" <psblib(a)psb.vib-ugent.be> References: <49F03DED.7060806(a)psb.vib-ugent.be> Bete Tom, wegens de grote vraag naar dit boek , wordt het aangekocht. Jacques Tom Michoel wrote: > Dag Jaques, > > Hebben wij op een of andere manier toegang tot de online versie van > dit boek? > > <http://www.springer.com/humana+press/book/978-1-58829-905-5> > > Zoniet, kan het eventueel aangekocht worden? > > Alvast bedankt, > Tom -- ================================================================== Jacques De Laet Tel:+32 (0)9 331 36 91 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM jalae(a)psb.vib-ugent.be http://www.psb.vib-ugent.be ================================================================== -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] FYI
by Yvan Saeys 27 Apr '09

27 Apr '09

http://users.cs.fiu.edu/~taoli/kdd09-workshop/ -- ================================================================== 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/ ==================================================================

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[Beg-sysbiol] Methods to reconstruct and compare transcriptional...[Methods Mol Biol. 2009] - PubMed Result
by Yves Van de Peer 26 Apr '09

26 Apr '09

http://www.ncbi.nlm.nih.gov/pubmed/19381525?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.vib-ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-sysbiol] Report on EU-USA workshop: how systems biology can...[Mol Oncol. 2009] - PubMed Result
by Yves Van de Peer 26 Apr '09

26 Apr '09

http://www.ncbi.nlm.nih.gov/pubmed/19383362?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.vib-ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-sysbiol] ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks -- Bindea et al. 25 (8): 1091 -- Bioinformatics
by Klaas Vandepoele 17 Apr '09

17 Apr '09

http://bioinformatics.oxfordjournals.org/cgi/content/full/25/8/1091 -- 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.vib-ugent.be Website: http://bioinformatics.psb.ugent.be/ --------------------------------------------------------- it's hard to keep the animo from driftin' away nowadays

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[Beg-sysbiol] dream interview
by Eric Bonnet 17 Apr '09

17 Apr '09

http://www.bio-itworld.com/pb/2009/04/16/dream3-update.html

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