May 2009 - beg-sysbiol@psb.ugent.be - maillist.psb.ugent.be

[Beg-sysbiol] Abstract | Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease
by Yves Van de Peer 23 May '09

23 May '09

http://genomebiology.com/2009/10/5/R55 -- 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] Brainstorm sysbiol presentation
by Anagha Joshi 20 May '09

20 May '09

Hi All, The almost final version of sysbiol part is in: /group/biocomp/doc/PRESENTATIONS/Brainstorm_2009/Brainstorm_sysbiol.ppt. We have tried to give a structure by asssembling everyone's input. If you have further suggestions/comments, pls feel free to make changes in the presentation itself or you can send the slides/comments to me and I will add/change. thanks, Anagha

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[Beg-sysbiol] With C$2M in Funding, 1000 Plants Initiative Takes On Transcriptomes | In Sequence | Sequencing | GenomeWeb
by Yves Van de Peer 20 May '09

20 May '09

http://www.genomeweb.com/sequencing/c2m-funding-1000-plants-initiative-take… -- 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] Methods section slides
by Anagha Joshi 18 May '09

18 May '09

Dear All, So far I have got slides for methods section from Vanessa, Sofie and Natalie. I am still waiting for input from Tom and Jens. If anyone else wants to contribute something .. It would be nice if I receive everything by noon today, then I can compile everything by evening and send it to Vanessa. thanks, Anagha

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Re: [Beg-sysbiol] text-mining for the sysbiol brainstorm part
by Anagha Joshi 15 May '09

15 May '09

Thanks Sofie, It would be nice if everyone can add one figure elaborating the method. thanks, Anagha On Fri, 15 May 2009, Sofie Van Landeghem wrote: > Hi guys, > > I've attached 3 presentations, and filled them with hopefully relevant > information for the sysbiol bit on the brainstorm :-) > > - text_data : should probably be included in the first bit about datatypes > (Vanessa?) > - text_integration : this belongs to the methods bit (Anagha?), showing some > examples how text-mining can be useful in a "bigger" setup > - text_discussion : these questions could be included in the last bit (who's > doing that?). They are just ideas to initiate discussion. > > Feel free to change the slides however you see fit, or ask me if you think > there's some information missing or unclear. > > Best, > Sofie >

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[Beg-sysbiol] brainstorm meeting
by Vanessa Vermeirssen 14 May '09

14 May '09

Hi all, on special request, the meeting this afternoon will start at 2 pm. In the meanwhile, if you have something on slides, please send it to me. I will combine that. Vanessa -- ================================================================== 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] brainstorm
by Vanessa Vermeirssen 14 May '09

14 May '09

Hi, since nobody added anything to the wiki yet, I would suggest that you use the wiki as a guideline and prepare everything directly on (PowerPoint) slides. e.g. if you have a nice figure illustrating a method, you can add it already. In that way we will save some time, putting everything together. If you could send me your information on slides then before tomorrow 11 am, I will make sure everything is compiled when we meet a 1 pm. Thanks, Vanessa -- ================================================================== 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] paper : Current progress in network research: toward reference networks for key model organisms
by Sofie Van Landeghem 13 May '09

13 May '09

Hi all, this paper "Current progress in network research: toward reference networks for key model organisms" (http://bib.oxfordjournals.org/cgi/content/full/8/5/318) was published in august 2007, so it's not completely up-to-date. Still I think it might be an interesting "overview" paper. You guys probably have a better idea about this. It introduces some general concepts in Systems biology, illustrated with quite some figures. The most interesting part for me, was (at the end) the description of reference networks that should be constructed using some sort of Network Ontology. The authors make a very valid point there, but I don't think much work has been done yet in this field. I might be wrong though ;-) This ontology-bit could be listed as both an opportunity and a threat, I think :-) Sofie

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[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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