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

[Beg-sysbiol] (no subject)
by Yves Van de Peer 30 Oct '06

30 Oct '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] Entrez PubMed
by Yves Van de Peer 29 Oct '06

29 Oct '06

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&dopt=Abstract&db…

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[Beg-sysbiol] Entrez PubMed
by Tom Michoel 24 Oct '06

24 Oct '06

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?tmpl=NoSidebarfile&db=PubMed&… how come we don't have access to the full text? (fortunately I have other sources too :-) tom

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[Beg-sysbiol] [math/0610034] Bayesian Variable Selection and Data Integration for Biological Regulatory Networks
by Tom Michoel 24 Oct '06

24 Oct '06

http://www.arxiv.org/abs/math.ST/0610034 Bayesian Variable Selection and Data Integration for Biological Regulatory Networks Authors: Shane T. Jensen, Guang Chen, Christian J. Stoeckert Jr Comments: Submitted to the Journal of the American Statistical Association Subj-class: Statistics; Molecular Networks A substantial focus of research in molecular biology is the network of factors which control the involvement of different genes in living cells. Previous statistical approaches for identifying gene regulatory networks have used gene expression data, ChIP binding data or promoter sequence data, but each of these resources provides only partial information. We present a Bayesian hierarchical model that integrates all three data types in a principled variable selection framework. The gene expression data is modeled as a function of the unknown gene regulatory network which has an informed prior distribution based upon both ChIP binding and promoter sequence data. We also present a variable weighting methodology for the principled balancing of multiple sources of prior information. We apply our procedure to the discovery of gene regulatory relationships in Yeast for which we can use several external sources of information to validate our results. Our inferred relationships show greater biological relevance on the external validation measures than previous data integration methods.

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[Beg-sysbiol] papers
by Eric Bonnet 23 Oct '06

23 Oct '06

2 sysbiol papers in plos biol: http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/… http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/…

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[Beg-sysbiol] to follow up (but still confidential I think ...)
by Yves Van de Peer 22 Oct '06

22 Oct '06

-------- Original Message -------- Subject: [Fwd: Re: Arabidopsis interactome .. 2nd attempt] Date: Tue, 17 Oct 2006 14:05:09 +0200 From: Pierre Hilson <pihil(a)psb.ugent.be> To: Yves Van de Peer (E-mail) <yvdp(a)psb.ugent.be> Dear Yves, I have received a request for a letter of support from Joe Ecker, David Hill and Marc Vidal (see below). I have already written a first draft of this letter (see attachment). In addition, I was wondering if you would be willing to help them establish orthologous relationships between rice and Arabidopsis genes (see in particular Dave's remarks). If you would, I could then add a paragraph stating something like this: Finally, besides AGRON-OMICS' input in the area of protein-protein interaction network, the group headed by my colleague Yves Van de Peer (Bioinformatics and Evolutionary Genomics, Department of Plant Systems Biology, VIB - Ghent University, Belgium) is volunteering to help establish orthologous relationships between proteins encoded in the genomes of Arabidopsis and other plant species, including rice. Such relationships will be essential to translate to economically relevant crops the knowledge acquired thanks to the Arabidopsis plant model. Yves is a world expert in the area of comparative genomics and his group has made key contributions for the annotation and comparative analysis of multiple plant genomes. If you are interested you could also discuss this directly with Marc visiting us on October 26th but there might not be time enough to write a separate letter since I'm told they'll submit their grant application tomorrow... I've received their request this morning! Let me know what you think of all this... may be by typing a long email with your fat fingers on your tiny blackberry keys! Or simply calling me if you feel like it. Cheers, Pierre -------- Original Message -------- Hi Pierre, Obviously, right now, the wealth of At resources far exceeds that of rice and other crop plants. But NSF was really insistent that PGRP has to have a crop plant element. Sharing info that will help us identify suitable rice orthologs to investigate specific pathways (disease resistance, drought, etc, or seed production, whatever) by cloning the respective rice ORFs and then doing Y2H on rice AD-cDNA libraries would be much appreciated. Also, as Joe mentioned, validation of interactions and possibly analysis of expression patterns comparing interacting proteins versus root expression, shoots and stems, etc. Thanks Dave PS – Will you be coming to the ORFeome Meeting in November? Website is: http://orfeomemeeting.dfci.harvard.edu/orfeome_httpd/htdocs/index.html On 10/16/06 8:04 PM, "Joseph R. Ecker" <ecker(a)salk.edu> wrote: Hi Pierre Marc/David and I will give one more shot at obtain funds for an Arabidopsis interactome. We consulted with NSF and they suggested that we need to add some experiments with rice- which is fine by us. One thing that could be helpful is to show some international collaboration/cooperation on this project. Can you send us a short letter describing your funded effort and indicate that you would be wiling to share your data with us to help with validation of our results and we could do the same for you? Sorry for the short notice, we would need the letter rather quickly to make the deadline. Marc/David Any thing else that should be indicated?? Joe Joseph R. Ecker Professor, The Salk Institute for Biological Studies Plant Biology/Genomic Analysis Laboratories 10010 North Torrey Pines Road La Jolla, CA 92037 Phone (858) 453-4100 x1752 FAX (858) 558-6379 Web addresses: http://www.salk.edu http://signal.salk.edu http://www.salk.edu/faculty/faculty/details.php?id=18 Administrative Assistant: Kim Emerson Phone (858) 453-4100 x1106 email: kemerson(a)salk.edu -- Pierre Hilson, PhD Functional Genomics Division Department of Plant Systems Biology VIB - Gent University Technologiepark 927 B-9052 Gent, Belgium Phone: + 32 (0)9 331 38 30 Fax: + 32 (0)9 331 38 09 pihil(a)psb.ugent.be www.psb.ugent.be -- 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] Entrez PubMed
by Yves Van de Peer 16 Oct '06

16 Oct '06

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&dopt=Abstract&db…

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[Beg-sysbiol] doc directory update
by Tom Michoel 11 Oct '06

11 Oct '06

I've updated the doc directory in /nas/biocomp/projects/segal/ with a copy of our paper, my lab meeting presentation and the embl/bbc poster, so you know where to go if you ever need stuff for your own presentations. Tom

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[Beg-sysbiol] poster draft
by Tom Michoel 11 Oct '06

11 Oct '06

Hi guys, What do you think of this as a poster? It's made in LaTeX (of course :-) so colors, fonts, etc. can be changed/added on the fly. Any suggestions please by tomorrow before it goes off to the printer. Tom

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[Beg-sysbiol] [Fwd: Re: joint paper on SynTren and module network learning for BMC Bioinformatics]
by Tom Michoel 10 Oct '06

10 Oct '06

something to consider for the revision and the future. tom -------- Original Message -------- Subject: Re: joint paper on SynTren and module network learning for BMC Bioinformatics Date: Tue, 10 Oct 2006 14:47:28 +0200 From: Tim Van den Bulcke <Tim.VandenBulcke(a)esat.kuleuven.be> To: tom.michoel(a)psb.ugent.be References: <4520DD47.7080902(a)psb.ugent.be> <4523D0F9.70209(a)esat.kuleuven.be> <452A5561.6000707(a)psb.ugent.be> [...] > > > P4: sensitivity, specificity, precision, recall: > > misschien hebben we hier niet de gangbare termen gebruikt? jouw > precision (tp/(tp+fp)) is wat wij specificity hebben genoemd; de > definities staan in "Methods -> Network comparison", maar als dat niet > de standaard benamingen zijn, kunnen we ze best aanpassen. > Ik denk dat dat niet de standaard benaming is. De definitie voor Specificity is TN/(FP+TN) [http://en.wikipedia.org/wiki/Sensitivity_and_specificity] en de precision = positive predictive value = tp/(tp+fp) [http://en.wikipedia.org/wiki/Information_retrieval#Precision] [...]

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