March 2007 - beg-sysbiol@psb.ugent.be

[Beg-sysbiol] (no subject)database
by Vanessa Vermeirssen 16 Mar '07

16 Mar '07

http://www.biomedcentral.com/1471-2105/8/87 GeneBins: a database for classifying gene expression data, with application to plant genome arrays <http://www.biomedcentral.com/1471-2105/8/87> *Goffard N, Weiller G */BMC Bioinformatics/, 2007* 8*:87 -- ================================================================== Vanessa Vermeirssen, PhD VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 3313809 GHENT UNIVERSITY, Technology Park 927, B-9052 Gent, Belgium Vlaams Interuniversitair Instituut voor Biotechnologie VIB mailto:vamei@psb.ugent.be http://www.psb.ugent.be ==================================================================

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[Beg-sysbiol] Discovery of microRNA-mRNA modules via population-based probabilistic learning -- Joung et al., 10.1093/bioinformatics/btm045 -- Bioinformatics
by Tom Michoel 15 Mar '07

15 Mar '07

http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm045v1

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[Beg-sysbiol] Entrez PubMed
by Tom Michoel 12 Mar '07

12 Mar '07

<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?tmpl=NoSidebarfile&db=PubMed&…>

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[Beg-sysbiol] shall we all buy (and read) a copy?
by Yves Van de Peer 11 Mar '07

11 Mar '07

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

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[Beg-sysbiol] CPIB
by Yves Van de Peer 11 Mar '07

11 Mar '07

http://www.cpib.info/

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[Beg-sysbiol] LeMoNe javadoc & new code
by Tom Michoel 09 Mar '07

09 Mar '07

It's been a while since we had any code update news ... I have started to write javadoc documentation for LeMoNe. You can have a look at it here: <file:///nas/biocomp/projects/segal/java/tomic/src/branches/InProgress2/index.html> (if you're in the PSB building ...) As you can see, this all refers to the latest working version which has a lot of new code compared with the current release. This is mainly to integrate Anagha's clustering into LeMoNe to generate different equally likely regulation programs for each module. You can get this code by svn from the InProgress2 branch. If you're interested I can explain what's new sometime next week. Tom -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] [Fwd: Re: Chapter]
by Yves Van de Peer 08 Mar '07

08 Mar '07

-------- Original Message -------- Subject: Re: Chapter Date: Tue, 6 Mar 2007 08:34:46 -0500 From: Erich Grotewold <grotewold.1(a)osu.edu> To: Yves Van de Peer <yves.vandepeer(a)psb.ugent.be> References: <p06110415be8af01d26ac(a)[10.250.15.85]> <42767A46.5080900(a)psb.ugent.be> <p0624083ac1f7745871c1(a)[128.146.132.31]> <45D22061.7000304(a)psb.ugent.be> <p06240804c200ece34ab7(a)[128.146.132.31]> <45DC08DF.5060405(a)psb.ugent.be> Dear Yves, The silence form your end could mean that the comments are so bad that you are afraid to send them or that you had no time... I will need to submit it in the next week, thus look forward to anything (good or bad) that you may have to say. How is the science going? As you can tell form the references, I have been following some of your pubs pretty closely - I still think that there is plenty of room for doing something together. I plan on spending a year (Oct 2007 - Sept. 2008) at the Mathematical Bioscience Institute here at OSU doing a sabbatical and becoming more familiar with how to apply mathematical tools to model regulatory networks, etc. I am also considering taking a few weeks here and there to visit labs doing research in these areas and become more familiar with areas in which I have little expertise on right now - would you see beneficial the possibility of me spending some time there? Just a thought.... Best regards, Erich >Erich Grotewold wrote: >>Dear Yves, >> >>Here goes the chapter - feel free to have those smarter ;-) >>postdocs read it as well, in particular to pint out significant >>omissions or mistakes that we may have made. Let me know when you >>get it so that I can ease my mind from the thought of the e-mail >>doing with the document whatever it pleases. >> >>Best regards, >>Erich >Dear Erich, > >Received your chapter loud and clear! >We'll try to give feedback as soon as possible. > >Best regrads, > >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/ -- Erich Grotewold, Professor Dept. of Plant Cellular and Molecular Biology Plant Biotechnology Center The Ohio State University 206 Rightmire Hall, 1060 Carmack Road Columbus, OH 43210 Phone: (614) 292-2483 FAX: (614) 292-5379 E-mail: grotewold.1(a)osu.edu Our lab website http://www.biosci.ohio-state.edu/~plantbio/osu_pcmb/people/Erich AGRIS - Arabidopsis Gene Regulatory Information Server http://arabidopsis.med.ohio-state.edu/ 2007 Gordon Conference in Plant Metabolic Engineering http://www.grc.org:80/programs.aspx?year=2007&program=plantmet -- 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 04 Mar '07

04 Mar '07

Dear All, Interesting paper ... We should start/try to think more how to study such particular issues (evolution of networks and gene duplication) as well ... Cheers, 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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