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

[Beg-sysbiol] A stele-enriched gene regulatory network in the Arabidopsis root
by Klaas Vandepoele 19 Jan '11

19 Jan '11

A stele-enriched gene regulatory network in the Arabidopsis root Siobhan M Brady^1 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a1>, ^2 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a2> , Lifang Zhang^3 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a3> , Molly Megraw^4 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a4> , Natalia J Martinez^5 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a5> , Eric Jiang^1 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a1> , Charles S Yi^1 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a1> , Weilin Liu^1 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a1> , Anna Zeng^2 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a2> , Mallorie Taylor-Teeples^2 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a2> , Dahae Kim^2 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a2> , Sebastian Ahnert^6 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a6> , Uwe Ohler^4 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a4> , Doreen Ware^3 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a3>, ^7 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a7> , Albertha J M Walhout^5 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a5> & Philip N Benfey^1 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a1> <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#top>*Abstract* Tightly controlled gene expression is a hallmark of multicellular development and is accomplished by transcription factors (TFs) and microRNAs (miRNAs). Although many studies have focused on identifying downstream targets of these molecules, less is known about the factors that regulate their differential expression. We used data from high spatial resolution gene expression experiments and yeast one-hybrid (Y1H) and two-hybrid (Y2H) assays to delineate a subset of interactions occurring within a gene regulatory network (GRN) that determines tissue-specific TF and miRNA expression in plants. We find that upstream TFs are expressed in more diverse cell types than their targets and that promoters that are bound by a relatively large number of TFs correspond to key developmental regulators. The regulatory consequence of many TFs for their target was experimentally determined using genetic analysis. Remarkably, molecular phenotypes were identified for 65% of the TFs, but morphological phenotypes were associated with only 16%. This indicates that the GRN is robust, and that gene expression changes may be canalized or buffered. http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html

2 2

[Beg-sysbiol] Network medicine: a network-based approach to huma... [Nat Rev Genet. 2011] - PubMed result
by Yves Van de Peer 20 Dec '10

20 Dec '10

http://www.ncbi.nlm.nih.gov/pubmed/21164525?dopt=Abstract -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Associate Department Director, VIB Department of Plant Systems Biology Group Leader Bioinformatics and 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.vib-ugent.be http://bioinformatics.psb.ugent.be/ Check out! http://www.plantgenomeevolution.com/

1 0

[Beg-sysbiol] Abstract | 2R and remodeling of vertebrate signal transduction engine
by Yves Van de Peer 20 Dec '10

20 Dec '10

http://www.biomedcentral.com/1741-7007/8/146 -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Associate Department Director, VIB Department of Plant Systems Biology Group Leader Bioinformatics and 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.vib-ugent.be http://bioinformatics.psb.ugent.be/ Check out! http://www.plantgenomeevolution.com/

1 0

[Beg-sysbiol] Scientists see fatal flaws in the NASA study of arsenic-based life.
by Cedric Simillion 08 Dec '10

08 Dec '10

It seems that some people are highly sceptical (or jealous?) about last week's Science paper on arsenic-base life. http://www.slate.com/id/2276919/pagenum/all/ Enjoy! Cedric -- ================================================================== Cedric Simillion, 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 http://bioinformatics.psb.ugent.be ==================================================================

1 0

[Beg-sysbiol] Reverse Engineering the Yeast RNR1 Transcriptional... [PLoS One. 2010] - PubMed result
by Yves Van de Peer 30 Nov '10

30 Nov '10

http://www.ncbi.nlm.nih.gov/pubmed/21103376?dopt=Abstract -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Associate Department Director, VIB Department of Plant Systems Biology Group Leader Bioinformatics and 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.vib-ugent.be http://bioinformatics.psb.ugent.be/

1 0

[Beg-sysbiol] anyone?
by Yves Van de Peer 19 Nov '10

19 Nov '10

-------- Original Message -------- Subject: SOM analysis Date: Mon, 25 Oct 2010 23:13:15 -0400 From: Gustavo Acevedo <gacevedo(a)uwo.ca> To: yves.vandepeer(a)psb.ugent.be, Miodrag Grbic <mgrbic(a)uwo.ca>, Vojislava Grbic <vgrbic(a)uwo.ca> Dear Yves, I have been using SOM as a clustering technique for the analysis of our expression data in the Arabidopsis response to spider mites. This method has been applied in the analysis of other microarray data and seems to be quite useful in determining differences in the expression profile of a defined group of genes. My knowledge on this analysis is limited to the way it has been used in published papers (attached) and I have done some initial attempts to apply it to our data set (which I showed during the meeting in Montenegro). I would like to perform this analysis in such a way that give us confidence on the information we can get from it. I would really appreciate if you could refer me to someone in your group with experience in this kind of analysis who could help me out. Best regards, Gustavo -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Associate Department Director, VIB Department of Plant Systems Biology Group Leader Bioinformatics and 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.vib-ugent.be http://bioinformatics.psb.ugent.be/

1 0

[Beg-sysbiol] RiboSys, a high-resolution, quantitative approach to measure the in vivo kinetics of pre-mRNA splicing and 3'-end processing in Saccharomyces cerevisiae.
by Pierre Rouze 31 Oct '10

31 Oct '10

http://www.ncbi.nlm.nih.gov/pubmed/20974745?dopt=Abstract This system permits pre-mRNA production, splicing, 3'-end maturation and degradation to be quantitatively monitored with unprecedented kinetic detail, suitable for mathematical modeling. for the ones willing to build a gene expression model that goes beyond transcription ;-) -- Pierre ROUZE Bioinformatics / Senior Expert Scientist VIB Department of Plant Systems Biology Ghent University Technologie park 927, B-9052 GENT BELGIUM Tel :32.933 13694 Cell.Phone : 32.476 638 304 Fax :32.933 13809 pierre.rouze(a)psb.vib-ugent.be http://www.psb.ugent.be/bioinformatics ¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨ prediction is very difficult, especially about the future Niels Bohr

1 0

[Beg-sysbiol] Interactional and functional centrality in transcriptional co-expression networks [Bioinformatics]
by Bram Slabbinck 21 Oct '10

21 Oct '10

FYI http://bioinformatics.oxfordjournals.org/content/early/2010/10/19/bioinform… (if you want to print it, take a coffee because it takes more than 5 minutes...) Bram -- ========================================================= Bram Slabbinck, PhD Bioinformatics & Systems Biology VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM Tel:+32 (0)9 33 13 822 Fax:+32 (0)9 33 13 809 Email: Bram.Slabbinck(a)psb.ugent.be WWW: http://bioinformatics.psb.ugent.be =========================================================

2 2

[Beg-sysbiol] Spring printer out of order
by Cedric Simillion 08 Oct '10

08 Oct '10

Dear all, In preparation of this afternoon's IWT session, I wanted to print out Ken's project. Apparently, spring doesn't like Ken's project, because I got an "900.43 Service RIP Software" error on the display. I'm afraid that means that spring will be out of order for a while, if it hasn't gone to meet its maker entirely. Cedric -- ================================================================== Cedric Simillion, 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 http://bioinformatics.psb.ugent.be ==================================================================

4 3

[Beg-sysbiol] Abstract | Inferring the conservative causal core of gene regulatory networks
by Klaas Vandepoele 05 Oct '10

05 Oct '10

includes a comparison of some gene regulatory network inference algorithms http://www.biomedcentral.com/1752-0509/4/132/abstract

1 0