November 2008 - beg-sysbiol@psb.ugent.be

[Beg-sysbiol] post-conference get-together?
by Tom Michoel 04 Dec '08

04 Dec '08

Sysbiol was all over the place last month, Anagha to Malaga, Nathalie & Tom to Bostom and Ying, Stephanie, Eric & Greg to Heidelbreg. Should we have a lazy friday afternoon meeting to keep each other up to date of what's going on in the rest of the world? Tom -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] might be interesting!
by Yves Van de Peer 27 Nov '08

27 Nov '08

-------- Original Message -------- Subject: Weekly Science Meeting CANCELLED Date: Thu, 27 Nov 2008 11:54:55 +0100 From: Nathalie Vanden Hautte <nahau(a)psb.UGent.be> To: <all(a)psb.ugent.be> Dear all, *This week’s Science Meeting has been cancelled.* Tomorrow, Friday 28^th November, Jonathan M. Flowers will give a talk at 10 am in the seminar room. The title of his talk is: “Adaptation and evolutionary constraint in the evolution of genetic networks”. You can find more details on the announcement enclosed. The next Weekly Science Meeting will be held on *5^th **December 2008*** at *12:00* in the meeting room Leaf. Jeffrey Fawcett will give a talk. The title of his presentation is: /Did plants with double genomes have a better chance to survive the Cretaceous–Tertiary extinction event?/ Please find herewith the planning for the upcoming Science Meetings: 12^th December Tim Lammens 19^th December/ no talk planned: Lab Meeting /26^th December/ no talk planned: Boxing Day/ In case you are interested in giving a talk next year (starting 16^th January 2009), please let Sofie Goormachtig (sogoo(a)psb.ugent.be <mailto:sogoo@psb.ugent.be>) and me know so we can add your name to the schedule. Thank you in advance for your reply. With kind regards, For Dirk and Sofie Nathalie __________________________________________ Nathalie Vanden Hautte Administrative Assistant VIB Department of Plant Systems Biology, UGent Technologiepark 927 9052 Gent (Zwijnaarde) Belgium Tel: +32 / 9 33 13 800 Fax: +32 / 9 33 13 809 Http://www.psb.ugent.be -- 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.ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-sysbiol] ice
by Eric Bonnet 25 Nov '08

25 Nov '08

I'll come later to the lab, since I'm not much of a ice-skater I'm waiting for the ice to melt... ;-) Eric

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[Beg-sysbiol] [Fwd: Talk on system theory and control for biochemical systems 02/12/08]
by Tom Michoel 18 Nov '08

18 Nov '08

-------- Original Message -------- Subject: Talk on system theory and control for biochemical systems 02/12/08 Date: Tue, 18 Nov 2008 11:30:20 +0100 (Romance Standard Time) From: Jonathan Rogge <Jonathan.Rogge(a)UGent.be> To: yvpee(a)psb.ugent.be, tomic(a)psb.ugent.be, krwab(a)psb.ugent.be, willy.govaerts(a)Ugent.be, leila.kheibarshekanasl(a)ugent.be, researchers(a)systems.ugent.be CC: margot.roels(a)ugent.be Dear colleagues, I would like to inform you of a lecture taking place at the SYSTeMS Research group, titled "Problems of control and system theory for biochemical reaction systems". Speaker is prof. Jan van Schuppen, who is affiliated with the CWI and Vrije Universiteit Amsterdam. An abstract of the talk is added below. The talk will take place on December 2nd, Tuesday afternoon at 2.30pm in the classroom on the 2nd floor of building 914 at Technologiepark Zwijnaarde. Kind regards, Jonathan Rogge ======================== Problems of control and system theory for biochemical reaction systems Jan H. van Schuppen (CWI/VU University Amsterdam) Progress in the life sciences can benefit, besides experimental and descriptive research, from the mathematical sciences for modeling, system identification, system theory, and control theory. The following research issues will be discussed during the lecture: (a) Modeling of glycolysis in Trypanosoma brucei and of part of the genetic network of Escherichia coli in regard to nitrogen assimilation. (b) Biochemical reaction systems and their algebraic properties. (c) Modeling of very large biochemical reaction systems preferably of the complete cell by methods of hierarchical system theory, modularity, and algebraic decomposition. (d) System identification of rational (positive) systems. (e) System reduction of biochemical reaction systems. (f) Control for biotechnology including rational drug design and production of food substances. -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] A protocol for unraveling gene regulatory networks. [Nat Protoc. 2008] - PubMed Result
by Yves Van de Peer 16 Nov '08

16 Nov '08

http://www.ncbi.nlm.nih.gov/pubmed/19008874?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.ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-sysbiol] @home
by Eric Bonnet 13 Nov '08

13 Nov '08

hi there, I'll be working at home this morning. Eric

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[Beg-sysbiol] PLoS Computational Biology: Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals
by Tom Michoel 07 Nov '08

07 Nov '08

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371% 2Fjournal.pcbi.1000216 When Noam Kaplan was in Leuven, he mentioned they were having difficulty getting their paper in one of the Nature journals. I wonder if this is that paper? Tom -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] An in silico method for detecting overlapping functional modules from composite biological networks
by Klaas Vandepoele 05 Nov '08

05 Nov '08

Might be applicable to find overlapping modules in coexpression networks (given that it works with a weighted graph). http://www.biomedcentral.com/1752-0509/2/93/abstract Research article An in silico method for detecting overlapping functional modules from composite biological networks *Ioannis A Maraziotis* email <http://www.biomedcentral.com/logon/logon.asp?msg=ce>, *Konstantina Dimitrakopoulou* email <http://www.biomedcentral.com/logon/logon.asp?msg=ce> and *Anastasios Bezerianos* email <http://www.biomedcentral.com/logon/logon.asp?msg=ce> /BMC Systems Biology/ 2008, *2**:*93doi:10.1186/1752-0509-2-93 Published: 1 November 2008 Abstract (provisional) Background The ever-increasing flow of gene expression and protein-protein interaction (PPI) data has assisted in understanding the dynamics of the cell. The detection of functional modules is the first step in deciphering the apparent modularity of biological networks. However most network-partitioning algorithms consider only the topological aspects and ignore the underlying functional relationships. Results In the current study we integrate proteomics and microarray data of yeast, in the form of a weighted PPI graph. We partition the enriched PPI network with the novel DetMod algorithm and we identify 335 modules. One of the main advantages of DetMod is that it manages to capture the inter-module cross-talk by allowing a controlled degree of overlap among the detected modules. The obtained modules are densely connected in terms of protein interactions, while their members share up to a high degree similar biological process GO terms. Moreover, known protein complexes are largely incorporated in the assessed modules. Finally, we display the prevalence of our method against modules resulting from other computational approaches. Conclusions The successful integration of heterogeneous data and the concept of the proposed algorithm provide confident functional modules. We also proved that our approach is superior to methods restricted to PPI data only.

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[Beg-sysbiol] back in town
by Tom Michoel 05 Nov '08

05 Nov '08

Not sure when I'll make it to the lab though: part of my luggage got lost in hyperspace and is supposed to make its way home sometime tomorrow. Tom -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] @home
by Eric Bonnet 04 Nov '08

04 Nov '08

hi there, I'll be working at home this morning. see you guys this afternoon. Eric

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