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

[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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[Beg-sysbiol] Biclustering via optimal re-ordering of data matri...[BMC Bioinformatics. 2008] - PubMed Result
by Yves Van de Peer 02 Nov '08

02 Nov '08

http://www.ncbi.nlm.nih.gov/pubmed/18954459?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] Applying intelligent computing techniques to model...[Genomics Proteomics Bioinformatics. 2008] - PubMed Result
by Yves Van de Peer 02 Nov '08

02 Nov '08

http://www.ncbi.nlm.nih.gov/pubmed/18973867?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] Reconstruction of transcriptional dynamics from ge...[Bioinformatics. 2008] - PubMed Result
by Yves Van de Peer 02 Nov '08

02 Nov '08

http://www.ncbi.nlm.nih.gov/pubmed/18974172?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] Could you guys (and girls) please read and comment?
by Yves Van de Peer 29 Oct '08

29 Oct '08

-------- Original Message -------- Subject: Networks from gene duplication -- project proposal Date: Wed, 8 Oct 2008 16:16:09 +0200 From: Zoran Nikoloski <Nikoloski(a)mpimp-golm.mpg.de> To: yves.vandepeer(a)psb.ugent.be <yves.vandepeer(a)psb.ugent.be> CC: Joachim Selbig <Selbig(a)mpimp-golm.mpg.de> Dear Prof. Van de Peer, During the Workshop "Evolution across Scales" which took in Potsdam, we had a discussion about possible collaboration with your group. At that time, we agreed that Prof. Selbig's group can prepare a write-up of possible problems/methods/proposed approaches on which the two groups could proceed working together. Included here, please, find the proposal of methods and approaches that we see suitable for analysis of networks obtained from gene duplication. We hope you would find the ideas (presented in the proposal) interesting and worth applying to the corpus of data on gene duplication from your research. I would appreciate it if you could let us know how we could proceed from here. Regards, Zoran Nikoloski post-doc in Prof. Selbig's group Institute of Biology and Biochemistry University Potsdam Max-Planck Institute for Molecular Plant Physiology This email was Anti Virus checked by the MPIMP-Golm Astaro Security Gateway. -- 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] at home this morning
by Eric Bonnet 28 Oct '08

28 Oct '08

hi there, I've been badly sick yesterday evening, some kind of food poisoning, I believe, so I'll stay at home this morning. Yves, I'll be there for the meeting this afternoon, no problemo. Eric

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