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

[Beg-sysbiol] An integrative approach to inferring biologically meaningful gene modules [BMC Sys. Biol. 2011]
by Bram Slabbinck 27 Jul '11

27 Jul '11

FYI Paper on integrating gene expression, protein interactions and GO enrichment to infer gene modules. Link: http://www.biomedcentral.com/1752-0509/5/117 regards Bram -- ========================================================== Bram Slabbinck, PhD Bioinformatics& Systems Biology Division VIB Department of Plant Systems Biology, UGent 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 ========================================================== Services and consulting in bioinformatics http://www.arctix.be ========================================================== Please consider the environment before printing this email

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[Beg-sysbiol] KEGG
by Bram Slabbinck 14 Jun '11

14 Jun '11

Hi For an Arctix project I need to list some software packages for KEGG analysis. If you have performed this kind of analysis, can you tell me which software packages you have used? thx 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 ========================================================= Services and consulting in bioinformatics http://www.arctix.be =========================================================

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[Beg-sysbiol] [article]Ancestral polyploidy in seed plants and angiosperms
by ying he 06 May '11

06 May '11

**http://www.nature.com/nature/journal/v473/n7345/full/nature09916.html Whole-genome duplication (WGD), or polyploidy, followed by gene loss and diploidization has long been recognized as an important evolutionary force in animals, fungi and other organisms^1 <http://www.nature.com/nature/journal/v473/n7345/full/nature09916.html#ref1>, 2 <http://www.nature.com/nature/journal/v473/n7345/full/nature09916.html#ref2>, 3 <http://www.nature.com/nature/journal/v473/n7345/full/nature09916.html#ref3> , especially plants. The success of angiosperms has been attributed, in part, to innovations associated with gene or whole-genome duplications^4 <http://www.nature.com/nature/journal/v473/n7345/full/nature09916.html#ref4>, 5 <http://www.nature.com/nature/journal/v473/n7345/full/nature09916.html#ref5>, 6 <http://www.nature.com/nature/journal/v473/n7345/full/nature09916.html#ref6> , but evidence for proposed ancient genome duplications pre-dating the divergence of monocots and eudicots remains equivocal in analyses of conserved gene order. Here we use comprehensive phylogenomic analyses of sequenced plant genomes and more than 12.6 million new expressed-sequence-tag sequences from phylogenetically pivotal lineages to elucidate two groups of ancient gene duplications—one in the common ancestor of extant seed plants and the other in the common ancestor of extant angiosperms. Gene duplication events were intensely concentrated around 319 and 192 million years ago, implicating two WGDs in ancestral lineages shortly before the diversification of extant seed plants and extant angiosperms, respectively. Significantly, these ancestral WGDs resulted in the diversification of regulatory genes important to seed and flower development, suggesting that they were involved in major innovations that ultimately contributed to the rise and eventual dominance of seed plants and angiosperms. -- ========================================================================================= ying he Tel:+32 (0)9 331 37 58 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM yinhe(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be/ Left brain has nothing right, right brain has nothing left. =========================================================================================

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[Beg-sysbiol] Smokey
by kenes 24 Feb '11

24 Feb '11

I'll be burdening smokey periodically really heavy this afternoon for long times (CPU, not really memory). If anyone should need smokey, let me know and I'll give smokey a breather. Kevin

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[Beg-sysbiol] Cluster jobs
by Cedric Simillion 18 Feb '11

18 Feb '11

Dear all, At the moment I'm occupying 64 cores (on 8 machines with 8 cores) on the cluster. There are still some 64-bit nodes available, but if anyone needs a large-ish number of nodes urgently, let me know and I'll kill a few of my jobs. With apologies for my computational greed, 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 ==================================================================

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[Beg-sysbiol] urgent ...
by Yves Van de Peer 18 Feb '11

18 Feb '11

Dear all, Does someone has high quality (high resolution) jpg or tiff figures of networks? We need to provide some nice figures for a University leaflet on the MRP (speerpunt). Thanks, Yves -- 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/

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[Beg-sysbiol] Plant systems biology: network matters. [Plant Cell Environ. 2011] - PubMed result
by Yves Van de Peer 13 Feb '11

13 Feb '11

http://www.ncbi.nlm.nih.gov/pubmed/21309807?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/

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[Beg-sysbiol] Fwd: Release of the AllegroMCODE plugin
by stefanie.debodt＠gmail.com 10 Feb '11

10 Feb '11

---------- Forwarded message ---------- From: Jun Yoon <junsungy...(a)gmail.com> Date: Feb 9, 9:28 am Subject: Release of the AllegroMCODE plugin To: cytoscape-announce Hi everyone, We are pleased to announce the first relase of the AllegroMCODE plugin. The AllegroMCODE plugin is a Cytoscape plugin that find clusters, or highly interconnected groups of nodes in a large complex network such as a protein interaction network and a social network. This plugin generates the same clustering results with the well-known MCODE plugin, but it can process several hundred times faster than the MCODE plugin for large complex networks by exploiting our high performance GPU computing architecture. You can also enjoy the processing speedup without any special graphics hardware since it interfaces with our free GPU computing server. Your analysis task of large complex network will be faster than ever by using the AllegroMCODE plugin. For example, it takes 0.52 seconds to find clusters from a large PPI netwrok which has 31,215 nodes and 317,706 edges by using the AllegroMCODE plugin with our free GPU computing server. Compatibility: Cytoscape 2.6, 2.7, and 2.8 Availability: through the Cytoscape plugin manager under the "Analysis" category. You can get more information from our website:http:// www.allegroviva.com/allegromcode Sincerely, Jun Yoon CEO & Co-Founder AllegroViva Corporation

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[Beg-sysbiol] figures
by Bram Slabbinck 28 Jan '11

28 Jan '11

Hi all, I am looking for some pictures for new.org stuff. If you think you have one or more nice/cool/superb/impressive/magnificent figures of a graph, network, genes, proteins, microarrays, spectrograms, etc. you can send it to me or put it in my PSB users folder. Preferably in vector format (eps, pdf)! thx a lot enjoy the weekend! 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 =========================================================

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[Beg-sysbiol] Abstract | A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation
by Klaas Vandepoele 23 Jan '11

23 Jan '11

*A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation* Nathaniel Robert Street, Stefan Jansson and Torgeir R Hvidsten BMC Plant Biology 2011, 11:13doi:10.1186/1471-2229-11-13 _Abstract_ Green plant leaves have always fascinated biologists as hosts for photosynthesis and providers of basic energy to many food webs. Today, comprehensive databases of gene expression data enable us to apply increasingly more advanced computational methods for reverse-engineering the regulatory network of leaves, and to begin to understand the gene interactions underlying complex emergent properties related to stress-response and development. These new systems biology methods are now also being applied to organisms such as Populus, a woody perennial tree, in order to understand the specific characteristics of these species. We present a systems biology model of the regulatory network of Populus leaves. The network is reverse-engineered from promoter information and expression profiles of leaf-specific genes measured over a large set of conditions related to stress and developmental. The network model incorporates interactions between regulators, such as synergistic and competitive relationships, by evaluating increasingly more complex regulatory mechanisms, and is therefore able to identify new regulators of leaf development not found by traditional genomics methods based on pair-wise expression similarity. The approach is shown to explain available gene function information and to provide robust prediction of expression levels in new data. We also use the predictive capability of the model to identify condition-specific regulation as well as conserved regulation between Populus and Arabidopsis. We outline a computationally inferred model of the regulatory network of Populus leaves, and show how treating genes as interacting, rather than individual, entities identifies new regulators compared to traditional genomics analysis. Although systems biology models should be used with care considering the complexity of regulatory programs and the limitations of current genomics data, methods describing interactions can provide hypotheses about the underlying cause of emergent properties and are needed if we are to identify target genes other than those constituting the "low hanging fruit" of genomic analysis. Fulltext: http://www.biomedcentral.com/1471-2229/11/13 Note that N. Street is an invited speaker at the Comparative & Regulatory Genomics Conference <http://bioinformatics.psb.ugent.be/crg_event/conference/about> (April 2011, Ghent) kind regards, Klaas Vandepoele

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