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

[Beg-sysbiol] guidelines examination surveillance
by Vanessa Vermeirssen 20 Jun '14

20 Jun '14

Hi, the program in Biochemistry and Biotechnology has recently spread new rules regarding examination surveillance (see attachment). I invite everybody who will supervise exams to read these thoroughly through. In case of unclarity or when immediate action is required, it is advisable to contact the course coordinator. Best regards, Vanessa -- ===================================================================== Vanessa Vermeirssen, PhD Tel:+32 (0)9 331 35 36 Fax:+32 (0)9 331 38 09 Bioinformatics and Systems Biology VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM room V311 vamei(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be/ ======================================================================

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[Beg-sysbiol] Paper: Combine Expression Data,and Protein–Protein Interaction Networks in Agrigenomics
by Bram Slabbinck 06 Jan '14

06 Jan '14

FYI An Integrated Approach (CLuster Analysis,Integration Method) to Combine Expression Data,and Protein–Protein Interaction Networks in Agrigenomics: Application on Arabidopsis thaliana http://online.liebertpub.com/doi/pdf/10.1089/omi.2013.0050 Abstract: Experimental co-expression data and protein–protein interaction networks are frequently used to analyze the interactions among genes or proteins. Recent studies have investigated methods to integrate these two sources of information. We propose a new method to integrate co-expression data obtained through DNA microarray analysis (MA) and protein–protein interaction (PPI) network data, and apply it to Arabidopsis thaliana. The proposed method identiﬁes small subsets of highly interacting proteins. Based on the analysis of the basis of co- localization and mRNA developmental expression, we show that these groups provide important biological insights; additionally, these subsets are signiﬁcantly enriched with respect to KEGG Pathways and can be used to predict successfully whether proteins belong to known pathways. Thus, the method is able to provide relevant biological information and support the functional identiﬁcation of complex genetic traits of economic value in plant agrigenomics research. The method has been implemented in a prototype software tool named CLAIM (CLuster Analysis Integration Method) and can be downloaded from http://bio.cs.put.poznan.pl/ research_ﬁelds. CLAIM is based on the separate clustering of MA and PPI data; the clusters are merged in a special graph; cliques of this graph are subsets of strongly connected proteins. The proposed method was successfully compared with existing methods. CLAIM appears to be a useful semi-automated tool for protein functional analysis and warrants further evaluation in agrigenomics research. -- ========================================================== Bram Slabbinck, PhD VIB Department of Plant Systems Biology, UGent Technologiepark 927, 9052 Gent, BELGIUM Tel:+32 (0)9 33 13 537 Fax:+32 (0)9 33 13 809 Email: Bram.Slabbinck(a)psb.ugent.be WWW: http://www.psb.ugent.be ========================================================== Please consider the environment before printing this email

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[Beg-sysbiol] cytoscape 3D
by Bram Slabbinck 14 Nov '13

14 Nov '13

fyi new tool for cytoscape in 3D: http://scape3d.sourceforge.net/ http://www.biomedcentral.com/1471-2105/14/322/abstract -- ========================================================== Bram Slabbinck, PhD VIB Department of Plant Systems Biology, UGent Technologiepark 927, 9052 Gent, BELGIUM Tel:+32 (0)9 33 13 537 Fax:+32 (0)9 33 13 809 Email: Bram.Slabbinck(a)psb.ugent.be WWW: http://www.psb.ugent.be ========================================================== Please consider the environment before printing this email

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[Beg-sysbiol] Mapping functional transcription factor networks from gene expression data
by Klaas Vandepoele 06 Aug '13

06 Aug '13

http://genome.cshlp.org/content/23/8/1319.full -- Prof. Dr. Klaas Vandepoele Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.vib-ugent.be Website: http://bioinformatics.psb.ugent.be/cig/ Twitter: http://twitter.com/plaza_genomics ---------------------------------------------------------

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[Beg-sysbiol] Joint EMBL-EBI-Wellcome Trust Course: In Silico Systems Biology | Training
by Klaas Vandepoele 28 Jun '13

28 Jun '13

http://www.ebi.ac.uk/training/course/joint-embl-ebi-wellcome-trust-course-s… -- Prof. Dr. Klaas Vandepoele Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.vib-ugent.be Website: http://bioinformatics.psb.ugent.be/cig/ Twitter: http://twitter.com/plaza_genomics ---------------------------------------------------------

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[Beg-sysbiol] Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules
by Klaas Vandepoele 11 Jun '13

11 Jun '13

*Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules* Sushmita Roy1,2,6,7, Ilan Wapinski1,3, Jenna Pfiffner1, Courtney French1, Amanda Socha1, Jay Konieczka1, Naomi Habib4, Manolis Kellis1,2, Dawn Thompson1 and Aviv Regev1,5,7 Abstract Comparative functional genomics studies the evolution of biological processes by analyzing functional data, such as gene expression profiles, across species. A major challenge is to compare profiles collected in a complex phylogeny. Here, we present Arboretum, a novel scalable computational algorithm that integrates expression data from multiple species with species and gene phylogenies to infer modules of coexpressed genes in extant species and their evolutionary histories. We also develop new, generally applicable measures of conservation and divergence in gene regulatory modules to assess the impact of changes in gene content and expression on module evolution. We used Arboretum to study the evolution of the transcriptional response to heat shock in eight species of Ascomycota fungi and to reconstruct modules of the ancestral environmental stress response (ESR). We found substantial conservation in the stress response across species and in the reconstructed components of the ancestral ESR modules. The greatest divergence was in the most induced stress, primarily through module expansion. The divergence of the heat stress response exceeds that observed in the response to glucose depletion in the same species. Arboretum and its associated analyses provide a comprehensive framework to systematically study regulatory evolution of condition-specific responses. http://genome.cshlp.org/content/23/6/1039.abstract -- Prof. Dr. Klaas Vandepoele Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.vib-ugent.be Website: http://bioinformatics.psb.ugent.be/cig/ Twitter: http://twitter.com/plaza_genomics ---------------------------------------------------------

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[Beg-sysbiol] RNA-seq analysis of allele-specific expression, hybrid effects and regulatory divergence...
by Bram Slabbinck 22 May '13

22 May '13

paper of keith http://gbe.oxfordjournals.org/content/early/2013/05/14/gbe.evt072.full.pdf+… -- ========================================================== Bram Slabbinck, PhD Bioinformatics & Systems Biology Division VIB Department of Plant Systems Biology, UGent Technologiepark 927, 9052 Gent, BELGIUM Tel:+32 (0)9 33 13 537 Fax:+32 (0)9 33 13 809 Email: Bram.Slabbinck(a)psb.ugent.be WWW: http://bioinformatics.psb.ugent.be ========================================================== Please consider the environment before printing this email

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[Beg-sysbiol] sysbiol share
by Vanessa Vermeirssen 09 Apr '13

09 Apr '13

Dear all, we have noticed that the sysbiol share is quite full and some folders/files are old and from previous persons in the lab. Could you indicate to Luc if you know of a folder that can be archived? Luc, according to me (others: correct me if I am wrong), the following folders can be archived: arabidopsis ath_cc ath_stress Brainstorm_2010 Chris_Town_data cropdesign_test cytoscape_anjos doc DREAM2/4/5/6 Gasch_trial IntroBioinfo-2010 macro MolBioSyst52009 napoc PNS sabot vamei/microarray vamei/ModuleNetwork2007 vamei/tabaccometab xiren yinghe Best regards, Vanessa -- ===================================================================== Vanessa Vermeirssen, PhD Tel:+32 (0)9 331 35 36 Fax:+32 (0)9 331 38 09 Bioinformatics and Systems Biology VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM room V311 vamei(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be/ ======================================================================

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[Beg-sysbiol] genefriends
by Bram Slabbinck 11 Feb '13

11 Feb '13

fyi http://genefriends.org/ GeneFriends is a functional genomics tool aimed at biologists and clinicians. It is based on a gene co-expression map that describes which genes tend to be activated (increase in expression) and deactivated (decrease in expression) simultaneously in a large number of microarray datasets. Because the microarray datasets come from a wide range of conditions, the co-expression map reflects which genes in general tend to be activated simultaneously and are thus under similar transcriptional regulation. This information can be used statistically, using a guilt-by-association approach, to identify and prioritize novel candidate genes involved in biological processes and complex diseases for which a seed list of genes associated with that disease or process is available. It can also be used to gain insights on genes of unknown function by looking at which genes they are co-expressed with. -- ========================================================== Bram Slabbinck, PhD Bioinformatics & Systems Biology Division VIB Department of Plant Systems Biology, UGent Technologiepark 927, 9052 Gent, BELGIUM Tel:+32 (0)9 33 13 537 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] next-gen ontology
by Bram Slabbinck 30 Jan '13

30 Jan '13

fyi http://www.nature.com/nmeth/journal/v10/n2/full/nmeth.2353.html An approach to cluster and organize systems biology data yields NeXO, a data-driven ontology. Where biology was small before, it now is frequently large. Data points have become data sets. Research studies now commonly examine not just one gene or protein but all of them. It has become a truism to say that this situation produces formidable challenges when it comes to analysis of the resulting vast data sets. The Gene Ontology (GO) has proven to be a widely used resource for analyzing systems biology data. Built manually from the literature by expert curators, GO attempts to synthesize available biological knowledge into an organized hierarchy of biological terms, linking genes to function. Large-scale data sets are frequently analyzed in light of GO to assess whether they capture meaningful patterns of gene function. In a recently published study, Trey Ideker and Janusz Dutkowski at the University of California, San Diego, and their colleagues, effectively turn this way of thinking on its head. They explore, in other words, whether 'omics' data sets themselves have meaningful ontological structure, akin to that of GO, and whether methods can be found to reveal it. The result is a parallel ontology to GO, which they call the network-extracted ontology, or NeXO. -- ========================================================== Bram Slabbinck, PhD Bioinformatics & Systems Biology Division VIB Department of Plant Systems Biology, UGent Technologiepark 927, 9052 Gent, BELGIUM Tel:+32 (0)9 33 13 537 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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