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

[Beg-sysbiol] The road to modularity. [Nat Rev Genet. 2007] - PubMed Result
by Yves Van de Peer 16 Dec '07

16 Dec '07

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&dopt=AbstractPlus&db=… -- 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] DREAM conference
by Tom Michoel 13 Dec '07

13 Dec '07

Hi, If you're interested, I got a copy of the proceedings of last year's DREAM conference (see <http://www.nyas.org/annals/detail.asp?annalID=891>). Vanessa asked for a small presentation of last week's conference. We would do it next week friday. Anyone else wants to join? Tom -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] [Fwd: ENFIN-DREAM meeting - Madrid - April 28-29, 2008]
by Yves Van de Peer 12 Dec '07

12 Dec '07

-------- Original Message -------- Subject: ENFIN-DREAM meeting - Madrid - April 28-29, 2008 Date: Tue, 11 Dec 2007 16:59:19 -0500 From: Gustavo Stolovitzky <gustavo(a)us.ibm.com> To: DREAM2 Call For Participation <DREAM2_Call_For_Participation%IBMUS(a)us.ibm.com> Sent on behalf of Pascal Kahlem ------------------------------- Dear colleagues, I would like to announce that the ENFIN-DREAM meeting on "assessment of computational methods in systems biology" will be hosted by Alfonso Valencia at CNIO in Madrid on April 28-29, 2008. Registrations are now possible from the webpage: http://www.enfin.org/page.php?page=enfin_dream There is also the possibility to apply abstracts for posters or for talks. Best regards, Pascal ________________________________________________________________________ Dr. Pascal KAHLEM Project Manager European Network of Excellence ENFIN on Systems Biology - www.enfin.org EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Line +44(0)1223492588 / Mob +49(0)1799582064 / Fax +44(0)1223494468 Email: pkahlem(a)ebi.ac.uk / Skype: pascalkahlem ________________________________________________________________________ -- 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] new share
by Eric Bonnet 12 Dec '07

12 Dec '07

hi there, The new sysbiol unix shared directory is almost ready. The new location will be /group/sysbiol. I propose to do the final move next week monday. The old location /group/biocomp/projects/segal will be set read-only monday morning, so it would be better not to create new files in the old location at that time (i.e. no job on the cluster producing an output on the old location). Please do not use the new location before monday. Eric

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[Beg-sysbiol] Evolutionary models for formation of network motif...[PLoS Comput Biol. 2007] - PubMed Result
by Yves Van de Peer 09 Dec '07

09 Dec '07

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&dopt=AbstractPlus&db=… -- 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] Using Likelihood-Free Inference to Compare Evoluti...[PLoS Comput Biol. 2007] - PubMed Result
by Yves Van de Peer 09 Dec '07

09 Dec '07

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&dopt=AbstractPlus&db=… -- 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] Network Inference, Analysis, and Modeling in Systems Biology
by Tom Michoel 07 Dec '07

07 Dec '07

http://www.plantcell.org/cgi/rapidpdf/tpc.107.054700v1 -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] fyi :: Predicting Gene Expression from Sequence: A Reexamination
by Klaas Vandepoele 03 Dec '07

03 Dec '07

*Predicting Gene Expression from Sequence: A Reexamination* Yuan Yuan, Lei Guo, Lei Shen, Jun S. Liu* Department of Statistics, Harvard University, Cambridge, Massachusetts, United States of America Although much of the information regarding genes' expressions is encoded in the genome, deciphering such information has been very challenging. We reexamined Beer and Tavazoie's (BT) approach to predict mRNA expression patterns of 2,587 genes in Saccharomyces cerevisiae from the information in their respective promoter sequences. Instead of fitting complex Bayesian network models, we trained na?¨ve Bayes classifiers using only the sequence-motif matching scores provided by BT. Our simple models correctly predict expression patterns for 79% of the genes, based on the same criterion and the same cross-validation (CV) procedure as BT, which compares favorably to the 73% accuracy of BT. The fact that our approach did not use position and orientation information of the predicted binding sites but achieved a higher prediction accuracy, motivated us to investigate a few biological predictions made by BT. We found that some of their predictions, especially those related to motif orientations and positions, are at best circumstantial. For example, the combinatorial rules suggested by BT for the PAC and RRPE motifs are not unique to the cluster of genes from which the predictive model was inferred, and there are simpler rules that are statistically more significant than BT's ones. We also show that CV procedure used by BT to estimate their method's prediction accuracy is inappropriate and may have overestimated the prediction accuracy by about 10%. http://compbiol.plosjournals.org/archive/1553-7358/3/11/pdf/10.1371_journal… -- ================================================================== Klaas Vandepoele, PhD 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.ugent.be Website: http://bioinformatics.psb.ugent.be/ ==================================================================

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[Beg-sysbiol] lemone update
by Eric Bonnet 21 Nov '07

21 Nov '07

Hi there, I updated the bingo class again, with some fresh code from Steven: - bingo parameters are read directly from the jar file, - some bingo param. are then overridden by values specified in the lemone property file (species, annotation file name, etc..) - output is now one (big) file for each module set, written in the bingo_results directory (created in the current directory). Be sure to link to the latest bingo jar file which is in: /group/biocomp/projects/segal/java/lib/BiNGO_11-2007/BiNGO.jar Bingo parameters example: #BiNGO parameters BiNGO=true signif_def=0.05 annotation_file_def=A_thaliana_default ontology_file_def=GO_Biological_Process annotation_default=true ontology_default=true -- Eric

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[Beg-sysbiol] This is (one of the things) that I hope we can start doing as well in the near future ...
by Yves Van de Peer 21 Nov '07

21 Nov '07

http://www.biomedcentral.com/1752-0509/1/49 -- 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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