January 2007 - beg-sysbiol@psb.ugent.be

[Beg-sysbiol] [q-bio/0701035] Hierarchy and Feedback in the Evolution of the E. coli Transcription Network
by Tom Michoel 25 Jan '07

25 Jan '07

<http://www.arxiv.org/abs/q-bio.MN/0701035>

1 0

[Beg-sysbiol] BioMed Central | Abstract | 1471-2164-8-21 | EDGEdb: a transcription factor-DNA Interaction database for the analysis of C. elegansdifferential gene expression
by Tom Michoel 22 Jan '07

22 Jan '07

<http://www.biomedcentral.com/1471-2164/8/21/abstract> could be another useful source of validation data. tom

1 0

[Beg-sysbiol] Entrez PubMed
by Yves Van de Peer 21 Jan '07

21 Jan '07

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&dopt=Abstract&db…

1 0

[Beg-sysbiol] PLoS Biology - Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles
by Tom Michoel 15 Jan '07

15 Jan '07

<http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/…> Interesting, I think we should test Lemone on this data set ASAP. They report 80% precision for their algorithm, but at 4% recall, that's F-measure 0.076 which is not that impressive (we get 0.22 on simulated data). I wonder why they didn't include Genomica in their comparison. Was it too good? Or was it because of this: "None of the publicly available Bayesian network learning software that we tried were designed to infer a network of the size we attempted with this study, nor would they run to completion. Those that did not crash due to memory problems were unable to generate a network after several weeks of computational time." A bit hard to believe for a network of some 4000 genes. Maybe we can write a comment if Lemone performs much better than whatever Bayesian network algorithm they tested? Tom

1 0

[Beg-sysbiol] paper
by Eric Bonnet 12 Jan '07

12 Jan '07

Evolutionary conservation and over-representation of functionally enriched network patterns in the yeast regulatory network http://www.biomedcentral.com/1752-0509/1/1

1 0

[Beg-sysbiol] paper
by Eric Bonnet 05 Jan '07

05 Jan '07

Clustering of Genes into Regulons using Integrated Modeling-COGRIM http://genomebiology.com/2007/8/1/R4

1 0

[Beg-sysbiol] [q-bio/0701001] MicroRNAs preferentially target the genes with high transcriptional regulation complexity
by Tom Michoel 03 Jan '07

03 Jan '07

http://www.arxiv.org/abs/q-bio.GN/0701001 -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

1 0

[Beg-sysbiol] Entrez PubMed
by Yves Van de Peer 01 Jan '07

01 Jan '07

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&dopt=Abstract&db…

1 0

[Beg-sysbiol] Entrez PubMed
by Yves Van de Peer 01 Jan '07

01 Jan '07

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&dopt=Abstract&db…

1 0