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

[Beg-sysbiol] gene regulatory networks [bioinformatics 2010]
by Bram Slabbinck 19 Jul '10

19 Jul '10

FYI Two papers on gene regulatory networks published in bioinformatics: - http://bioinformatics.oxfordjournals.org/cgi/content/full/26/15/1879 - http://bioinformatics.oxfordjournals.org/cgi/reprint/btq421v1 regards Bram ========================================================= ir. 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 =========================================================

1 0

[Beg-sysbiol] Fwd: Re: Apple full transcripts array
by Yves Van de Peer 09 Jul '10

09 Jul '10

-------- Original Message -------- Subject: Re: Apple full transcripts array Date: Fri, 9 Jul 2010 13:51:54 +0200 From: Jean-Pierre Renou <jeprenou(a)angers.inra.fr> To: Yves Van de Peer <yves.vandepeer(a)psb.vib-ugent.be> CC: jean-pierre renou <renou(a)evry.inra.fr>, rogerb(a)u.washington.edu, riccardo.velasco(a)iasma.it, Jean-Marc Celton <jcelton(a)mail.biotech.uwc.ac.za>, zharkikh(a)myriad.com, michael.egholm(a)roche.com, sgardiner(a)hortresearch.co.nz, Charles Eric Durel <Charles-Eric.Durel(a)angers.inra.fr>, laurens <francois.laurens(a)angers.inra.fr>, Elisabeth Chevreau <chevreau(a)angers.inra.fr>, bogden(a)genomex.com, yves.vandepeer(a)psb.ugent.be, ananth(a)eecs.wsu.edu, rhellens(a)hortresearch.co.nz, stefano.toppo(a)unipd.it, martin.kater(a)unimi.it, alessandra.stella(a)tecnoparco.org, durel <durel(a)angers.inra.fr> Dear Yves For sure I will keep you informed, it is obvious that we can make significant benefits by joining our efforts and expertise to make sense of the data. Currently I am just beginning to work on apple in Angers, so I need few months to set up the probe design. My plan is to produce numerous apple transcriptome data with the chips in 2011 on dozens of samples. If the other apple-scientists plan to use the same array for their experiments and are interested to share the results, we can expect to begin meta-analyses quite soon. I will do my best to be as quick as possible, we do have numerous samples in the -80°C already waiting for us. Best regards JP Le 9 juil. 2010 à 08:58, Yves Van de Peer a écrit : > > Dear all, > > For what it's worth, we would be highly interested in having a look > at such transcriptome data for apple, with the aim to reconstruct > transcriptional regulatory networks. Recently, we have developed > sophisticated software to identify regulators such as transcription > factors, signal transducers, but also microRNAs, based on > transcriptome and other data. Please keep us in the loop if you > think we might be able to help or if you'd like to collaborate on > such a 'transcriptome' project. > > Best regards, > > Yves >> Dear colleague >> Charles-Eric Durel informed me that you expect to have very soon an >> apple microarray based on the genome sequence. Actually I am deeply >> involved in functional genomics and transcriptomics since numerous >> years (http://www.versailles.inra.fr/urgv/renou.htm) and I will >> join the "Genhort" laboratory of Angers, to work on apple, next >> month. Indeed we had exactly the same feeling as you, and I got >> financial support from INRA to design a full transcript microarray >> based on on the genome sequence very soon. We totally agree with >> you that such a powerful tool should be available for the whole >> apple community without restriction. Moreover we all know that we >> can expect much more power in the future meta-analyse we could plan >> if we avoid to multiply the platforms, the homogeneity of the data >> being a guarantee of quality. >> We think that, regarding to high throughput sequencing methods >> which are supposed to be more powerful in terms of gene discovery >> (yet not so sure for transcript quantification), the major interest >> of a microarray remains its low price. This would provide the >> opportunity to analyze hundreds of samples such as many biological >> replicates, time course experiments, various types of samples etc >> etc...... The higher is the quantity of analysed samples, the >> higher is the value of a transcriptomic resource! For this reasons, >> after having considered all the possibilites, we are most in favour >> of the "Maskless Arrays Synthetiser" technology which provides very >> cheap, powerful and evolutive chips. Currently we have very good >> experiences with the new multiplex Nimblegen chips (12 X 120.000 >> probes) which would provide full transcript arrays for 85€ per >> unit. Agilent chips are good too and use the same technology but >> are more expensive and provide less probes per unit. The same for >> Illumina (which are rather cheap). Affymetrix chips are definetely >> expensive and not evolutive, due to the Mask technology. The >> bioinformatic team of my current lab has developed an algorithm >> (derived from SPDAS, Thareau et al. 2003) to design very specific >> oligoprobes that we plan to use, because Nimblegen doesn't have >> such skills (at least it's that they told us). >> François Laurens and I will meet Ricardo and his staff next July to >> discuss all these points and to optimize our collaboration. If you >> are interested by this initiative we would be happy to share this >> resource with you and all the apple community. I am pretty sure >> that we can all make a very good job altogether and make fast >> progress in terms of deciphering apple gene regulation networks, >> thanks to the highly valuable genetic resources already available. >> I think that it would be a nice opportunity to meet altogether >> during the next Rosacae Symposium in SA. Maybe we could organize a >> workshop? >> Best Regards >> Jean Pierre >> > > > -- > 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/ >

1 0

[Beg-sysbiol] Revisiting date and party hubs: novel approaches t... [PLoS Comput Biol. 2010] - PubMed result
by Yves Van de Peer 09 Jul '10

09 Jul '10

http://www.ncbi.nlm.nih.gov/pubmed/20585543?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/

1 0

[Beg-sysbiol] BioMed Central | Full text | Duplicability of self-interacting human genes
by Klaas Vandepoele 01 Jul '10

01 Jul '10

http://www.biomedcentral.com/1471-2148/10/160 -- 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.vib-ugent.be Website: http://bioinformatics.psb.ugent.be/ --------------------------------------------------------- PLAZA, a resource for Plant Comparative Genomics http://bioinformatics.psb.ugent.be/plaza/ ---------------------------------------------------------

1 0

[Beg-sysbiol] tornado
by Klaas Vandepoele 23 Jun '10

23 Jun '10

Dear all, I will use tornado for approx. 24h to do some high-memory calculations. best, Klaas -- 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.vib-ugent.be Website: http://bioinformatics.psb.ugent.be/ --------------------------------------------------------- PLAZA, a resource for Plant Comparative Genomics http://bioinformatics.psb.ugent.be/plaza/ ---------------------------------------------------------

1 0

[Beg-sysbiol] svdPPCS: ... method for conserved and divergent co-expression gene module identification (Paper)
by Bram Slabbinck 22 Jun '10

22 Jun '10

fyi http://www.biomedcentral.com/1471-2105/11/338 regards Bram -- ========================================================= ir. 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 =========================================================

1 0

[Beg-sysbiol] Deciphering the Arabidopsis Floral Transition Proc... [Plant Physiol. 2010] - PubMed result
by Yves Van de Peer 13 Jun '10

13 Jun '10

http://www.ncbi.nlm.nih.gov/pubmed/20530214?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/

1 0

[Beg-sysbiol] [Fwd: DREAM5 Systems Biology Prediction Challenges v2]
by Tom Michoel 10 Jun '10

10 Jun '10

-------- Original Message -------- Subject: DREAM5 Systems Biology Prediction Challenges v2 Date: Wed, 9 Jun 2010 22:12:41 -0400 From: Gustavo Stolovitzky <gustavo(a)us.ibm.com> To: gustavo(a)us.ibm.com PLEASE LET ME KNOW IF YOU PREFER NOT TO RECEIVE ANNOUNCEMENTS FROM THE DREAM PROJECT SINCERE APOLOGIES IF YOU RECEIVE THIS ANNOUNCEMENT MORE THAN ONCE *Call for Systems Biology Predictions* *DREAM5: The 5^th DIALOGUE ON REVERSE ENGINEERING ASSESSMENT AND METHODS* Dear Colleague, We would like to you to participate in the following DREAM5 challenges (the first two challenges had been announced earlier) *RELEASED EARLIER: *1. *_Epitope-Antibody Recognition (EAR) Challenge_* <http://wiki.c2b2.columbia.edu/dream/index.php/D5c1>* *- Predict the binding specificity of peptide-antibody interactions. *RELEASED EARLIER:* 2. *_TF-DNA Motif Recognition Challenge_* <http://wiki.c2b2.columbia.edu/dream/index.php/D5c2>* - *Predict the specificity of a Transcription Factor binding to a 35-mer probe. *NEW: *3. *_Systems Genetics Challenge_* <http://wiki.c2b2.columbia.edu/dream/index.php/D5c3>* -* Predict disease phenotypes and infer gene networks from Systems Genetics data *NEW:* 4. *_Network Inference Challenge_* <http://wiki.c2b2.columbia.edu/dream/index.php/D5c4>* -*Infer simulated and in vivo gene regulatory networks from gene expression data We are releasing only one half of Challenge 3. The other half will be posted in our website shortly. To access the data sets, and descriptions of the DREAM5 challenges, please go to _http://wiki.c2b2.columbia.edu/dream/index.php/Challenges_ . The best performers in these challenges will be invited to present in the joint RECOMB Systems Biology/Regulatory Genomics/DREAM5 conference. See _http://recombsat.c2b2.columbia.edu/_ for details on this conference. To learn more about the DREAM project, please go to _http://wiki.c2b2.columbia.edu/dream/index.php/The_DREAM_Project_ *DREAM5 Challenge Submission Timeline* *Late May-Early June, 2010* Call for participation in the challenges. Challenges posted. *September 20, 2010* Predictions Submission Deadline. *Nov 16-20, 2010* RECOMB Systems Biology/Regulatory Genomics/DREAM5 conference. (The DREAM5 conference track is on November 16th.) Sincerely, DREAM5 Challenge Organizers: Gustavo Stolovitzky (chair), IBM Research Robert J Prill, IBM Research Julio Saez Rodriguez, Sys Bio Dept, Harvard University DREAM5 is part of a project we call the DREAM (Dialogue for Reverse Engineering Assessments and Methods) project. Its main objective is to catalyze the interaction between experiment and theory in the area of rigorous assessment of systems biology prediction methods. ===================================== Gustavo Stolovitzky, PhD. Manager, Functional Genomics and Systems Biology IBM Computational Biology Center P.O.Box 218, Yorktown Heights, NY 10598 Office: (914) 945- -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

1 0

[Beg-sysbiol] Paper: Gene Set-Based Module Discovery Decodes cis-Regulatory Codes Governing Diverse Gene Expression across Human Multiple Tissues
by Bram Slabbinck 10 Jun '10

10 Jun '10

FYI (pdf) http://www.plosone.org/article/fetchObjectAttachment.action?uri=info%3Adoi%… regards Bram -- ========================================================= ir. 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 =========================================================

1 0

[Beg-sysbiol] Ordered structure of the transcription network inherited from the yeast whole-genome duplication
by Tom Michoel 09 Jun '10

09 Jun '10

<http://www.biomedcentral.com/1752-0509/4/77/abstract> -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

2 1