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

[Beg-sysbiol] greetings from Yokohama ;-)
by Eric Bonnet 09 Jun '10

09 Jun '10

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[Beg-sysbiol] Fwd: EXPANDER version 5.1 released
by Steven Maere 07 Jun '10

07 Jun '10

Some inspiration for lemone/enigma functionality increase. Thomas and Bram, is 'the organization' part of the sysbiol mailing list ? S Begin forwarded message: > From: EXPANDER Development Team <click(a)POST.TAU.AC.IL> > Date: June 7, 2010 11:00:47 AM GMT+02:00 > To: TAU-CS-EXPANDER-USERS(a)LISTSERV.TAU.AC.IL > Subject: EXPANDER version 5.1 released > Reply-To: EXPANDER Development Team <click(a)POST.TAU.AC.IL> > > Dear EXPANDER user, > > We are pleased to inform our large community of users that version 5.1 of > EXPANDER is now available. > > Version highlights include: > > * Analysis wizard: perform a pre-planned sequence of analysis steps > * KEGG pathway enrichment analysis > * Use differential expression analysis (t-test or SAM) to identify gene > groups > * Rule-based grouping: identify a set of genes with patterns similar to a > user-provided pattern > * View a clustering solution “projected" on another dataset > * Support for Aspergillus Fumigatus > > The version can be downloaded from: > http://acgt.cs.tau.ac.il/expander/registration.html. > Users of previous versions of EXPANDER do not have to re-register: From > the EXPANDER menu, select Help >> Open Download Page. > > > If you wish to be removed from the mailing list, please reply this message > with the word "Remove" in the title. > > As always, your comments, questions, problem reports and suggestions are > welcome. > > Sincerely yours, > The EXPANDER development team, > Ron Shamir's Computational Genomics Group > Tel-Aviv University > http://acgt.cs.tau.ac.il/expander/ ================================================================== Steven Maere, PhD Group leader, Evolutionary Systems Biology group Dept. of Plant Systems Biology VIB / Ghent University Technologiepark 927 B-9052 Gent BELGIUM tel: +32 9 331 3805 fax: +32 9 331 3809 email: stmae(a)psb.vib-ugent.be http://www.psb.ugent.be/esb/ ==================================================================

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[Beg-sysbiol] Network evolution
by Cedric Simillion 02 Jun '10

02 Jun '10

Hi Everyone, For those of you who don't know me yet: My name is Cedric. I've done my PhD with Yves, a long time ago. After having spent 4 years abroad, I've returned to PSB. My new project will (most likely) focus on the evolution of networks. Since it seems that some of you are also interested in this topic, it's probably a good idea to sit down together and discuss on how we can collaborate. Therefore, I suggest to have a meeting on Thursday, at 14h00 with everyone interested in network evolution. I'll give a brief presentation on the things I'm interested in. Maybe the rest of you can then give a brief summary of their project(s). Could you please confirm your attendance to this meeting? Also, let me know if you really would like to attend but can't make Thursday afternoon, so we can arrange another time. Hope to see you then, Cedric P.S. Does anyone know if we have to book a meeting room? -------------------------------------------------- The point, you see, is not the answers themselves, but the mental development we enjoy through striving for those answers. Arthur C. Clarke -- The Light of Other Days

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[Beg-sysbiol] FYI
by Bram Slabbinck 31 May '10

31 May '10

http://www.biomedcentral.com/1752-0509/4/74 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.vib-ugent.be WWW: http://www.psb.vib-ugent.be =========================================================

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[Beg-sysbiol] Process-based network decomposition reveals backbo... [Proc Natl Acad Sci U S A. 2010] - PubMed result
by Yves Van de Peer 30 May '10

30 May '10

http://www.ncbi.nlm.nih.gov/pubmed/20498084?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/

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[Beg-sysbiol] Revealing differences in gene network inference al... [Bioinformatics. 2010] - PubMed result
by Yves Van de Peer 30 May '10

30 May '10

http://www.ncbi.nlm.nih.gov/pubmed/20501553?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/

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[Beg-sysbiol] (no subject)
by Yves Van de Peer 23 May '10

23 May '10

-- 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/

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[Beg-sysbiol] A global protein kinase and phosphatase interactio... [Science. 2010] - PubMed result
by Yves Van de Peer 23 May '10

23 May '10

http://www.ncbi.nlm.nih.gov/pubmed/20489023?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/

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[Beg-sysbiol] Genes encoding hub and bottleneck enzymes of the A... [BMC Evol Biol. 2010] - PubMed result
by Yves Van de Peer 23 May '10

23 May '10

http://www.ncbi.nlm.nih.gov/pubmed/20478072?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/

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[Beg-sysbiol] Fwd: DREAM5 Systems Biology Prediction Challenges
by Tom Michoel 23 May '10

23 May '10

Begin forwarded message: > From: Gustavo Stolovitzky <gustavo(a)us.ibm.com> > Date: Sun 23 May 2010 07:19:48 GMT+02:00 > To: DREAM N-Z <DREAM_N-Z%IBMUS(a)us.ibm.com> > Subject: DREAM5 Systems Biology Prediction Challenges > > > 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 5th DIALOGUE ON REVERSE ENGINEERING ASSESSMENT AND METHODS > > Dear Colleague, > > We would like to invite you to participate in the following DREAM5 > challenges > > 1. Epitope-Antibody Recognition (EAR) Challenge - Predict the > binding specificity of peptide-antibody interactions. > 2. TF-DNA Motif Recognition Challenge - Predict the specificity of a > Transcription Factor binding to a 35-mer probe. > > These are two of the four challenges that we will be having this > year. The remaining two challenges > > 3. Systems Genetics Challenge - Predict disease phenotypes and infer > gene networks from Systems Genetics data > 4. Network Inference Challenge -Infer simulated and in-vivo gene > regulatory networks. > > 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, 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. -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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