May 2007 - beg-sysbiol@psb.ugent.be - maillist.psb.ugent.be

[Beg-sysbiol] paper: Estimating the annotation error rate of curated GO database sequence annotations
by Eric Bonnet 31 May '07

31 May '07

http://www.biomedcentral.com/1471-2105/8/170/abstract

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[Beg-sysbiol] [Fwd: Mini Review: Approaches for Extracting Practical Information from Gene Co-expression Networks in Plant Biology]
by Yves Van de Peer 29 May '07

29 May '07

-------- Original Message -------- Subject: Mini Review: Approaches for Extracting Practical Information from Gene Co-expression Networks in Plant Biology Date: Tue, 29 May 2007 09:16:01 +0200 From: Klaas Vandepoele <Klaas.Vandepoele(a)psb.ugent.be> To: Tineke Casneuf <ticas(a)psb.ugent.be>, Steven Maere <stmae(a)psb.ugent.be> CC: Yves Van de Peer <yvdp(a)psb.ugent.be> Mini Review Approaches for Extracting Practical Information from Gene Co-expression Networks in Plant Biology Gene co-expression, in many cases, implies the presence of a functional linkage between genes. Co-expression analysis has uncovered gene regulatory mechanisms in model organisms such as Escherichia coli and yeast. Recently, accumulation of Arabidopsis microarray data has facilitated a genome-wide inspection of gene co-expression profiles in this model plant. An approach using network analysis has provided an intuitive way to represent complex co-expression patterns between many genes. Co-expression network analysis has enabled us to extract modules, or groups of tightly co-expressed genes, associated with biological processes. Furthermore, integrated analysis of gene expression and metabolite accumulation has allowed us to hypothesize the functions of genes associated with specific metabolic processes. Co-expression network analysis is a powerful approach for data-driven hypothesis construction and geneprioritization, and provides novel insights into the system-level understanding of plant cellular processes. Aoki et al. (2007)PlantCellPhysiol48,381.pdf -- ================================================================== Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, UGent Technologiepark 927, B-9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ ================================================================== -- 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://www.psb.ugent.be/bioinformatics/

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[Beg-sysbiol] Entrez PubMed
by Yves Van de Peer 27 May '07

27 May '07

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

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[Beg-sysbiol] Machine Learning in Systems Biology
by Yvan Saeys 25 May '07

25 May '07

Hi all, In september this year, there will be a special workshop on machine learning in systems biology, organized by our colleagues in Liege. As the deadline for papers is june 30, I think we should make an effort to prepare something for this conference. Maybe the work of Tom and Anagha on clustering and the work of Michiel on feature selection for splicing are suitable candidates for a submission (publication in the conference proceedings will not preclude from publishing elsewhere). http://mlsb07.ibisc.fr/opencms/opencms/mlsb2007 best regards, yvan -- ================================================================== Dr. Yvan Saeys, PhD DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 331 38 09 BIOINFORMATICS TEAM Tel:32 (0)9 331 36 95 GHENT UNIVERSITY, Technologiepark 927, B-9052 Gent, Belgium Vlaams Instituut voor Biotechnologie VIB mailto:yvan.saeys@ugent.be http://bioinformatics.psb.ugent.be/ http://www.psb.ugent.be/~yvsae/ ==================================================================

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[Beg-sysbiol] Network motifs: theory and experimental approaches : Article : Nature Reviews Genetics
by Tom Michoel 22 May '07

22 May '07

http://www.nature.com/nrg/journal/v8/n6/full/nrg2102.html

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[Beg-sysbiol] another vidal paper
by Vanessa Vermeirssen 21 May '07

21 May '07

the localizome paper :-) -- ================================================================== Vanessa Vermeirssen, PhD VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 3313809 GHENT UNIVERSITY, Technology Park 927, B-9052 Gent, Belgium Vlaams Interuniversitair Instituut voor Biotechnologie VIB mailto:vamei@psb.ugent.be http://www.psb.ugent.be ==================================================================

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[Beg-sysbiol] new paper from vidal's group
by Eric Bonnet 21 May '07

21 May '07

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[Beg-sysbiol] kennen jullie die Koen Vanhoof? Groeten, Yves
by Yves Van de Peer 17 May '07

17 May '07

-------- Original Message -------- Subject: From Ricardo Grau Date: Tue, 15 May 2007 13:44:54 -0500 From: Ricardo Grau <rgrau(a)cei.uclv.edu.cu> To: <yves.vandepeer(a)psb.ugent.be> CC: <ibonetc(a)gmail.com> Dear Yves: I am sorry; I don’t know what has happened with my emails for you. It’s possible you haven read it because I have been using the account of the event (iwobi08(a)cei.uclv.edu.cu <mailto:iwobi08@cei.uclv.edu.cu>). In any way, It will be very nice that Ivan, Katlheen and you could participate in our Workshop and it is an official invitation. If definitively you agree, please Mail-me and immediately we inform it to Ann Nowe. In regards with the Gladis Casas and Maria del C. visit to Belgium, it is a good notice they can work with you. They have already ticket and will arrive to Belgium at 17^th Sept. We are proposing you, they could stay the first month in Hasselt, working with Professor Koen Vanhoof (who is specialist in Bayesian networks too). They, they could go to Ghent at 14^th October and stay there until December 13^th . Is it a good date for you? Best regards. Yours Ricardo Grau From: Yovanny Izquierdo Nuñez [mailto:iwobi08@cei.uclv.edu.cu] Sent: Thursday, March 22, 2007 9:34 PM To: yves.vandepeer(a)psb.ugent.be <mailto:yves.vandepeer@psb.ugent.be> Subject: IWOBI ´08 Programme Committee Importance: High Dear Yves and Katlheen: The UCLV is currently organizing the Second International Workshop on Bioinformatics (IWOBI) to be held in our campus from February 5th to 8th, 2008. We´re inviting you to be part of our programme committee given your expertise in the field and the excelent relationships between our workgroups. If you decide to join us, contact us for further details. You will find our first call for papers attached. I am looking forward to see you in Santa Clara next year, and would also appreciate if you could spread the news among potential participants. My best wishes for you and the rest of the colleagues in Ghent and Leuven. Give them my regards. Ricardo Grau ------------------------------------------------------------------------ Servicio de Correos del Grupo de Redes. UCLV Participe en Universidad 2008 del 11 al 15 de febrero del 2008. Palacio de Convenciones. La Habana. Cuba. http: //www.universidad2008.cu ------------------------------------------------------------------------ -- 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://www.psb.ugent.be/bioinformatics/

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[Beg-sysbiol] (no subject)
by Yves Van de Peer 16 May '07

16 May '07

Dear All, Yesterday in Manchester I have met David Robertson and one of his postdocs John Pinney. They are doing really nice work on networks. John is even developing software to look at networks in 3-D. Of course they work on yeast, and I hope we can do similar things one day (I'm not pushy though :-) on Arabidopsis or other eukaryotes. They are looking at interaction networks and then map duplicated genes onto those (discriminating between duplicates created in whole versus small-scale gene duplication events). Nice work. Greg Amoutzias (who will join us in August) did his PhD there. Cheers, Yves -- 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://www.psb.ugent.be/bioinformatics/

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[Beg-sysbiol] Otto Warburg International Summer School
by Yves Van de Peer 16 May '07

16 May '07

http://ows.molgen.mpg.de/

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