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

[Beg-evodevo] Comparative genomic analysis of the Odorant-Bindin...[Genome Biol. 2007] - PubMed Result
by Yves Van de Peer 28 Oct '07

28 Oct '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-evodevo] Genome Biology | Abstract | gb-2007-8-10-r225 | Phylogenetic Simulation of Promoter Evolution: Estimation and Modeling of Binding Site Turnover Events and Assessing Their Impact on Alignment Tools
by Yves Van de Peer 28 Oct '07

28 Oct '07

http://genomebiology.com/2007/8/10/R225 -- 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-evodevo] Ohno's dilemma: Evolution of new genes under conti...[Proc Natl Acad Sci U S A. 2007] - PubMed Result
by Yves Van de Peer 22 Oct '07

22 Oct '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-evodevo] Gene duplication and the adaptive evolution of a c...[Nature. 2007] - PubMed Result
by Yves Van de Peer 14 Oct '07

14 Oct '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-evodevo] Plant Genome Duplication Database
by Yves Van de Peer 09 Oct '07

09 Oct '07

http://chibba.agtec.uga.edu/duplication/index/dotplot_app?species1=at&speci… -- 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-evodevo] Genome Biology | Abstract | gb-2007-8-10-r209 | All duplicates are not equal: the difference between small-scale and genome duplication
by Klaas Vandepoele 08 Oct '07

08 Oct '07

http://genomebiology.com/2007/8/10/R209 -- ================================================================== 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-evodevo] Expression Partitioning between Genes
by Stefanie De Bodt 17 Sep '07

17 Sep '07

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&dopt=AbstractPlus&db=…

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[Beg-evodevo] Pubmed :: Natural history and evolutionary principles of gene duplication in fungi
by Klaas Vandepoele 06 Sep '07

06 Sep '07

Natural history and evolutionary principles of gene duplication in fungi Ilan Wapinski^1 <http://www.nature.com/nature/journal/v449/n7158/full/nature06107.html#a1>, ^2 <http://www.nature.com/nature/journal/v449/n7158/full/nature06107.html#a2>, ^3 <http://www.nature.com/nature/journal/v449/n7158/full/nature06107.html#a3> , Avi Pfeffer^3 <http://www.nature.com/nature/journal/v449/n7158/full/nature06107.html#a3> , Nir Friedman^4 <http://www.nature.com/nature/journal/v449/n7158/full/nature06107.html#a4> & Aviv Regev^1 <http://www.nature.com/nature/journal/v449/n7158/full/nature06107.html#a1>, ^5 <http://www.nature.com/nature/journal/v449/n7158/full/nature06107.html#a5> 1. Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA 2. FAS Center for Systems Biology, Harvard University, 7 Divinity Avenue 3. School of Engineering and Applied Sciences, Harvard University, 33 Oxford Street, Cambridge, Massachusetts 02138, USA 4. School of Computer Science and Engineering, Hebrew University, Jerusalem 91904, Israel 5. Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA Correspondence to: Aviv Regev^1 <http://www.nature.com/nature/journal/v449/n7158/full/nature06107.html#a1>, ^5 <http://www.nature.com/nature/journal/v449/n7158/full/nature06107.html#a5> Correspondence and requests for materials should be addressed to A.R. (Email: aregev(a)broad.mit.edu <mailto:aregev@broad.mit.edu>). Top of page <http://www.nature.com/nature/journal/v449/n7158/full/nature06107.html#top> Abstract Gene duplication and loss is a powerful source of functional innovation. However, the general principles that govern this process are still largely unknown. With the growing number of sequenced genomes, it is now possible to examine these events in a comprehensive and unbiased manner. Here, we develop a procedure that resolves the evolutionary history of all genes in a large group of species. We apply our procedure to seventeen fungal genomes to create a genome-wide catalogue of gene trees that determine precise orthology and paralogy relations across these species. We show that gene duplication and loss is highly constrained by the functional properties and interacting partners of genes. In particular, stress-related genes exhibit many duplications and losses, whereas growth-related genes show selection against such changes. Whole-genome duplication circumvents this constraint and relaxes the dichotomy, resulting in an expanded functional scope of gene duplication. By characterizing the functional fate of duplicate genes we show that duplicated genes rarely diverge with respect to biochemical function, but typically diverge with respect to regulatory control. Surprisingly, paralogous modules of genes rarely arise, even after whole-genome duplication. Rather, gene duplication may drive the modularization of functional networks through specialization, thereby disentangling cellular systems. -- ================================================================== 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-evodevo] The floral genome: an evolutionary history of gene...[Trends Plant Sci. 2007] - PubMed Result
by Yves Van de Peer 05 Aug '07

05 Aug '07

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&dopt=AbstractPlus&db=…

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[Beg-evodevo] dating early plant evolution
by Stefanie De Bodt 03 Jul '07

03 Jul '07

http://www.springerlink.com/content/y2443540636qx52w/fulltext.pdf -- ================================================================== Stefanie De Bodt, PhD VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Technologiepark 927 B-9052 Gent Belgium Tel: 32 (0)9 3313692 Website: http://bioinformatics.psb.ugent.be ==================================================================

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