October 2007 - beg-evodevo@psb.ugent.be

[Beg-evodevo] gene duplication in mammals
by Stefanie De Bodt 29 Oct '07

29 Oct '07

The Pattern of Evolution of Smaller-Scale Gene Duplicates in Mammalian Genomes is More Consistent with Neo- than Subfunctionalisation -- ================================================================== 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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[Beg-evodevo] Reconcilation with non-binary species trees :: NOTUNG update
by Klaas Vandepoele 29 Oct '07

29 Oct '07

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&dopt=AbstractPlus&db=… Apparently the only shortcoming of NOTUNG (ie cannot handle multifurcated trees when preforming tree reconciliation) is now partially resolved: they now can handle such species trees, but apparently still require binary gene trees... Klaas *1: *Comput Syst Bioinformatics Conf. <javascript:AL_get(this, 'jour', 'Comput Syst Bioinformatics Conf.');> 2007;6:441-52.[image: Click here to read]<http://www.ncbi.nlm.nih.gov/entrez/utils/fref.fcgi?PrId=5265&itool=Abstract…> Links <javascript:PopUpMenu2_Set(Menu17951846);> Reconcilation with non-binary species trees.*Vernot B*<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=PubMed&Cmd=Search&Term=%22Verno…>, *Stolzer M*<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=PubMed&Cmd=Search&Term=%22Stolz…>, *Goldman A*<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=PubMed&Cmd=Search&Term=%22Goldm…>, *Durand D*<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=PubMed&Cmd=Search&Term=%22Duran…> . Departments of Biological Sciences and Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA. durand(a)cs.cmu.edu. Reconciliation is the process of resolving disagreement between gene and species trees, by invoking gene duplications and losses to explain topological incongruence. The resulting inferred duplication histories are a valuable source of information for a broad range of biological applications, including ortholog identification, estimating gene duplication times, and rooting and correcting gene trees. Reconciliation for binary trees is a tractable and well studied problem. However, a striking proportion of species trees are non-binary. For example, 64% of branch points in the NCBI taxonomy have three or more children. When applied to non-binary species trees, current algorithms overestimate the number of duplications because they cannot distinguish between duplication and deep coalescence. We present the first formal algorithm for reconciling binary gene trees with non-binary species trees under a duplication-loss parsimony model. Using a space efficient mapping from gene to species tree, our algorithm infers the minimum number of duplications and losses in O(|V(G)| . (k(S) + h(S))) time, where V(G) is the number of nodes in the gene tree, h(S) is the height of the species tree and k(S) is the width of its largest multifurcation. We also present a dynamic programming algorithm for a combined loss model, in which losses in sibling species may be represented as a single loss in the common ancestor. Our algorithms have been implemented in NOTUNG, a robust, production quality tree-fitting program, which provides a graphical user interface for exploratory analysis and also supports automated, high-throughput analysis of large data sets.

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[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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