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

[Beg-evodevo] Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment
by Klaas Vandepoele 30 May '07

30 May '07

-- ================================================================== 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/ ==================================================================

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[Beg-evodevo] Gene essentiality, gene duplicability and protein connectivity in human and mouse
by Klaas Vandepoele 29 May '07

29 May '07

-- ================================================================== 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/ ==================================================================

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[Beg-evodevo] Homeodomain proteins belong to the ancestral molecular toolkit of eukaryotes
by Stefanie De Bodt 29 May '07

29 May '07

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&dopt=Abstract&db… -- ================================================================== 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] regulatory vs protein coding
by Stefanie De Bodt 14 May '07

14 May '07

-- ================================================================== 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] PhyloGena—a user-friendly system for automated phylogenetic annotation of unknown sequences
by Klaas Vandepoele 11 May '07

11 May '07

PhyloGena—a user-friendly system for automated phylogenetic annotation of unknown sequences * Kristian Hanekamp ^1 ^,2 , Uta Bohnebeck ^3 , Bánk Beszteri ^4 and Klaus Valentin ^4 ^,* * *for those people who do not like programming UNIX pipelines... Note the taxonomic-based reduction procedure to control the number of taxa in the tree!* ** -- ================================================================== 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/ ==================================================================

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[Beg-evodevo] Entrez PubMed
by Yves Van de Peer 06 May '07

06 May '07

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

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[Beg-evodevo] Entrez PubMed
by Yves Van de Peer 06 May '07

06 May '07

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

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[Beg-evodevo] More genes underwent positive selection in chimpanzee evolution than in human evolution (PNAS)
by Cindy Martens 01 May '07

01 May '07

*More genes underwent positive selection in chimpanzee evolution than in human evolution* * Margaret A. Bakewell, Peng Shi, and Jianzhi Zhang * Observations of numerous dramatic and presumably adaptive phenotypic^ modifications during human evolution prompt the common belief^ that more genes have undergone positive Darwinian selection^ in the human lineage than in the chimpanzee lineage since their^ evolutionary divergence 6--7 million years ago. Here, we^ test this hypothesis by analyzing nearly 14,000 genes of humans^ and chimps. To ensure an accurate and unbiased comparison, we^ select a proper outgroup, avoid sequencing errors, and verify^ statistical methods. Our results show that the number of positively^ selected genes is substantially smaller in humans than in chimps,^ despite a generally higher nonsynonymous substitution rate in^ humans. These observations are explainable by the reduced efficacy^ of natural selection in humans because of their smaller long-term^ effective population size but refute the anthropocentric view^ that a grand enhancement in Darwinian selection underlies human^ origins. Although human and chimp positively selected genes^ have different molecular functions and participate in different^ biological processes, the differences do not ostensibly correspond^ to the widely assumed adaptations of these species, suggesting^ how little is currently known about which traits have been under^ positive selection. Our analysis of the identified positively^ selected genes lends support to the association between human^ Mendelian diseases and past adaptations but provides no evidence^ for either the chromosomal speciation hypothesis or the widespread^ brain-gene acceleration hypothesis of human origins. PNAS | *May 1, 2007* | vol. 104 | no. 18 | *7489-7494* http://www.pnas.org/cgi/content/abstract/104/18/7489?etoc -- ========================================================= Cindy Martens VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY, UGent Bioinformatics and Evolutionary Genomics Technologiepark 927 B-9052 Gent Belgium Tel: +32 (0)9 331 38 22 Fax: +32 (0)9 331 38 09 E-mail: cindy.martens(a)psb.ugent.be Website: http://www.psb.ugent.be/bioinformatics =========================================================

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