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

[Beg-evodevo] The Functional Role of Pack-MULEs in Rice Inferred from Purifying Selection and Expression Profile.
by Klaas Vandepoele 19 Jan '09

19 Jan '09

http://www.ncbi.nlm.nih.gov/pubmed/19136648?dopt=Abstract -- 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] allopolyploidization and cold
by Stefanie De Bodt 12 Jan '09

12 Jan '09

Terashima A, Takumi S. Allopolyploidization reduces alternative splicing efficiency for transcripts of the wheat DREB2 homolog, WDREB2. Genome. 2009 Jan;52(1):100-5. -- ================================================================== Stefanie De Bodt, PhD VIB Department of Plant Systems Biology, UGent Technologiepark 927 B-9052 Gent Belgium Tel: 32 (0)9 3313692 Website: http://www.psb.ugent.be ==================================================================

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[Beg-evodevo] Two-phase increase in the maximum size of life over 3.5 billion years reflects biological innovation and environmental opportunity — PNAS
by Klaas Vandepoele 07 Jan '09

07 Jan '09

http://www.pnas.org/content/106/1/24.abstract?etoc -- 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] Questioning the ubiquity of neofunctionalization.
by Klaas Vandepoele 04 Jan '09

04 Jan '09

PLoS Comput Biol. 2009 Jan;5(1):e1000252. Epub 2009 Jan 2. Questioning the ubiquity of neofunctionalization. Gibson TA, Goldberg DS. Gene duplication provides much of the raw material from which functional diversity evolves. Two evolutionary mechanisms have been proposed that generate functional diversity: neofunctionalization, the de novo acquisition of function by one duplicate, and subfunctionalization, the partitioning of ancestral functions between gene duplicates. With protein interactions as a surrogate for protein functions, evidence of prodigious neofunctionalization and subfunctionalization has been identified in analyses of empirical protein interactions and evolutionary models of protein interactions. However, we have identified three phenomena that have contributed to neofunctionalization being erroneously identified as a significant factor in protein interaction network evolution. First, self-interacting proteins are underreported in interaction data due to biological artifacts and design limitations in the two most common high-throughput protein interaction assays. Second, evolutionary inferences have been drawn from paralog analysis without consideration for concurrent and subsequent duplication events. Third, the theoretical model of prodigious neofunctionalization is unable to reproduce empirical network clustering and relies on untenable parameter requirements. In light of these findings, we believe that protein interaction evolution is more persuasively characterized by subfunctionalization and self-interactions. http://www.ncbi.nlm.nih.gov/pubmed/19119408?dopt=Abstract

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[Beg-evodevo] PASTAA: identifying transcription factors associat...[Bioinformatics. 2008] - PubMed Result
by lieven sterck 22 Dec '08

22 Dec '08

http://www.ncbi.nlm.nih.gov/pubmed/19073590?dopt=Abstract -- ============================================================== Lieven Sterck, PhD Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck(a)psb.ugent.be Website: http://bioinformatics.psb.ugent.be ============================================================== "Facts are meaningless. You could use facts to prove anything that's even remotely true!" H. Simpson

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[Beg-evodevo] Next-generation genetics in plants : Article : Nature
by Klaas Vandepoele 11 Dec '08

11 Dec '08

http://www.nature.com/nature/journal/v456/n7223/full/nature07629.html -- 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/ --------------------------------------------------------- You would be nothing without me, I could be nothing Said the waves to the sand

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[Beg-evodevo] lethality in interploidy crosses
by Stefanie De Bodt 09 Dec '08

09 Dec '08

<http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/…> *The Maternally Expressed WRKY Transcription Factor /TTG2/ Controls Lethality in Interploidy Crosses of /Arabidopsis/* Brian P. Dilkes, Melissa Spielman, Renate Weizbauer, Brian Watson, Diana Burkart-Waco, Rod J. Scott, and Luca Comai Hybrid lethality in crosses between diploids and tetraploids, plants with whole genome duplication, is determined by an epidermal regulator expressed in the maternal tissue that envelops the seed. Full-text <http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/…> | Author Summary <http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/…> | Screen PDF (768K) <http://biology.plosjournals.org/perlserv/?request=get-pdf&file=10.1371_jour…>

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[Beg-evodevo] PLoS Genetics: Evolutionary Diversification of Plant Shikimate Kinase Gene Duplicates
by Klaas Vandepoele 09 Dec '08

09 Dec '08

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.100… -- 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] Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids, -- Lyons et al. 148 (4): 1772 -- PLANT PHYSIOLOGY
by Cindy Martens 06 Dec '08

06 Dec '08

http://www.plantphysiol.org/cgi/content/abstract/148/4/1772?etoc

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[Beg-evodevo] EnsemblCompara GeneTrees: Analysis of complete, du...[Genome Res. 2008] - PubMed Result
by Yves Van de Peer 30 Nov '08

30 Nov '08

http://www.ncbi.nlm.nih.gov/pubmed/19029536?dopt=Abstract -- 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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