January 2009 - beg-evodevo@psb.ugent.be

[Beg-evodevo] Divergent Evolution of Duplicate Genes Leads to Genetic Incompatibilities Within A. thaliana -- Bikard et al. 323 (5914): 623 -- Science
by Cindy Martens 31 Jan '09

31 Jan '09

http://www.sciencemag.org/cgi/content/abstract/323/5914/623?sa_campaign=Ema… -- ================================================================== Cindy Martens VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM Tel: +32 (0)9 331 38 22 Fax: +32 (0)9 331 38 09 E-mail: cindy.martens(a)psb.vib-ugent.be Website: http://bioinformatics.psb.ugent.be/ ==================================================================

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[Beg-evodevo] Sorghum genome
by Klaas Vandepoele 28 Jan '09

28 Jan '09

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[Beg-evodevo] The life and death of gene families. [Bioessays. 2009] - PubMed Result
by Klaas Vandepoele 25 Jan '09

25 Jan '09

http://www.ncbi.nlm.nih.gov/pubmed/19153999?dopt=Abstract

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[Beg-evodevo] Bias in Plant Gene Content Following Different Sor...[Annu Rev Plant Biol. 2008] - PubMed Result
by Klaas Vandepoele 25 Jan '09

25 Jan '09

http://www.ncbi.nlm.nih.gov/pubmed/19152483?dopt=Abstract

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[Beg-evodevo] who can help? Thanks. Yves
by Yves Van de Peer 24 Jan '09

24 Jan '09

-------- Original Message -------- Subject: A problem with i-ADHoRe Date: Fri, 23 Jan 2009 13:21:43 -0800 (PST) From: Sahar N.Malakshah <snohz001(a)ucr.edu> To: yves.vandepeer(a)psb.ugent.be <yves.vandepeer(a)psb.ugent.be> Hi professor Vandepeer; I'm a PhD student and trying to run i-ADHoRe on its sample datasets using this command: /home/sahar/PhD_thesis/iADHoRe/i-ADHoRe testset.ini But I encountered Segmentation fault at the middle of running the program(i've pasted what I get at the end of this email). I've not installed the Perl API, yet, but I think it's not related to the error that I've received. So I would appreciate if you can help me to solve this problem. Our machine information:Linux liulab01.ucr.edu 2.6.18-53.1.19.el5 #1 SMP Tue Apr 22 03:01:10 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux This is the error: [sahar@liulab01 testset]$ /home/sahar/PhD_thesis/iADHoRe/i-ADHoRe testset.ini This is i-ADHoRe 2.0 Written by Koen Janssens Algorithm designed by Koen Janssens, Cedric Simillion, Klaas Vandepoele, Yvan Saeys and Yves Van de Peer (c) 2006, Flanders Interuniversity Institute of Biotechnology, VIB Parsing settings file... Done! Creating dataset... Done! Mapping gene pairs... Done! Remapping tandem duplicates................. Done! Detecting level 2 multiplicons ................. ................ ............... .............. ............. ............ ........... .......... ......... ........ ....... ...... ..... .... ... .. . Done! Higher Level Detection 857 multiplicons to evaluate - evaluating level 2 multiplicon... Segmentation fault [sahar@liulab01 testset]$ /home/sahar/PhD_thesis/iADHoRe/i-ADHoRe testset.ini Sahar Nohzadeh-Malakshah 3133 Batchelor Hall Department of Botany and Plant Sciences UC Riverside, CA, USA E-mail: snohz001(a)ucr.edu -- 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] 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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