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druvus's Mao:L [4 articles]

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	Arabidopsis gene co-expression network and its functional modules BMC Bioinformatics, Vol. 10, No. 1. (2009), 346. by Linyong Mao, John Van Hemert, Sudhansu Dash, Julie Dickerson posted to network module arabidopsis by druvus on 2009-10-21 16:19:12 along with 7 people maren hchuang icecrown zchen dolchan venancio Borelli Abstract Copy My Attachments My Copy Abstract BACKGROUND:Biological networks characterize the interactions of biomolecules at a systems-level. One important property of biological networks is the modular structure, in which nodes are densely connected with each other, but between which there are only sparse connections. In this report, we attempted to find the relationship between the network topology and formation of modular structure by comparing gene co-expression networks with random networks. The organization of gene functional modules was also investigated.RESULTS:We constructed a genome-wide Arabidopsis gene co-expression network (AGCN) by ...
	Evidence-based gene predictions in plant genomes Genome Research, Vol. 19, No. 10. (18 October 2009), pp. 1912-1923. by Chengzhi Liang, Long Mao, Doreen Ware, Lincoln Stein posted to annotation plant by druvus on 2009-07-22 11:31:44 along with 3 people megraw natstreet kshameer Abstract Copy My Attachments My Copy Abstract 10.1101/gr.088997.108 Automated evidence-based gene building is a rapid and cost-effective way to provide reliable gene annotations on newly sequenced genomes. One of the limitations of evidence-based gene builders, however, is their requirement for transcriptional evidenceâknown proteins, full-length cDNAs, or expressed sequence tags (ESTs)âin the species of interest. This limitation is of particular concern for plant genomes, where the rate of genome sequencing is greatly outpacing the rate of EST- and cDNA-sequencing projects. To overcome this limitation, we have developed an evidence-based ...
	Phylogeny, gene structures, and expression patterns of the ERF gene family in soybean (Glycine max L.) J. Exp. Bot., Vol. 59, No. 15. (1 November 2008), pp. 4095-4107. by Gaiyun Zhang, Ming Chen, Xueping Chen, et al.Zhaoshi Xu, Shan Guan, Lian-Cheng Li, Aili Li, Jiaming Guo, Long Mao, Youzhi Ma posted to family phylogeny plant proteome by druvus on 2009-03-31 12:39:53 Abstract Copy My Attachments My Copy Abstract Members of the ERF transcription factor family play important roles in regulating gene expression in response to biotic and abiotic stresses. In soybean (Glycine max L.), however, only a few ERF genes have been studied so far. In this study, 98 unigenes that contained a complete AP2/ERF domain were identified from 63 676 unique sequences in the DFCI Soybean Gene Index database. The phylogeny, gene structures, and putative conserved motifs in soybean ERF proteins were analysed, and compared with those of ...
	Genome-wide analysis of the MADS-box gene family in Populus trichocarpa. Gene, Vol. 378 (15 August 2006), pp. 84-94. by C. H. Leseberg, A. Li, H. Kang, M. Duvall, L. Mao posted to populus tf by druvus on 2008-12-19 16:10:37 Abstract Copy My Attachments My Copy Abstract Populus trichocarpa (poplar) is distinguished from its herbaceous counterparts Arabidopsis and rice by its woody structure, perennial life cycle, and dioecious, two-whorled flowers. MADS-box genes are known to be involved in many important processes during plant development. Investigation of the poplar genome revealed 105 putative functional MADS-box genes and 12 pseudogenes. These numbers are comparable to those in Arabidopsis. However, poplar has 64 type II MADS-box genes, implying a higher birth rate when compared with Arabidopsis (64 vs.47). In addition to ...

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