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Group: bioinplant - Deng [3 articles]

Papers posted to the group bioinplant by author Deng. You can also see everyone's Deng.

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	Prediction of structured non-coding RNAs in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae. J Exp Zoolog B Mol Dev Evol, Vol. 306, No. 4. (15 July 2006), pp. 379-392. by K. Missal, X. Zhu, D. Rose, et al.W. Deng, G. Skogerbø, R. Chen, P. F. Stadler posted to ncrna prediction by bsmagic to the group bioinplant on 2006-11-16 13:22:59 along with 3 people and 2 groups NicholasErho thegoose2 tharris C. elegans / WormBase Bioinformatics Abstract Copy My Attachments My Copy Abstract We present a survey for non-coding RNAs and other structured RNA motifs in the genomes of Caenorhabditis elegans and Caenorhabditis briggsae using the RNAz program. This approach explicitly evaluates comparative sequence information to detect stabilizing selection acting on RNA secondary structure. We detect 3,672 structured RNA motifs, of which only 678 are known non-translated RNAs (ncRNAs) or clear homologs of known C. elegans ncRNAs. Most of these signals are located in introns or at a distance from known protein-coding genes. With ...
	Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray Nucl. Acids Res., Vol. 34, No. 10. (31 May 2006), pp. 2976-2983. by Housheng He, Lun Cai, Geir Skogerbo, et al.Wei Deng, Tao Liu, Xiaopeng Zhu, Yudong Wang, Dong Jia, Zhihua Zhang, Yong Tao, Haipan Zeng, Muhammad N. Aftab, Yan Cui, Guozhen Liu, Runsheng Chen posted to expression transcriptome ncrna microarray profiling by bsmagic to the group bioinplant on 2006-11-16 13:19:45 along with 5 people and 3 groups thegoose2 tharris tardigrade mtagaya cdawson C. elegans / WormBase Bioinformatics GIG Abstract Copy My Attachments My Copy Abstract Small non-coding RNAs (ncRNAs) are encoded by genes that function at the RNA level, and several hundred ncRNAs have been identified in various organisms. Here we describe an analysis of the small non-coding transcriptome of Caenorhabditis elegans, microRNAs excepted. As a substantial fraction of the ncRNAs is located in introns of protein-coding genes in C.elegans, we also analysed the relationship between ncRNA and host gene expression. To this end, we designed a combined microarray, which included probes against ncRNA as well ...
	Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression. Genome Res, Vol. 16, No. 1. (January 2006), pp. 20-29. by W. Deng, X. Zhu, G. Skogerbø, et al.Y. Zhao, Z. Fu, Y. Wang, H. He, L. Cai, H. Sun, C. Liu, B. Li, B. Bai, J. Wang, D. Jia, S. Sun, H. He, Y. Cui, Y. Wang, D. Bu, R. Chen posted to function ncrna transcriptome by bsmagic to the group bioinplant on 2006-11-16 13:18:54 along with 4 people and 4 groups thegoose2 tharris imouthesmp marcius C. elegans / WormBase Bioinformatics BioinfoCIPF SGU-CIPF Abstract Copy My Attachments My Copy Abstract Recent evidence points to considerable transcription occurring in non-protein-coding regions of eukaryote genomes. However, their lack of conservation and demonstrated function have created controversy over whether these transcripts are functional. Applying a novel cloning strategy, we have cloned 100 novel and 61 known or predicted Caenorhabditis elegans full-length ncRNAs. Studying the genomic environment and transcriptional characteristics have shown that two-thirds of all ncRNAs, including many intronic snoRNAs, are independently transcribed under the control of ncRNA-specific upstream promoter elements. Furthermore, the transcription ...

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