Zheng, Qi, Zhang, Yong, Chen, Ying, Yang, Ning, Wang, Xiu-Jie, Zhu, Dahai
Abstract Background The genetic closeness and divergent muscle growth rates of broilers and layers make them great models for myogenesis study. In order to discover the molecular mechanisms...
GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis (2008)
Gene Ontology (GO) analysis has become a commonly used approach for functional studies of large-scale genomic or transcriptomic data. Although there have been a lot of software with GO-related...
A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii (2007)
Zhao, Tao, Li, Guanglin, Mi, Shijun, Li, Shan, Hannon, Gregory J., Wang, Xiu-Jie, ...
Endogenous small RNAs function in RNA interference (RNAi) pathways to control gene expression through mRNA cleavage, translational repression, or chromatin modification. Plants and animals contain...
Prediction of trans-antisense transcripts in Arabidopsis thaliana (2006)
Wang, Huan, Chua, Nam-Hai, Wang, Xiu-Jie
Abstract Background Natural antisense transcripts (NATs) are coding or non-coding RNAs with sequence complementarity to other transcripts (sense transcripts). These RNAs could potentially regulate...
Genome Biology 2006, 7:R92 doi:10.1186/gb-2006-7-10-r92 (2006)
Huan Wang, Nam-hai Chua, Xiu-jie Wang, Huan Wang, Nam-hai Chua, Xiu-jie Wang, ...
This Provisional PDF corresponds to the article as it appeared upon acceptance. Copyedited and fully formatted PDF and full text (HTML) versions will be made available soon.
Wang, Xiu-Jie, Gaasterland, Terry, Chua, Nam-Hai
Abstract Background Natural antisense transcripts (NAT) are a class of endogenous coding or non-protein-coding RNAs with sequence complementarity to other transcripts. Several lines of evidence have...
Prediction and identification of Arabidopsis thalianamicroRNAs and their mRNA targets (2004)
Wang, Xiu-Jie, Reyes, José L, Chua, Nam-Hai, Gaasterland, Terry
Abstract Background A class of eukaryotic non-coding RNAs termed microRNAs (miRNAs) interact with target mRNAs by sequence complementarity to regulate their expression. The low abundance of some...
Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets
Wang, Xiu-Jie, Reyes, José L, Chua, Nam-Hai, Gaasterland, Terry
Using bioinformatic methods, 83 novel Arabidopsis miRNAs have been predicted. Putative target mRNAs have been identified for most of the candidate genes.
Wang, Xiu-Jie, Gaasterland, Terry, Chua, Nam-Hai
A new computational method for predicting cis-encoded natural antisense transcripts (NATs) in Arabidopsis identified 1,340 potential NAT pairs. The expression of both sense and antisense transcripts...
Prediction and Identification of Herpes Simplex Virus 1-Encoded MicroRNAs
Cui, Can, Griffiths, Anthony, Li, Guanglin, Silva, Lindsey M., Kramer, Martha F., Gaasterland, Terry, ...
MicroRNAs (miRNAs) are key regulators of gene expression in higher eukaryotes. Recently, miRNAs have been identified from viruses with double-stranded DNA genomes. To attempt to identify miRNAs...
Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets
Wang, Xiu-Jie, Reyes, José L, Chua, Nam-Hai, Gaasterland, Terry
Using bioinformatic methods, 83 novel Arabidopsis miRNAs have been predicted. Putative target mRNAs have been identified for most of the candidate genes.
Wang, Xiu-Jie, Gaasterland, Terry, Chua, Nam-Hai
A new computational method for predicting cis-encoded natural antisense transcripts (NATs) in Arabidopsis identified 1,340 potential NAT pairs. The expression of both sense and antisense transcripts...
Prediction and Identification of Herpes Simplex Virus 1-Encoded MicroRNAs
Cui, Can, Griffiths, Anthony, Li, Guanglin, Silva, Lindsey M., Kramer, Martha F., Gaasterland, Terry, ...
MicroRNAs (miRNAs) are key regulators of gene expression in higher eukaryotes. Recently, miRNAs have been identified from viruses with double-stranded DNA genomes. To attempt to identify miRNAs...
Prediction of trans-antisense transcripts in Arabidopsis thaliana
Wang, Huan, Chua, Nam-Hai, Wang, Xiu-Jie
A genome-wide screen for trans-natural antisense transcripts in Arabidopsis thaliana suggests that antisense transcripts could be involved in complex regulatory networks in eukaryotes.
Li, XiaoChing, Wang, Xiu-Jie, Tannenhauser, Jonathan, Podell, Sheila, Mukherjee, Piali, Hertel, Moritz, ...
Vocal learning and neuronal replacement have been studied extensively in songbirds, but until recently, few molecular and genomic tools for songbird research existed. Here we describe new...
A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii
Zhao, Tao, Li, Guanglin, Mi, Shijun, Li, Shan, Hannon, Gregory J., Wang, Xiu-Jie, ...
Endogenous small RNAs function in RNA interference (RNAi) pathways to control gene expression through mRNA cleavage, translational repression, or chromatin modification. Plants and animals contain...
GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis
Gene Ontology (GO) analysis has become a commonly used approach for functional studies of large-scale genomic or transcriptomic data. Although there have been a lot of software with GO-related...
LEAFY COTYLEDON1 Is a Key Regulator of Fatty Acid Biosynthesis in Arabidopsis1[C][W][OA]
Mu, Jinye, Tan, Helin, Zheng, Qi, Fu, Fuyou, Liang, Yan, Zhang, Jian, ...
In plants, fatty acids are de novo synthesized predominantly in plastids from acetyl-coenzyme A. Although fatty acid biosynthesis has been biochemically well studied, little is known about the...
Discovery of Herpes B Virus-Encoded MicroRNAs▿
Besecker, Michael I., Harden, Mallory E., Li, Guanglin, Wang, Xiu-Jie, Griffiths, Anthony
Herpes B virus (BV) naturally infects macaque monkeys and is a close relative of herpes simplex virus. BV can zoonotically infect humans to cause a rapidly ascending encephalitis with ∼80%...
Ha, Misook, Lu, Jie, Tian, Lu, Ramachandran, Vanitharani, Kasschau, Kristin D., Chapman, Elisabeth J., ...
Small RNAs, including microRNAs (miRNAs), small interfering RNAs (siRNAs), and trans-acting siRNAs (tasiRNAs), control gene expression and epigenetic regulation. Although the roles of miRNAs and...
Systematic identification and characterization of chicken (Gallus gallus) ncRNAs
Zhang, Yong, Wang, Jie, Huang, Shoujun, Zhu, Xiaopeng, Liu, Jun, Yang, Ning, ...
Recent studies have demonstrated that non-coding RNAs (ncRNAs) play important roles during development and evolution. Chicken, the first genome-sequenced non-mammalian amniote, possesses unique...