In our previous work, we developed four major bioinformatics tools/databases: (1) the web-based ANOVA-FDR software to provide user-friendly microarray data analysis (http://lgsun.grc.nia.nih.gov/ANOVA/);(2) an algorithm and a fully-automated computational pipeline for transcript assembly from expressed sequences aligned to the mouse genome;(3) a web-based browser to visualize all transcripts and alternative spliced forms of mouse genes (NIA Mouse Gene Index: http://lgsun.grc.nia.nih.gov/geneindex/mm9/);(4) a web-based database and tool to visualize and map the transcription factor binding sites of the mouse genome (CisView: http://lgsun.grc.nia.nih.gov/geneindex/mm6/cisview.html);and (5) a web-based tool to identify consensus sequence motifs based on the genome-wide chromatin-immunoprecipitation coupled with sequencing (ChIP-Seq) method (CisFinder: http: http://lgsun.grc.nia.nih.gov/CisFinder/). During the last year, we have been working on maintaining and updating these bioinformatics resources. We have also developed a new algorithm to simulate the gene expression regulated by two competing transcription factors. We continue to apply our software tools to various biological problems of our own and in collaboration, which yielded a few publications. We are working constantly to maintain and update the bioinformatics resources that we have developed and made available to the research community. We will continue the development of new algorithms and websites for bioinformatics needs.
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|Amano, Tomokazu; Hirata, Tetsuya; Falco, Geppino et al. (2013) Zscan4 restores the developmental potency of embryonic stem cells. Nat Commun 4:1966|
|Xu, Dongyi; Shen, Weiping; Guo, Rong et al. (2013) Top3* is an RNA topoisomerase that works with fragile X syndrome protein to promote synapse formation. Nat Neurosci 16:1238-47|
|Hung, Sandy S C; Wong, Raymond C B; Sharov, Alexei A et al. (2013) Repression of global protein synthesis by eif1a-like genes that are expressed specifically in the two-cell embryos and the transient zscan4-positive state of embryonic stem cells. DNA Res 20:391-402|
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