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 (;(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:;(4) a web-based database and tool to visualize and map the transcription factor binding sites of the mouse genome (CisView:;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: 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.

National Institute of Health (NIH)
National Institute on Aging (NIA)
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National Institute on Aging
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Sharov, Alexei A; Schlessinger, David; Ko, Minoru S H (2015) ExAtlas: An interactive online tool for meta-analysis of gene expression data. J Bioinform Comput Biol :1550019
Akiyama, Tomohiko; Xin, Li; Oda, Mayumi et al. (2015) Transient bursts of Zscan4 expression are accompanied by the rapid derepression of heterochromatin in mouse embryonic stem cells. DNA Res 22:307-18
Monti, Manuela; Zanoni, Mario; Calligaro, Alberto et al. (2013) Developmental arrest and mouse antral not-surrounded nucleolus oocytes. Biol Reprod 88:2
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
Nishiyama, Akira; Sharov, Alexei A; Piao, Yulan et al. (2013) Systematic repression of transcription factors reveals limited patterns of gene expression changes in ES cells. Sci Rep 3:1390
Morgani, Sophie M; Canham, Maurice A; Nichols, Jennifer et al. (2013) Totipotent embryonic stem cells arise in ground-state culture conditions. Cell Rep 3:1945-57
Xu, Dongyi; Shen, Weiping; Guo, Rong et al. (2013) Top3β is an RNA topoisomerase that works with fragile X syndrome protein to promote synapse formation. Nat Neurosci 16:1238-47
Livigni, Alessandra; Peradziryi, Hanna; Sharov, Alexei A et al. (2013) A conserved Oct4/POUV-dependent network links adhesion and migration to progenitor maintenance. Curr Biol 23:2233-44
Yang, Hsih-Te; Ko, Minoru S H (2012) Stochastic modeling for the expression of a gene regulated by competing transcription factors. PLoS One 7:e32376
Sharov, Alexei A; Nishiyama, Akira; Piao, Yulan et al. (2011) Responsiveness of genes to manipulation of transcription factors in ES cells is associated with histone modifications and tissue specificity. BMC Genomics 12:102

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