In our previous work, we developed four major bioinformatics tools/databases: (1) a 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/); and (4) an web-based database and tool to visualize and map transcription factor binding sites of the mouse genome (CisView: http://lgsun.grc.nia.nih.gov/geneindex/mm6/cisview.html). The unrestricted community access to the resource can accelerate a wide range of research, particularly in reproductive and regenerative medicine.? During the last year, we have updated all of these databases based on the latest mouse genome sequence assembly. We are currently developing tools to carry out quality control (QC) of 2-color DNA microarray results and a software tool to identify consensus transcription factor binding sequences based on genome-wide chromatin immunoprecipitation analysis (ChIP-Seq) and expression profiling data.
| Sharov, Alexei A (2009) Role of Utility and Inference in the Evolution of Functional Information. Biosemiotics 2:101-115 |
| Sharov, Alexei A; Masui, Shinji; Sharova, Lioudmila V et al. (2008) Identification of Pou5f1, Sox2, and Nanog downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data. BMC Genomics 9:269 |
