GT-Scan: identifying unique genomic targets

GT-Scan: identifying unique genomic targets

UNLABELLED A number of technologies, including CRISPR/Cas, transcription activator-like effector nucleases and zinc-finger nucleases, allow the user to target a chosen locus for genome editing or regulatory interference. Specificity, however, is a major problem, and the targeted locus must be chosen with care to avoid inadvertently affecting other loci ('off-targets') in the genome. To address ...

ChromoScan: a scan statistic application for identifying chromosomal regions in genomic studies

UNLABELLED ChromoScan is an implementation of a genome-based scan statistic that detects genomic regions, which are statistically significant for targeted measurements, such as genetic associations with disease, gene expression profiles, DNA copy number variations, as well as other genome-based measurements. A Java graphic user interface (GUI) is provided to allow users to select appropriate da...

Identifying Master Regulators of Cancer and Their Downstream Targets by Integrating Genomic and Epigenomic Features

Vast amounts of molecular data characterizing the genome, epigenome and transcriptome are becoming available for a variety of cancers. The current challenge is to integrate these diverse layers of molecular biology information to create a more comprehensive view of key biological processes underlying cancer. We developed a biocomputational algorithm that integrates copy number, DNA methylation,...

Identifying genomic targets for protein over-expression by “omics” analysis of Quiescent Escherichia coli cultures

BACKGROUND A cellular stress response is triggered upon induction of recombinant protein expression which feedback inhibits both growth as well as protein synthesis. In order to separate these two effects, it was decided to study "quiescent cultures" which continue to be metabolically active and express recombinant proteins even after growth cessation. The idea was to identify and up-regulate g...

A Genomic Approach to Identifying Novel Targets For Early Detection and Intervention of Prostate Cancer