Engineered nucleases such as CRISPR/Cas9 are powerful tools to alter genetic information in cells and animals, and treating human diseases. Engineered nucleases can create a DNA double strand break (DSB) at the intended, user-specified cut-site. The DSB is then repaired by DNA repair machinery in the cell through either non-homologous end joining (NHEJ) which often induces small or large insertions/ deletions (indels), or homology-directed repair (HDR) that requires a donor template. The Bao lab has been developing genome editing tools to address safety issues of CRISPR/Cas9 based genome editing. One tool LongAmpSeq, accurately quantifies and profiles unintended gene modifications due to Cas9 induced double-stranded breaks including large deletions, insertions, and complex chromosomal arrangements. Our lab has also developed in silico tools that predict and quantify genome editing outcomes. These tools include COSMID, an online bioinformatics tool for identifying and ranking the potential off-target sites of CRISPR/Cas9 as well as tools for gene editing systems such as SAPTA, a design tool for improving the activity of TALENs and PROGNOS, an online bioinformatics tool for predicting the off-target cleavage of ZFNs and TALENs. The Bao lab has also been developing viral-vector and nanoparticle-based delivery vehicles for in vivo genome editing.