A Swiss Army Knife for Genomic Data

A good way to find out what a cell is doing—whether it is growing out of control as in cancers, or is under the control of an invading virus, or is simply going about the routine business of a healthy cell—is to look at its gene expression. Lior Pachter, Bren Professor of Computational Biology and Computing and Mathematical Sciences, has developed a complex software tool that enables the processing of large sets of genomic data in about 30 minutes, using the computing power of an average laptop. Like a Swiss Army knife, the tool can be used in myriad ways for different biological needs, and will help ensure the reproducibility of scientific studies. "The interdisciplinarity of our team was crucial to conceiving of and executing this project," says Pachter. "There are people in the lab who are computer scientists, biologists, engineers. Sina Booeshaghi is in the mechanical engineering department and brings the perspective of his design background and engineering." [Caltech story]