He received his PhD in Computer Science from the University of Maryland where he was co-advised by researchers at University of California at Berkeley. He spent several years in Berkeley as a visiting student where he wrote TopHat and Cufflinks and co-wrote Bowtie with Ben Langmead. It was during a postdoc at Harvard in the Department of Stem Cell and Regenerative Biology where he started to work with stem cells and became interested in single-cell analysis. This led to the development of the Monocle algorithm and eventually the monocle Bioconductor package. Cole will be speaking at the BioC 2015 conference in Seattle this year and will talk in detail about the biological questions behind his research interests. In this interview he shares his perspective as a software developer in the context of past projects, e.g., TopHat, Cufflinks, as well as the recent ‘monocle’ package.