Jake Chen has been conducting research and development in bioinformatics and computational biology since 1995. Prior to coming back to academia, in 2002-3, he was the head of computational proteomics at Myriad Proteomics, Inc. (now Prolexys Pharmaceuticals, Inc.), Salt Lake City, Utah, where he led a team of bioinformatics researchers and developers to process and study the "human protein interactome" data, a proprietary network map of human protein-protein interactions consisting more than 10,000 human proteins and 80,000 interactions from more than 1TB of collected raw data.

In 1998-2002, he worked as a senior consultant and then a bioinformatics computer scientist at Affymetrix, Inc., Santa Clara, California, where he developed several gene/mRNA selection databases of more than 100GB in size, which resulted in the commercialization of human U95, mouse U74, and rat U34 GeneChip microarrays. In 1996-8, he was a research assistant and consultant to the Computational Biology Center of the University of Minnesota, where he developed algorithms and databases to analyze Expressed Sequence Tags from several plant genome sequencing projects in the US. He has given many scientific presentations at leading US biotech firms, research institutes, universities, ACM/IEEE local meetings, and national/international conferences.