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Lin has been a trailblazer since his postdoctoral work with Allan Spradling, which established the Drosophila ovary as a powerful model for stem cell research. Lin located germline stem cells and demonstrated their asymmetric division. He identified the first niche cells and key genes (pumilio, nanos, hedgehog and piwi) that maintain the stem cell fate. Lin's most significant contribution is the discovery of the Argonaute/Piwi protein family and elucidation of its evolutionarily conserved function in stem cell maintenance, germline specification, epigenetic programming, and post-transcriptional regulation. He and three other labs independently discovered an extremely complex class of small non-coding RNAs called Piwi-interacting RNAs (piRNAs). This discovery was hailed by Science as one of the ten breakthroughs of 2006. His latest work revealed that transposons and pseudogenes regulate mRNA and lncRNA expression via the Piwi/piRNA pathway. These discoveries address central questions in genetics and epigenetics, with broad impact to biomedical research.