These included studying rice finishing,[8] silkworm sequencing,[9] and genetic variation in chickens.
[10] From 2006 to 2009, Li worked on a postdoctoral research fellowship with Richard M. Durbin at the Wellcome Trust Sanger Institute.
[15] Li joined the Broad Institute in 2009, working in the core faculty lab of David Altshuler,[11][16] which investigates the discovery and understanding of the genetic causes of disease.
As of December 2018, Li's papers on SAMtools[12] and BWA[13] (sequence alignment using the Burrows–Wheeler transform) have both been cited over 16,000 times.
Li became the fourth former member of Richard Durbin's lab to win the award, following Sean Eddy, Ewan Birney and Alex Bateman.