[1] In 2002, Lee was joint recipient of the Newcomb Cleveland Prize, for the best paper published in the journal Science that year.

[2] In 2024, Lee's 1993 paper was cited as the seminal discovery for which the Nobel Prize in Physiology or Medicine was awarded that year, to co-author Victor Ambros, her husband.

Her work on the cloning of lin-4 began in January, 1989, in Ambros's lab at Harvard University, and she was joined on the project in the fall of 1989 by Rhonda Feinbaum, a postdoc.

[10][11] The 1993 paper was soon accepted for publication, and in a change of journal policy, it was published with a notice on the front page that it was jointly first-authored by Lee and Feinbaum,[6] clarifying that both contributed equally to the research.

[6] Lee's co-authored 1993 paper is widely regarded as the seminal contribution in the discovery of microRNA, for which her husband Ambros and Ruvkun were both awarded the Nobel Prize in 2024.