[4] He completed his doctorate in mathematics from the Massachusetts Institute of Technology in 1999, supervised by Bonnie Berger,[2] with Eric Lander and Daniel Kleitman as co-advisors.

[4] As well as for his technical contributions, Pachter is known for using new media to promote open science[8] and for a thought experiment he posted on his blog according to which 'the nearest neighbor to the "perfect human"' is from Puerto Rico.

[9] This received considerable media attention,[10] and a response was published in Scientific American.

[11] He is also known for criticisms of the All-of-us project's use of UMAP to visualize and interpret population genetics data.

[12] In 2017, Pachter was elected a Fellow of the International Society for Computational Biology (ISCB).