American Born Chinese, Gene's first graphic novel, was the first-ever graphic novel ever to be named a finalist for the National Book Award. The book went on to win the Printz Award, the ALA's award for the best young adult book published that year, and an Eisner Award, one of the most prestigious honors in the comic book world. His follow-up solo graphic novel, Boxers & Saints, was also a National Book Award finalist and won the Printz Honor and the LA Times Book Prize for Young Readers. 

In addition, Gene was named the next National Ambassador for Young People's Literature by the Library of Congress in early 2016. He is the first writer who works primarily in graphic novels to be named ambassador. 

Currently, Gene is writing the graphic novel series Secret Coders, illustrated by Mike Holmes. This middle-grade series uses narrative to teach kids about computer programming.