He has collaborated with The Smashing Pumpkins, Felix da Housecat, Daft Punk, Rachael Yamagata, Soulwax, LCD Soundsystem, Prince, Bloc Party, Mandy Moore, Interpol, Bauhaus, Justice, Joshua Radin, Spank Rock, Fischerspooner, Yeah Yeah Yeahs, Hanson, Peaches, Sean "Diddy" Combs, The Chemical Brothers, MSTRKRFT, Beck, Hot Chip, and Mark Ronson.

[5][6] In the 1990s, Holmes hosted a show, “In Advance of the Landing,” on the University of Chicago's WHPK, during which he explored extraterrestrial phenomena and cults.

[4] The album was re-released in 2018 on Omnivore Records with 10 bonus tracks, including covers of Prince, The Ronettes, and The Muppets' “Rainbow Connection.”[11] After Yum-Yum, Holmes stopped releasing music for many years, but took on other endeavors: In 2009 Holmes contributed to a remake of The Velvet Underground & Nico as part of Beck's Record Club with noted producer Nigel Godrich and others.

[6] From 2008 to 2011, Holmes was part of Ashtar Command, an indie rock band composed of him and former Filter guitarist Brian Liesegang.

Their album American Sunshine was put out on Holmes’ Privateer label and Shepard Fairey’s Obey imprint.

It features Joshua Radin, Taylor Hanson, Har Mar Superstar, Alex Ebert, Rachael Yamagata, Priscilla Ahn, and Z Berg.

[15] Holmes has worked with immersive technology company Cosm to create audio-visual experience “The Journey Within” in Los Angeles.