In the 1990s, he recorded in the trio, Miniature, with Roberts and Joey Baron,[1] and in the band Caos Totale with Django Bates, Mark Dresser, Marc Ducret, Steve Swell, and Bobby Previte.

He led a trio with Michael Formanek and Jim Black, then added Chris Speed to form the quartet Bloodcount (which was occasionally a quintet with the addition of Ducret).

[2] Screwgun's first release was a 3-disc set by Bloodcount called Unwound, the music of which exemplified Berne's characteristic style of "explod[ing] the walls of traditional compositional form: instead of adhering to anything remotely resembling theme and variations, he intersperses thematic material–sometimes repeated, elongated, or truncated–with the careening pleasures of free improvisation.

Berne formed the band Snakeoil with Matt Mitchell, Oscar Noriega, and Ches Smith, which released a self-titled album in 2012, and six more recordings, with slight personnel changes, over the next decade.

With ARTE Quartet With BB&C With Gregg Belisle-Chi With Gregg Belisle-Chi and Tom Rainey With Big Satan With Bloodcount With Broken Shadows With Buffalo Collision With Caos Totale With Bruno Chevillon With Marilyn Crispell With Michael Formanek With Bill Frisell With Hardcell With Miniature With Matt Mitchell With Aurora Nealand and Hank Roberts With Aurora Nealand and Marc Helias With Paraphrase With Hank Roberts With Herb Robertson, Marc Ducret and the Copenhagen Art Ensemble With Science Friction With Snakeoil With Nasheet Waits With Ray Anderson With Nels Cline With Marc Ducret With Enten Eller With Umberto Petrin With Jazzophone Compagnie With Simon Fell With Figure 8 With Michael Formanek With Vinny Golia With Drew Gress With Mark Helias With Julius Hemphill With Ingrid Laubrock With Mr. Rencore With Ivo Perelman With Hank Roberts With Herb Robertson With Samo Salamon & Tom Rainey With George Schuller With Ches Smith With Spring Heel Jack With Chloe Sobek With David Torn, Craig Taborn, and Tom Rainey With David Torn, Trevor Dunn, and Tom Rainey With David Torn and Ches Smith as Sun of Goldfinger With Stefan Winter With Yōsuke Yamashita With John Zorn