Raised in Detroit, Thomas learned piano and guitar as a child. They recorded one European Parliament together and played a few short tours, where she met Damien Jurado and David Bazan. Thomas" appearance on the song "Parking Lot", from Damien Jurado"s album Ghost of David, brought her to the attention of Sub People’s Records, who signed her in 2000.
Her first recording for the label was a duet with Jurado on "Wages of Sin" on Badlands: A Tribute To Bruce Springsteen"s Nebraska.
Her debut album When We Were Small was released on January 22, 2001. The album featured Eric Fisher (who Thomas met at Cornish College) on guitar and keyboards and Andy Myers on drums.
Thomas released her third album, If Songs Could Be Held, in 2005. In March 2006, her song "Faith"s Silver Elephant" appeared on the Paper Bag Records compilation See You on the Moon!.
In April 2006, Pitchfork erroneously reported that Thomas and American musician Sufjan Stevens were having a baby together, but later published a retraction.
Denison Witmer and Thomas later admitted it was an April Fools" prank. Thomas acted in the 2009 film Calvin Marshall and was the subject of the 2009 documentary All the Way from Michigan Not Mars. She suffered from a thyroid condition that affected her for two years, leading to a gap of four years until her next album.