In 1958 Joe finished ten years of study with Joseph Schmid, a student of Alban Berg, completing Schoenberg's harmony, counterpoint and composition courses. Joe went on to teach harmony, 16th century counterpoint and composition at the Brooklyn Conservatory while continuing to compose and in 1963 was commissioned by Erich Leinsdorf of the Boston Symphony Orchestra to write a piano concerto. It was premiered in 1985 by the American Composers Orchestra at Alice Tully Hall. As a soloist in the 50's and early 60's he performed Greek, Syrian, Jewish and Turkish music on clarinet and saxophone as well as pop music of the day. In 1965, his reputation as a diverse performer led to an invitation to be the saxophone soloist in the premiere of a composition by David Reck dedicated to Ornette Coleman. Joe premiered the piece as part of the 20th Century Innovation Series conducted by Gunther Schuller at Carnegie Hall.
Also in 1965, encouraged by his friend and drummer Peter Dolger, Joe recorded an album with drums, bass, piano, clarinet & saxophone. His written tunes and subsequent improvisations contained elements of jazz, Greek melodies and rhythms, and twelve-tone compositional ideas. The album was recorded for Atlantic but remained unreleased until 1996, when John Zorn heard it and enthusiastically issued it on his Avant Label under the title Paniot's Nine. Paniot pays homage to Joe's friend who inspired the making of this record.