While attending Barnard College in the early 1950s she became friends with Joyce Johnson (at that time Joyce Glassman). It was also during this period that she was first introduced to Allen Ginsberg by philosophy professor Alex Greer. The two discovered a mutual acquaintance in Carl Solomon, whom they had both met while spending time separately in a mental hospital. A romantic involvement followed in the spring and summer of 1953, however it was during this time that Ginsberg began to embrace his homosexuality, and the relationship gradually dissolved. Despite this, Cowen remained emotionally attached to Ginsberg for the rest of her life.
In February 1956 she and her lover Sheila moved into an apartment with Ginsberg and Peter Orlovsky. At the time Cowen had a job as a typist. She was fired and removed from the office by police officers who beat her. When her father came to pick her up from the station he warned her, "If your mother ever hears of this it will kill her." Upon being fired she moved to San Francisco, in order to experience its growing Beat scene. While in San Francisco Cowen became pregnant and was forced to undergo a hysterectomy during a late-stage abortion. She returned to New York, then made another trip to California, later returning permanently to Manhattan.
A life-long depressive, Cowen began to be afflicted by increasingly severe psychological breakdowns, eventually being admitted to Bellevue Hospital in order to obtain treatment for hepatitis and psychosis. She checked herself out against doctors' orders and returned to her parents' apartment on Bennett Avenue under the guise that she was going to go on vacation with her parents to Miami Beach. At her parents' home she committed suicide, jumping through the locked living room window and falling seven stories to the ground.
After her death her parents destroyed the bulk of her writings; however, Leo Skir, a friend, had 83 of her poems in his possession at the time of her death, and saw to their publication.
A short biography and several of her works are included in "Women of the Beat Generation: Writers, Artists and Muses at the Heart of a Revolution" edited by Brenda Knight. Cowen features prominently in Minor Characters by Joyce Johnson.