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In 1984 he was awarded the Louisa Gross Horwitz Prize from Columbia University together with Joseph L. Goldstein (Co-recipient of 1985 Nobel Prize in Physiology or Medicine).
Cech's work has been recognised by many awards and prizes including: lifetime Professorship by the American Cancer Society (1987),the Louisa Gross Horwitz Prize from Columbia University(1988), the Heineken Prize of the Royal Netherlands Academy of Sciences (1988), the Albert Lasker Basic Medical Research Award (1988), the Nobel Prize in Chemistry (1989, shared with Sidney Altman) and the National Medal of Science (1995).