The former Wigan Athletic and Chesterfield boss took over from Alan Archibald last October but leaves after the Jags picked up just two points from their opening five matches in 2019/20.
Assistant Brian Kerr also moves on and the Firhill club have confirmed that chief executive Gerry Britton, academy director Scott Allison and experienced striker Kenny Miller will take charge of the team for Saturday's home game against Dunfermline Athletic.
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