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In 1875 he earned his doctorate at the University of Berlin, and later became an assistant to Karl Gegenbaur (1826-1903) in Heidelberg. At Heidelberg he performed important research involving primate morphology, particularly studies of its muscular system. In the mid-1880s he authored works that provided a foundation for comparative anatomical and phylogenetic studies on facial muscles in mammals.
In 1888 Ruge became a professor of anatomy at the University of Amsterdam, and in 1897 obtained the same position at the University of Zurich.