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Keen was born in Philadelphia on January 19, 1837. He attended Philadelphia Central High School.

He studied at Brown University, where he graduated in 1859. He graduated in medicine from Jefferson Medical College in 1862. During the American Civil War, he worked for the U.S. Army as a surgeon. After the war, and two years of studies in Paris and Berlin.

He married around 1870 and had as his children: Dora Keen, the Alpinist.

He started lecturing surgical pathology in Philadelphia. He was president of the Philadelphia School of Anatomy from 1875 to 1889.

He became known in the medical community around the world for inventing several new procedures in brain surgery, including drainage of the cerebral ventricles and removals of large brain tumors. Keen also performed the first successful removal of a brain tumor.

Keen also participated in a secret surgical operation to remove a cancerous jaw tumor on Grover Cleveland in 1893.

Keen died in Philadelphia on June 7, 1932.

He received honorary degrees from Jefferson Medical Collegeand Brown, Northwestern, Toronto, Edinburgh, Yale, St. Andrews, Greifswald, and Upsala universities, and served as president of the American Surgical Association (1898), the American Medical Association (1900), the Congress of American Physicians and Surgeons (1903), and the American Philosophical Society (after 1907). New International Encyclopedia In 1914, at a meeting of the International Surgical Association, he was elected president for the meeting of 1917. After 1894 he was foreign corresponding member of the Société de Chirurgie de Paris, the Société Belge de Chirurgie, and the Clinical Society of London; honorary fellow of the Royal College of Surgeons of England, the Royal College of Surgeons of Edinburgh, the Deutsche Gesellschaft für Chirurgie, the Palermo Surgical Society, and the Berliner Medicinische Gesellschaft, and associate fellow of the American Academy of Arts and Sciences. New International Encyclopedia

He published:

• Clinical Charts of the Human Body (1870)
• Early History of Practical Anatomy (1875)
• Surgical Complications and Sequels of Typhoid Fever (1898)
• Addresses and Other Papers (1905)
• Animal Experimentation and Medical Progress (1914)
• an edition of Heath's Practical Anatomy (1870)
• the New American from the Eleventh English Edition of Gray's Anatomy (Sept 1887)
• the New American from the Thirteenth English Edition of Gray's Anatomy (Sept 1893)
• the American Text-Book of Surgery (1899, 1903)
• Keen's System of Surgery (1905—13)

Co-authored:

• Gunshot Wounds, and Other Injuries of Nerves, together with Silas Weir Mitchell, George Read Morehouse (1864)