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Do I have rights as the first co-author of the paper behind the invention (Shan et al PNAS)? This was filed without my knowledge since I left this institution.

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Did you contribute to any claims to the said invention? Have you been included as a joint inventor of the invention? If yes, then being a joint inventor will give the right over an invention. The best thing to do is to consult an expert on what legal process you could take to excercise your right to the invention.

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    Depending upon the institution and any agreement you had with them you, have likely signed away your rights the day you joined. – George White Nov 11 '14 at 6:31

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