I prefer to be referred to by my middle name. How should I list my name on publications?
I'm not sure if this is correct, but in the past I have written: First initial. Middle name Last name.
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You can write your name however you prefer, so long as it is clear and consistent.
A good example of a person with your same situation, however, is Chris Anderson at Berkeley, whose publications list:
J. Christopher Anderson
As you can see, he has come to the exact same solution that you suggest.