What influence does brain chemistry have on the soul?

Many thanks to fundevogel for inspiring this question which began in discussing why new incarnations of The Doctor (Doctor Who) behave so differently with regeneration into a new body.

fundevogel suggested that while memories are retained, the organic chemistry of the new body’s brain causes a change in the personality of the new Doctor.

This thought led me to ponder the nature of the “soul”. Assume for the purpose of this question, that the existence of a soul is real and that it is perpetual; existing after the death of the body. (If you are compelled to say “I don’t believe in the idea of souls, I can’t stop you but I wish you wouldn’t.) If the personality that defines who you are is effected by brain chemistry, how would your soul change after the death of the brain?

Would others recognize you? Would you recognize yourself?