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Handling ISR

I have a general question regarding handling ISRs which stems from my inexperience. My understanding of ISR is that the execution branches, from the main code, to the ISR upon a condition being satisfied. After executing the ISR code it goes back to the main code, essentially back to the point where it paused to go to the ISR.
My question is can I call another function within the ISR instead of having the execution go back to where it had left off? Would it cause any adverse effects?
I am sure I must have confused some people by now for which i would like to apologize. Your criticisms/comments are welcome.

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