As Arash mentioned a DNA ladder is used to confirm the size of your amplified product after PCR.Without which you cant tell wether the band obtained is a specific one or not.For publications you need not show your ladder,it is expected that the the picture you provide is of the band of your specific gene.
I am unable to understand... you have studied the effect of drugs on protein expression by Western Blotting or you have done expression analysis by RT-PCR etc.
if u have done western blotting then you have to use protein marker rather than DNA or as said above.
Again it is important to use marker/ladder to know that the band is of your interest.