"...is that a cow?"
Peter Bishop explains that since cows are genetically very similar to humans and experiments can simulate the effect on humans: they are an "ethically" acceptable test subject, when using a human might be lethal.
Gene appears multiple times throughout the series, mostly in the background.
In the flash forward of the third season finale, Gene was not seen in the future version of this universe, and had likely passed, as the adult Ella Dunham states that she misses the cow.
In the fifth season, Gene can be seen trapped in the amber triggered by Walter in his lab at Harvard.
- Gene has been "re-cast" several times since the Pilot episode, mostly because of the change in venue between studios in Toronto, New York and Vancouver.