When people refer to Genetically Modified Organisms (GMOs), they are referring to precision plant breeding using genetic engineering. It allows plant breeders to take a desirable trait (like resistance to drought, insects, weeds, and disease) from one plant or organism and transfer it to the plant they want to improve, as well as make a change to an existing trait in a plant they are developing.
As for cooking processes, any food products that may contain GMO ingredients (such as corn syrup that was derived from a GE corn plant) OR a GE whole food like the Hawaiian papaya variety engineered to resist the RingSpot Virus, would be cooked, eaten and enjoyed in the exact same way as it conventional or (if available) conventional or organic counterpart. In other words, these foods are nutritionally equivalent. In a more detailed response on the topic, Angela Culler, Lead of Compositional Biology Center at Monsanto states,
“…before a GM crop is commercialized, extensive scientific analyses are conducted, including a compositional analysis, that contribute to the overall safety assessment of these crops. These are very comprehensive studies that include multiple geographies that span up to 1000 miles to get a variety of environmental and soil conditions, with multiple plots within a location and analysis of up to 80 analytes. The overwhelming conclusion of these studies is that the composition of the GM crops is nutritionally equivalent to the non-modified variant, and that factors such as environment have a much bigger effect on composition.”