Bryan is correct.
As for references as Chris Rogers requests, there are many, given the plethora of texts and papers on the subject. One good text is:
Ritter, J., Flower, R. J., Henderson, G., Loke, Y. K., MacEwan, D. J., & Rang, H. P. (2019). Rang and Dale’s pharmacology. St. Louis, Missouri: Elsevier.
To expand on the subject, a good food to avoid if taking prescriptions is grapefruit (although other citrus fruits are currently being studied). Grapefruit irreversibly bind to CYP3A4 and can cause an increase in the drug the patient is taking, potentially elevating it to toxic levels. There is extensive literature on this subject and a literature review would yield pages of references. It is just one example of a food interacting with a drug, and since a large percentage of drugs use the CYP3A4 pathway, it is a big interaction which is highly studied.
The OP used doxycycline as an example, and as Graham pointed out, metals such as Ca++ bind to doxy and cause it to become insoluble and therefore less able to be absorbed. However, doxycycline also commonly causes nausea; thus, often providers will advise patients they can eat something small with the doxycycline to help alleviate the nausea. Therefore, if someone ate something with doxy -- once -- most providers wouldn't worry. However, in the clinical setting of a patient who does not respond to doxycycline and reports taking the medication with breakfast and dinner, it could be prudent to consider that the doxycycline was not ineffective against the offending organism, but was taken inappropriately. It is also worth noting that while doxycycline is typically given as 100mg BID, it can be taken as 200mg OD (this could enhance patient compliance, since it is hard to to follow the instructions twice a day).
It is worth noting that while the three interactions that Bryan mentioned are the primary types of drug interactions, there is one interaction that does not fall into this category, which I discuss with my patients regularly. Flagyl and drinking alcohol (EtOH) has long been thought to produce a disulfiram-like reaction; a disulfiram reaction is what is used by antabuse to "treat" alcoholism. If EtOH is used while on Antabuse the patient vomits violently and has severe abdominal cramping. It is questionable if Flagyl does indeed produce a disulfiram-like reaction or if there is something else going on (say something with serotonin). Regardless, drinking alcohol while on Flagyl is not a good idea, and it doesn't fall into any of those three categories.
I think that as a society we have become complacent with medications, and feel like they are all pretty safe. We know that there are these serious drugs (like chemo) that are out there, but we forget that many commonly used drugs can have serious interactions and consequences. As a recommendation, if you have any questions about drugs, call the pharmacist or your provider. The pharmacists today are typically 4-year trained in a PharmD program and are highly knowledgeable about interactions (more so typically than providers) and they are a great resource for questions like this one.