The neural regulators and feedback mechanisms which control the rhythmic nature of breathing in mammals (and many other organisms) are currently the subject of intense research.
Mammalian central pattern generators producing rhythmic movements exhibit robust but flexible behavior. However, brainstem network architectures that enable these features are not well understood.
Source Respir Physiol Neurobiol. 2009 Aug 31; 168(1-2): 19–25.
It's known that the 'Respiratory Center' is located in the medulla oblongata and pons in the brainstem. But the exact mechanisms which generate and regulate the rhythms are unknown.
One area of interest is the pre-Bötzinger Complex (preBötC) which is a cluster of interneurons in the ventral respiratory group of the medulla of the brainstem. It has been suggested that it may be crucial for the generation of the respiratory rhythm in mammals, though it's currently unclear how this system is regulated.
The location of neurons generating the rhythm of breathing in mammals is unknown.
[…] the respiratory rhythm in the mammalian neonatal nervous system may result from a population of conditional bursting pacemaker neurons in the pre-Bötzinger Complex.
Source: Science. 254(5032): 726–729.
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