The present invention provides systems and methods for monitoring subjects, especially during sleep. Respiratory and sound data are recorded and coughs arousal are recognized as joint events in both of these signals having selected characteristics. Further, cough-arousal events during sleep are recognized when a likely cough occurs in association with a recognized EEG arousal. Cough arousal events are combined into a cough arousal index that reflects disease severity and sleep disruption due to cough. The methods of this invention are computer-implemented and can be provided as a program product including a computer readable medium. Measurements and indices provided by this invention can be used to monitor and to treat respiratory diseases.