ECs, GPA, etc for schools like Upenn, UMich, and Boston College

Can you re-calculate your uwGPA without subgrades? That is the UMich’s way. Assuming it is still 3.89, your GPA and ACT put you right at the 75th percentile of admitted students. So your chance should be much higher than the average for OOS which is around 20%. With a research publication with your name on it, it is a pretty good achievement and that should help your admission.