A detailed study of the effects of hydrodynamic interaction (HI) and excluded volume (EV), on isolated bead-rod chains in shear flows, where the "rods" are mimicked by stiff Fraenkel springs is presented. It is observed that the deformation behavior at weak and intermediate shear rates is qualitatively similar to that observed for polymer chains in the absence of EV and HI, while that at high-shear rates is sensitive to modeling details and chain resolution. Our simulations with varying degrees of resolution reveal universality in chain behavior in the presence of EV (without HI), while the onset of the transition to a compressed chain in the presence of HI (without EV) shifts to higher shear rates with increasing chain resolution. The results also highlight the success of the bead-spring models in predicting the chain behavior in shear flows in the presence of HI, when the HI parameter is appropriately chosen. (c) 2014 American Institute of Chemical Engineers AIChE J, 60: 1400-1412, 2014