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Accurate estimation of the state of charge in battery systems is of essential importance for battery system management. Due to nonlinearity, high sensitivity of the inverse mapping from external measurements, and measurement errors, SOC estimation has remained a challenging task. This is further compounded by the fact that battery characteristic model parameters change with time and operating conditions. This paper introduces an adaptive nonlinear observer design that compensates nonlinearity and achieves better estimation accuracy. A two-time-scale signal processing method is employed to attenuate the effects of measurement noises on SOC estimates. The results are further expanded to derive an integrated algorithm to identify model parameters and initial SOC jointly. Simulations were performed to illustrate the capability and utility of the algorithms. Experimental verifications are conducted on Li-ion battery packs of different capacities under different load profiles.